PDB Short entry for 3MDC HEADER LYASE,TRANSFERASE/DNA 30-MAR-10 3MDC TITLE DNA POLYMERASE LAMBDA IN COMPLEX WITH DFDCTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL LAMBDA, DNA POLYMERASE KAPPA, DNA POLYMERASE BETA-2, POL COMPND 5 BETA2; COMPND 6 EC: 2.7.7.7, 4.2.99.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 MOL_ID: 4; SOURCE 16 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, LYASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.GARCIA-DIAZ,M.MURRAY,T.KUNKEL,K.M.CHOU REVDAT 4 21-FEB-24 3MDC 1 REMARK SEQADV HETSYN LINK REVDAT 3 08-NOV-17 3MDC 1 REMARK REVDAT 2 09-JUN-10 3MDC 1 JRNL REVDAT 1 28-APR-10 3MDC 0 JRNL AUTH M.GARCIA-DIAZ,M.S.MURRAY,T.A.KUNKEL,K.M.CHOU JRNL TITL INTERACTION BETWEEN DNA POLYMERASE LAMBDA AND ANTICANCER JRNL TITL 2 NUCLEOSIDE ANALOGS. JRNL REF J.BIOL.CHEM. V. 285 16874 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20348107 JRNL DOI 10.1074/JBC.M109.094391 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 29110 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1455 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.6810 - 4.2990 0.99 3236 168 0.2380 0.2490 REMARK 3 2 4.2990 - 3.4150 0.97 3071 152 0.1780 0.2310 REMARK 3 3 3.4150 - 2.9840 0.97 3007 154 0.1910 0.2690 REMARK 3 4 2.9840 - 2.7120 0.95 2948 164 0.1990 0.2420 REMARK 3 5 2.7120 - 2.5170 0.93 2840 154 0.2030 0.2900 REMARK 3 6 2.5170 - 2.3690 0.89 2733 141 0.2130 0.2860 REMARK 3 7 2.3690 - 2.2510 0.85 2636 122 0.2340 0.3190 REMARK 3 8 2.2510 - 2.1530 0.82 2478 131 0.2370 0.3200 REMARK 3 9 2.1530 - 2.0700 0.83 2512 150 0.2550 0.3120 REMARK 3 10 2.0700 - 1.9980 0.73 2194 119 0.2700 0.3150 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 52.71 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.31900 REMARK 3 B22 (A**2) : 4.50500 REMARK 3 B33 (A**2) : -1.18600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2989 REMARK 3 ANGLE : 1.119 4137 REMARK 3 CHIRALITY : 0.061 448 REMARK 3 PLANARITY : 0.003 460 REMARK 3 DIHEDRAL : 19.100 1154 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3MDC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.504 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30728 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-PROPANOL, PH 5.5, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 27.60300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.00400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.88650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.00400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.60300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.88650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 251 REMARK 465 HIS A 252 REMARK 465 ASN A 253 REMARK 465 VAL A 536 REMARK 465 VAL A 537 REMARK 465 ARG A 538 REMARK 465 ASN A 539 REMARK 465 THR A 540 REMARK 465 HIS A 541 REMARK 465 GLY A 542 REMARK 465 CYS A 543 REMARK 465 LYS A 544 REMARK 465 VAL A 545 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 254 CG CD1 CD2 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 256 CG1 CG2 CD1 REMARK 470 LYS A 287 CG CD CE NZ REMARK 470 THR A 294 OG1 CG2 REMARK 470 SER A 295 OG REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 390 CG CD OE1 OE2 REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG D 1 P DG D 1 OP3 -0.130 REMARK 500 REMARK 500 REMARK: NULL 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 T 2 C3' - C2' - C1' ANGL. DEV. = -6.5 DEGREES REMARK 500 DG T 2 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG T 5 O4' - C1' - N9 ANGL. DEV. = -6.8 DEGREES REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT T 10 O4' - C1' - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG P 3 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT P 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA P 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC D 2 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 255 -126.62 75.22 REMARK 500 ILE A 256 -37.60 -37.36 REMARK 500 HIS A 290 -5.90 -56.77 REMARK 500 PRO A 292 106.99 -58.87 REMARK 500 ILE A 316 -76.10 -71.93 REMARK 500 LEU A 317 1.75 -68.95 REMARK 500 ASN A 407 95.66 -164.43 REMARK 500 CYS A 415 -143.14 -113.63 REMARK 500 ARG A 438 -24.19 -152.92 REMARK 500 SER A 463 92.57 -168.76 REMARK 500 PRO A 547 109.32 -45.59 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 NA A 1 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 98.5 REMARK 620 3 ALA A 344 O 81.7 83.8 REMARK 620 4 DA P 5 OP1 159.8 100.8 94.4 REMARK 620 5 HOH P 7 O 92.8 107.1 168.5 87.4 REMARK 620 6 HOH P 86 O 70.7 167.2 87.7 89.3 80.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 11 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 153 O REMARK 620 2 CYS A 300 O 70.3 REMARK 620 3 ILE A 305 O 113.6 66.2 REMARK 620 4 DC D 3 OP1 96.9 143.5 90.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 580 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 20 O REMARK 620 2 HOH A 172 O 163.6 REMARK 620 3 HOH A 234 O 64.8 99.7 REMARK 620 4 ASP A 382 OD1 72.0 123.3 136.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 579 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 93 O REMARK 620 2 ASP A 427 OD2 96.8 REMARK 620 3 ASP A 429 OD2 87.7 101.5 REMARK 620 4 GTF A 576 O1A 163.5 88.5 75.9 REMARK 620 5 GTF A 576 O1B 89.2 172.3 83.6 87.1 REMARK 620 6 GTF A 576 O3G 122.5 92.2 145.3 72.7 80.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 577 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 159 O REMARK 620 2 SER A 463 O 70.2 REMARK 620 3 HOH T 88 O 138.1 95.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 578 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD1 111.1 REMARK 620 3 ASP A 490 OD1 94.0 97.4 REMARK 620 4 GTF A 576 O1A 98.7 90.7 161.5 REMARK 620 5 DC P 6 O3' 144.4 100.2 64.7 97.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTF A 576 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 577 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 578 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 579 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 580 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MDA RELATED DB: PDB DBREF 3MDC A 252 575 UNP Q9UGP5 DPOLL_HUMAN 252 575 DBREF 3MDC T 1 11 PDB 3MDC 3MDC 1 11 DBREF 3MDC P 1 6 PDB 3MDC 3MDC 1 6 DBREF 3MDC D 1 4 PDB 3MDC 3MDC 1 4 SEQADV 3MDC ALA A 251 UNP Q9UGP5 EXPRESSION TAG SEQRES 1 A 325 ALA HIS ASN LEU HIS ILE THR GLU LYS LEU GLU VAL LEU SEQRES 2 A 325 ALA LYS ALA TYR SER VAL GLN GLY ASP LYS TRP ARG ALA SEQRES 3 A 325 LEU GLY TYR ALA LYS ALA ILE ASN ALA LEU LYS SER PHE SEQRES 4 A 325 HIS LYS PRO VAL THR SER TYR GLN GLU ALA CYS SER ILE SEQRES 5 A 325 PRO GLY ILE GLY LYS ARG MET ALA GLU LYS ILE ILE GLU SEQRES 6 A 325 ILE LEU GLU SER GLY HIS LEU ARG LYS LEU ASP HIS ILE SEQRES 7 A 325 SER GLU SER VAL PRO VAL LEU GLU LEU PHE SER ASN ILE SEQRES 8 A 325 TRP GLY ALA GLY THR LYS THR ALA GLN MET TRP TYR GLN SEQRES 9 A 325 GLN GLY PHE ARG SER LEU GLU ASP ILE ARG SER GLN ALA SEQRES 10 A 325 SER LEU THR THR GLN GLN ALA ILE GLY LEU LYS HIS TYR SEQRES 11 A 325 SER ASP PHE LEU GLU ARG MET PRO ARG GLU GLU ALA THR SEQRES 12 A 325 GLU ILE GLU GLN THR VAL GLN LYS ALA ALA GLN ALA PHE SEQRES 13 A 325 ASN SER GLY LEU LEU CYS VAL ALA CYS GLY SER TYR ARG SEQRES 14 A 325 ARG GLY LYS ALA THR CYS GLY ASP VAL ASP VAL LEU ILE SEQRES 15 A 325 THR HIS PRO ASP GLY ARG SER HIS ARG GLY ILE PHE SER SEQRES 16 A 325 ARG LEU LEU ASP SER LEU ARG GLN GLU GLY PHE LEU THR SEQRES 17 A 325 ASP ASP LEU VAL SER GLN GLU GLU ASN GLY GLN GLN GLN SEQRES 18 A 325 LYS TYR LEU GLY VAL CYS ARG LEU PRO GLY PRO GLY ARG SEQRES 19 A 325 ARG HIS ARG ARG LEU ASP ILE ILE VAL VAL PRO TYR SER SEQRES 20 A 325 GLU PHE ALA CYS ALA LEU LEU TYR PHE THR GLY SER ALA SEQRES 21 A 325 HIS PHE ASN ARG SER MET ARG ALA LEU ALA LYS THR LYS SEQRES 22 A 325 GLY MET SER LEU SER GLU HIS ALA LEU SER THR ALA VAL SEQRES 23 A 325 VAL ARG ASN THR HIS GLY CYS LYS VAL GLY PRO GLY ARG SEQRES 24 A 325 VAL LEU PRO THR PRO THR GLU LYS ASP VAL PHE ARG LEU SEQRES 25 A 325 LEU GLY LEU PRO TYR ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 T 11 DC DG DG DC DG DG DT DA DC DT DG SEQRES 1 P 6 DC DA DG DT DA DC SEQRES 1 D 4 DG DC DC DG HET GTF A 576 30 HET NA A 11 1 HET NA A 1 1 HET NA A 577 1 HET MG A 578 1 HET MG A 579 1 HET NA A 580 1 HETNAM GTF 2'-DEOXY-2',2'-DIFLUOROCYTIDINE 5'-(TETRAHYDROGEN HETNAM 2 GTF TRIPHOSPHATE) HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETSYN GTF GEMCITABINE-TRIPHOSPHATE FORMUL 5 GTF C9 H14 F2 N3 O13 P3 FORMUL 6 NA 4(NA 1+) FORMUL 9 MG 2(MG 2+) FORMUL 12 HOH *369(H2 O) HELIX 1 1 HIS A 255 GLN A 270 1 16 HELIX 2 2 ASP A 272 SER A 288 1 17 HELIX 3 3 SER A 295 SER A 301 1 7 HELIX 4 4 GLY A 306 GLY A 320 1 15 HELIX 5 5 LEU A 322 ILE A 328 5 7 HELIX 6 6 SER A 331 ASN A 340 1 10 HELIX 7 7 GLY A 345 GLN A 355 1 11 HELIX 8 8 SER A 359 ALA A 367 1 9 HELIX 9 9 THR A 370 HIS A 379 1 10 HELIX 10 10 SER A 381 GLU A 385 5 5 HELIX 11 11 ARG A 389 ASN A 407 1 19 HELIX 12 12 CYS A 415 ARG A 420 1 6 HELIX 13 13 GLY A 442 GLU A 454 1 13 HELIX 14 14 PRO A 495 SER A 497 5 3 HELIX 15 15 GLU A 498 GLY A 508 1 11 HELIX 16 16 SER A 509 LYS A 523 1 15 HELIX 17 17 THR A 555 LEU A 563 1 9 HELIX 18 18 GLU A 569 ASP A 574 5 6 SHEET 1 A 2 MET A 387 PRO A 388 0 SHEET 2 A 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 B 5 LEU A 411 ALA A 414 0 SHEET 2 B 5 VAL A 428 THR A 433 -1 O THR A 433 N LEU A 411 SHEET 3 B 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 430 SHEET 4 B 5 LYS A 472 CYS A 477 -1 N CYS A 477 O ARG A 487 SHEET 5 B 5 LEU A 457 VAL A 462 -1 N ASP A 459 O VAL A 476 SHEET 1 C 2 MET A 525 LEU A 527 0 SHEET 2 C 2 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 LINK NA NA A 1 O SER A 339 1555 1555 2.53 LINK NA NA A 1 O ILE A 341 1555 1555 2.51 LINK NA NA A 1 O ALA A 344 1555 1555 2.62 LINK NA NA A 1 OP1 DA P 5 1555 1555 2.44 LINK NA NA A 1 O HOH P 7 1555 1555 2.54 LINK NA NA A 1 O HOH P 86 1555 1555 2.96 LINK NA NA A 11 O HOH A 153 1555 1555 3.19 LINK NA NA A 11 O CYS A 300 1555 1555 2.88 LINK NA NA A 11 O ILE A 305 1555 1555 3.08 LINK NA NA A 11 OP1 DC D 3 1555 1555 2.97 LINK O HOH A 20 NA NA A 580 1555 1555 3.02 LINK O HOH A 93 MG MG A 579 1555 1555 2.47 LINK O HOH A 159 NA NA A 577 1555 1555 3.04 LINK O HOH A 172 NA NA A 580 1555 1555 2.97 LINK O HOH A 234 NA NA A 580 1555 1555 2.94 LINK OD1 ASP A 382 NA NA A 580 1555 1555 2.58 LINK OD1 ASP A 427 MG MG A 578 1555 1555 2.22 LINK OD2 ASP A 427 MG MG A 579 1555 1555 2.13 LINK OD1 ASP A 429 MG MG A 578 1555 1555 2.33 LINK OD2 ASP A 429 MG MG A 579 1555 1555 2.52 LINK O SER A 463 NA NA A 577 1555 1555 2.92 LINK OD1 ASP A 490 MG MG A 578 1555 1555 2.40 LINK O1A GTF A 576 MG MG A 578 1555 1555 2.16 LINK O1A GTF A 576 MG MG A 579 1555 1555 2.08 LINK O1B GTF A 576 MG MG A 579 1555 1555 2.16 LINK O3G GTF A 576 MG MG A 579 1555 1555 2.54 LINK NA NA A 577 O HOH T 88 1555 1555 3.06 LINK MG MG A 578 O3' DC P 6 1555 1555 2.60 CISPEP 1 GLY A 508 SER A 509 0 4.25 SITE 1 AC1 25 HOH A 52 HOH A 54 HOH A 162 HOH A 241 SITE 2 AC1 25 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 3 AC1 25 CYS A 425 GLY A 426 ASP A 427 ASP A 429 SITE 4 AC1 25 TYR A 505 PHE A 506 THR A 507 GLY A 508 SITE 5 AC1 25 SER A 509 ALA A 510 ASN A 513 MG A 578 SITE 6 AC1 25 MG A 579 HOH A 626 HOH A 675 DC P 6 SITE 7 AC1 25 DG T 5 SITE 1 AC2 4 CYS A 300 ILE A 302 ILE A 305 DC D 3 SITE 1 AC3 6 SER A 339 ILE A 341 ALA A 344 DA P 5 SITE 2 AC3 6 HOH P 7 HOH P 86 SITE 1 AC4 3 HOH A 159 SER A 463 HOH T 88 SITE 1 AC5 6 ASP A 427 ASP A 429 ASP A 490 GTF A 576 SITE 2 AC5 6 MG A 579 DC P 6 SITE 1 AC6 5 HOH A 93 ASP A 427 ASP A 429 GTF A 576 SITE 2 AC6 5 MG A 578 SITE 1 AC7 6 HOH A 20 HOH A 172 HOH A 234 ASP A 382 SITE 2 AC7 6 ARG A 485 HIS A 486 CRYST1 55.206 59.773 142.008 90.00 90.00 90.00 P 21 21 21 4 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 0.018114 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007042 0.00000