PDB Full entry for 1R2O HEADER DNA 29-SEP-03 1R2O TITLE D(GCATGCT) + NI2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS METAL ION, DNA QUADRUPLEX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.C.CARDIN,Y.GAN,J.H.THORPE,S.C.M.TEIXEIRA,B.C.GALE,M.I.A.MORAES REVDAT 3 14-FEB-24 1R2O 1 REMARK LINK REVDAT 2 24-FEB-09 1R2O 1 VERSN REVDAT 1 21-OCT-03 1R2O 0 JRNL AUTH J.C.CARDIN,Y.GAN,J.H.THORPE,S.C.M.TEIXEIRA,B.C.GALE, JRNL AUTH 2 M.I.A.MORAES JRNL TITL METAL ION DISTRIBUTION AND STABILIZATION OF THE DNA JRNL TITL 2 QUADRUPLEX STRUCTURE FORMED BY D(GCATGCT) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 801 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.700 REMARK 3 FREE R VALUE TEST SET COUNT : 22 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.45 REMARK 3 REFLECTION IN BIN (WORKING SET) : 52 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : 7 REMARK 3 BIN FREE R VALUE : 0.1900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 140 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26000 REMARK 3 B22 (A**2) : 0.26000 REMARK 3 B33 (A**2) : -0.39000 REMARK 3 B12 (A**2) : 0.13000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.661 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.277 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.499 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.910 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 178 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 81 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 273 ; 2.467 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 202 ; 1.191 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 24 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 83 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 3 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 12 ; 0.121 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 62 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 45 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 2 ; 0.136 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 11 ; 0.159 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 9 ; 0.233 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.103 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 178 ; 2.173 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 273 ; 3.214 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1R2O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000020361. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8126 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 857 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 30.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 13.47 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 17.10 REMARK 200 R MERGE FOR SHELL (I) : 0.21600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: XTALVIEW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, NICKEL DICHLORIDE, REMARK 280 POTASSIUM CHLORIDE, MPD, PH 5.7, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.38733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.69367 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 61.38733 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.69367 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.38733 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 30.69367 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 61.38733 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 30.69367 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 30.69367 REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 30.69367 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 N3 DT X 7 LIES ON A SPECIAL POSITION. REMARK 375 C4 DT X 7 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 201 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG X 1 N3 - C2 - N2 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC X 2 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA X 3 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC X 6 O5' - P - OP2 ANGL. DEV. = 7.6 DEGREES REMARK 500 DT X 7 N1 - C2 - O2 ANGL. DEV. = 6.9 DEGREES REMARK 500 DT X 7 N3 - C2 - O2 ANGL. DEV. = -7.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI X 101 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG X 1 N7 REMARK 620 2 DG X 5 N7 174.7 REMARK 620 3 HOH X 202 O 94.8 82.7 REMARK 620 4 HOH X 203 O 86.9 88.3 87.9 REMARK 620 5 HOH X 204 O 94.3 88.3 170.7 94.3 REMARK 620 6 HOH X 205 O 92.2 92.6 91.7 179.0 86.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI X 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QYK RELATED DB: PDB REMARK 900 D(GCATGCT) + BARIUM REMARK 900 RELATED ID: 1QYL RELATED DB: PDB REMARK 900 D(GCATGCT) + VANADIUM REMARK 900 RELATED ID: 1QZL RELATED DB: PDB REMARK 900 D(GCATGCT) + CO2+ DBREF 1R2O X 1 7 PDB 1R2O 1R2O 1 7 SEQRES 1 X 7 DG DC DA DT DG DC DT HET NI X 101 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ FORMUL 3 HOH *8(H2 O) LINK N7 DG X 1 NI NI X 101 1555 1555 2.25 LINK N7 DG X 5 NI NI X 101 12555 1555 2.24 LINK NI NI X 101 O HOH X 202 1555 1555 1.82 LINK NI NI X 101 O HOH X 203 1555 1555 2.16 LINK NI NI X 101 O HOH X 204 1555 1555 2.14 LINK NI NI X 101 O HOH X 205 1555 1555 2.06 SITE 1 AC1 6 DG X 1 DG X 5 HOH X 202 HOH X 203 SITE 2 AC1 6 HOH X 204 HOH X 205 CRYST1 24.807 24.807 92.081 90.00 90.00 120.00 P 62 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.040311 0.023273 0.000000 0.00000 SCALE2 0.000000 0.046547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010860 0.00000 ATOM 1 O5' DG X 1 7.025 4.604 9.108 1.00 25.95 O ATOM 2 C5' DG X 1 7.085 5.542 10.194 1.00 27.59 C ATOM 3 C4' DG X 1 6.893 4.924 11.559 1.00 27.24 C ATOM 4 O4' DG X 1 5.557 4.419 11.741 1.00 28.99 O ATOM 5 C3' DG X 1 7.740 3.701 11.838 1.00 29.19 C ATOM 6 O3' DG X 1 7.981 3.542 13.281 1.00 32.59 O ATOM 7 C2' DG X 1 6.910 2.555 11.298 1.00 25.54 C ATOM 8 C1' DG X 1 5.536 2.990 11.739 1.00 26.82 C ATOM 9 N9 DG X 1 4.391 2.647 10.893 1.00 27.57 N ATOM 10 C8 DG X 1 4.378 2.564 9.516 1.00 26.78 C ATOM 11 N7 DG X 1 3.215 2.277 9.011 1.00 23.76 N ATOM 12 C5 DG X 1 2.408 2.191 10.097 1.00 23.42 C ATOM 13 C6 DG X 1 1.044 1.910 10.109 1.00 26.06 C ATOM 14 O6 DG X 1 0.335 1.692 9.102 1.00 27.02 O ATOM 15 N1 DG X 1 0.530 1.847 11.420 1.00 22.56 N ATOM 16 C2 DG X 1 1.241 2.082 12.579 1.00 22.31 C ATOM 17 N2 DG X 1 0.467 1.947 13.727 1.00 19.10 N ATOM 18 N3 DG X 1 2.564 2.369 12.569 1.00 21.54 N ATOM 19 C4 DG X 1 3.079 2.402 11.294 1.00 26.30 C ATOM 20 P DC X 2 9.103 2.457 13.718 1.00 33.32 P ATOM 21 OP1 DC X 2 9.860 3.153 14.773 1.00 34.64 O ATOM 22 OP2 DC X 2 9.720 1.799 12.555 1.00 34.36 O ATOM 23 O5' DC X 2 8.194 1.276 14.271 1.00 33.29 O ATOM 24 C5' DC X 2 7.250 1.574 15.317 1.00 32.11 C ATOM 25 C4' DC X 2 6.337 0.394 15.435 1.00 31.82 C ATOM 26 O4' DC X 2 5.436 0.457 14.302 1.00 29.87 O ATOM 27 C3' DC X 2 7.001 -0.990 15.351 1.00 30.26 C ATOM 28 O3' DC X 2 6.916 -1.691 16.586 1.00 31.93 O ATOM 29 C2' DC X 2 6.177 -1.727 14.310 1.00 29.71 C ATOM 30 C1' DC X 2 4.927 -0.852 14.130 1.00 29.10 C ATOM 31 N1 DC X 2 4.245 -0.970 12.828 1.00 26.74 N ATOM 32 C2 DC X 2 2.867 -1.216 12.705 1.00 28.76 C ATOM 33 O2 DC X 2 2.134 -1.343 13.715 1.00 27.99 O ATOM 34 N3 DC X 2 2.321 -1.291 11.429 1.00 26.39 N ATOM 35 C4 DC X 2 3.085 -1.176 10.326 1.00 27.18 C ATOM 36 N4 DC X 2 2.496 -1.291 9.118 1.00 23.02 N ATOM 37 C5 DC X 2 4.493 -0.940 10.439 1.00 27.64 C ATOM 38 C6 DC X 2 5.005 -0.819 11.681 1.00 29.59 C ATOM 39 P DA X 3 8.243 -2.166 17.375 1.00 32.00 P ATOM 40 OP1 DA X 3 9.279 -1.196 17.008 1.00 31.31 O ATOM 41 OP2 DA X 3 8.308 -3.623 17.124 1.00 30.38 O ATOM 42 O5' DA X 3 7.923 -1.869 18.925 1.00 29.88 O ATOM 43 C5' DA X 3 7.872 -0.510 19.453 1.00 27.08 C ATOM 44 C4' DA X 3 6.836 -0.468 20.595 1.00 25.82 C ATOM 45 O4' DA X 3 5.483 -0.816 20.143 1.00 22.23 O ATOM 46 C3' DA X 3 7.210 -1.462 21.710 1.00 21.06 C ATOM 47 O3' DA X 3 7.115 -0.822 22.943 1.00 24.44 O ATOM 48 C2' DA X 3 6.225 -2.606 21.512 1.00 19.87 C ATOM 49 C1' DA X 3 4.997 -1.939 20.872 1.00 24.02 C ATOM 50 N9 DA X 3 4.243 -2.840 20.023 1.00 26.11 N ATOM 51 C8 DA X 3 4.329 -2.916 18.652 1.00 27.38 C ATOM 52 N7 DA X 3 3.589 -3.847 18.120 1.00 25.45 N ATOM 53 C5 DA X 3 2.963 -4.422 19.190 1.00 25.98 C ATOM 54 C6 DA X 3 2.044 -5.457 19.240 1.00 28.45 C ATOM 55 N6 DA X 3 1.597 -6.085 18.135 1.00 27.93 N ATOM 56 N1 DA X 3 1.621 -5.818 20.478 1.00 28.70 N ATOM 57 C2 DA X 3 2.068 -5.176 21.570 1.00 24.86 C ATOM 58 N3 DA X 3 2.945 -4.184 21.634 1.00 27.90 N ATOM 59 C4 DA X 3 3.372 -3.854 20.391 1.00 27.75 C ATOM 60 P DT X 4 8.035 0.417 23.422 1.00 26.38 P ATOM 61 OP1 DT X 4 7.315 1.693 23.364 1.00 29.06 O ATOM 62 OP2 DT X 4 9.300 0.291 22.655 1.00 25.77 O ATOM 63 O5' DT X 4 8.159 -0.004 24.963 1.00 27.65 O ATOM 64 C5' DT X 4 8.980 -1.182 25.389 1.00 26.92 C ATOM 65 C4' DT X 4 8.402 -1.754 26.681 1.00 26.36 C ATOM 66 O4' DT X 4 8.472 -0.729 27.694 1.00 27.17 O ATOM 67 C3' DT X 4 6.916 -2.099 26.580 1.00 26.31 C ATOM 68 O3' DT X 4 6.683 -3.278 27.272 1.00 24.90 O ATOM 69 C2' DT X 4 6.155 -0.886 27.148 1.00 24.43 C ATOM 70 C1' DT X 4 7.166 -0.353 28.149 1.00 26.66 C ATOM 71 N1 DT X 4 7.232 1.123 28.386 1.00 25.19 N ATOM 72 C2 DT X 4 7.070 1.579 29.707 1.00 24.83 C ATOM 73 O2 DT X 4 6.839 0.880 30.683 1.00 23.35 O ATOM 74 N3 DT X 4 7.174 2.917 29.834 1.00 26.05 N ATOM 75 C4 DT X 4 7.441 3.837 28.817 1.00 28.03 C ATOM 76 O4 DT X 4 7.515 5.043 29.044 1.00 27.37 O ATOM 77 C5 DT X 4 7.609 3.287 27.481 1.00 26.19 C ATOM 78 C7 DT X 4 7.898 4.191 26.313 1.00 29.75 C ATOM 79 C6 DT X 4 7.501 1.972 27.334 1.00 21.52 C ATOM 80 P DG X 5 5.510 -4.224 26.769 1.00 27.13 P ATOM 81 OP1 DG X 5 5.595 -5.566 27.388 1.00 24.74 O ATOM 82 OP2 DG X 5 5.403 -4.086 25.302 1.00 27.51 O ATOM 83 O5' DG X 5 4.196 -3.524 27.371 1.00 30.06 O ATOM 84 C5' DG X 5 3.697 -3.855 28.658 1.00 27.71 C ATOM 85 C4' DG X 5 2.503 -3.006 28.992 1.00 24.08 C ATOM 86 O4' DG X 5 2.968 -1.642 29.028 1.00 24.15 O ATOM 87 C3' DG X 5 1.354 -2.985 27.980 1.00 24.71 C ATOM 88 O3' DG X 5 0.417 -4.082 28.201 1.00 26.08 O ATOM 89 C2' DG X 5 0.734 -1.599 28.213 1.00 23.43 C ATOM 90 C1' DG X 5 1.862 -0.763 28.825 1.00 22.98 C ATOM 91 N9 DG X 5 2.351 0.301 27.978 1.00 24.73 N ATOM 92 C8 DG X 5 2.416 0.293 26.608 1.00 23.54 C ATOM 93 N7 DG X 5 2.963 1.394 26.117 1.00 24.06 N ATOM 94 C5 DG X 5 3.307 2.169 27.211 1.00 24.46 C ATOM 95 C6 DG X 5 3.891 3.458 27.288 1.00 25.76 C ATOM 96 O6 DG X 5 4.281 4.213 26.378 1.00 25.21 O ATOM 97 N1 DG X 5 4.070 3.859 28.620 1.00 28.94 N ATOM 98 C2 DG X 5 3.705 3.096 29.724 1.00 29.67 C ATOM 99 N2 DG X 5 3.935 3.634 30.939 1.00 25.28 N ATOM 100 N3 DG X 5 3.133 1.880 29.634 1.00 27.81 N ATOM 101 C4 DG X 5 2.955 1.490 28.366 1.00 25.89 C ATOM 102 P DC X 6 -0.075 -4.963 26.957 1.00 25.55 P ATOM 103 OP1 DC X 6 -0.791 -4.031 26.050 1.00 26.09 O ATOM 104 OP2 DC X 6 -0.800 -6.071 27.567 1.00 23.23 O ATOM 105 O5' DC X 6 1.278 -5.279 26.193 1.00 30.41 O ATOM 106 C5' DC X 6 2.052 -6.354 26.452 1.00 36.42 C ATOM 107 C4' DC X 6 1.699 -7.488 25.529 1.00 39.09 C ATOM 108 O4' DC X 6 2.062 -7.266 24.127 1.00 39.43 O ATOM 109 C3' DC X 6 2.422 -8.742 25.980 1.00 42.65 C ATOM 110 O3' DC X 6 1.417 -9.739 26.018 1.00 48.42 O ATOM 111 C2' DC X 6 3.526 -8.921 24.930 1.00 40.98 C ATOM 112 C1' DC X 6 2.817 -8.393 23.677 1.00 39.98 C ATOM 113 N1 DC X 6 3.709 -7.944 22.534 1.00 37.30 N ATOM 114 C2 DC X 6 3.509 -8.440 21.226 1.00 35.84 C ATOM 115 O2 DC X 6 2.611 -9.273 21.019 1.00 29.97 O ATOM 116 N3 DC X 6 4.301 -7.962 20.222 1.00 33.98 N ATOM 117 C4 DC X 6 5.268 -7.083 20.468 1.00 34.40 C ATOM 118 N4 DC X 6 6.059 -6.661 19.457 1.00 31.10 N ATOM 119 C5 DC X 6 5.486 -6.596 21.797 1.00 36.20 C ATOM 120 C6 DC X 6 4.678 -7.030 22.770 1.00 35.10 C ATOM 121 P A DT X 7 1.518 -10.946 27.070 0.50 54.52 P ATOM 122 P B DT X 7 1.567 -11.108 26.845 0.50 48.98 P ATOM 123 OP1A DT X 7 1.332 -10.417 28.444 0.50 52.95 O ATOM 124 OP1B DT X 7 0.384 -11.259 27.731 0.50 49.17 O ATOM 125 OP2A DT X 7 2.741 -11.732 26.786 0.50 53.26 O ATOM 126 OP2B DT X 7 2.930 -11.135 27.424 0.50 47.00 O ATOM 127 O5'A DT X 7 0.205 -11.722 26.564 0.50 57.71 O ATOM 128 O5'B DT X 7 1.440 -12.177 25.658 0.50 47.08 O ATOM 129 C5'A DT X 7 0.274 -12.480 25.356 0.50 62.87 C ATOM 130 C5'B DT X 7 1.152 -11.741 24.312 0.50 46.08 C ATOM 131 C4'A DT X 7 -0.980 -12.371 24.501 0.50 65.90 C ATOM 132 C4'B DT X 7 1.205 -12.882 23.312 0.50 44.82 C ATOM 133 O4'A DT X 7 -2.059 -13.110 25.133 0.50 67.77 O ATOM 134 O4'B DT X 7 2.021 -12.504 22.161 0.50 43.71 O ATOM 135 C3'A DT X 7 -1.494 -10.953 24.264 0.50 67.63 C ATOM 136 C3'B DT X 7 1.870 -14.139 23.865 0.50 43.80 C ATOM 137 O3'A DT X 7 -1.854 -10.790 22.893 0.50 67.86 O ATOM 138 O3'B DT X 7 1.379 -15.279 23.154 0.50 41.60 O ATOM 139 C2'A DT X 7 -2.694 -10.827 25.201 0.50 68.68 C ATOM 140 C2'B DT X 7 3.351 -13.775 23.649 0.50 42.57 C ATOM 141 C1'A DT X 7 -3.178 -12.273 25.351 0.50 69.58 C ATOM 142 C1'B DT X 7 3.278 -13.193 22.228 0.50 42.23 C ATOM 143 N1 A DT X 7 -3.781 -12.636 26.698 0.50 71.39 N ATOM 144 N1 B DT X 7 4.380 -12.261 21.715 0.50 39.85 N ATOM 145 C2 A DT X 7 -5.003 -13.297 26.746 0.50 71.85 C ATOM 146 C2 B DT X 7 5.361 -11.603 22.471 0.50 38.23 C ATOM 147 O2 A DT X 7 -5.653 -13.612 25.761 0.50 71.91 O ATOM 148 O2 B DT X 7 5.565 -11.622 23.656 0.50 35.24 O ATOM 149 N3 A DT X 7 -5.453 -13.580 28.012 0.50 72.27 N ATOM 150 N3 B DT X 7 6.220 -10.831 21.749 0.50 39.52 N ATOM 151 C4 A DT X 7 -4.830 -13.280 29.214 0.50 73.06 C ATOM 152 C4 B DT X 7 6.235 -10.628 20.395 0.50 36.50 C ATOM 153 O4 A DT X 7 -5.332 -13.581 30.295 0.50 73.61 O ATOM 154 O4 B DT X 7 7.077 -9.900 19.918 0.50 35.00 O ATOM 155 C5 A DT X 7 -3.559 -12.597 29.102 0.50 73.14 C ATOM 156 C5 B DT X 7 5.212 -11.313 19.653 0.50 38.56 C ATOM 157 C7 A DT X 7 -2.777 -12.219 30.332 0.50 72.77 C ATOM 158 C7 B DT X 7 5.100 -11.182 18.153 0.50 39.91 C ATOM 159 C6 A DT X 7 -3.103 -12.313 27.867 0.50 72.25 C ATOM 160 C6 B DT X 7 4.358 -12.086 20.339 0.50 39.06 C TER 161 DT X 7 HETATM 162 NI NI X 101 3.037 2.014 6.781 1.00 23.53 NI HETATM 163 O HOH X 201 2.878 1.676 15.337 0.50 18.49 O HETATM 164 O HOH X 202 1.442 1.150 6.856 1.00 18.32 O HETATM 165 O HOH X 203 1.941 3.869 6.767 1.00 23.13 O HETATM 166 O HOH X 204 4.922 2.937 6.359 1.00 17.01 O HETATM 167 O HOH X 205 4.073 0.234 6.829 1.00 19.11 O HETATM 168 O HOH X 207 0.647 -1.876 24.856 0.50 21.26 O HETATM 169 O HOH X 209 -3.064 -6.958 26.149 1.00 42.37 O HETATM 170 O HOH X 210 3.374 -2.681 23.986 1.00 30.72 O CONECT 11 162 CONECT 162 11 164 165 166 CONECT 162 167 CONECT 164 162 CONECT 165 162 CONECT 166 162 CONECT 167 162 MASTER 338 0 1 0 0 0 2 6 149 1 7 1 END