PDB Short entry for 4NRQ HEADER OXIDOREDUCTASE 27-NOV-13 4NRQ TITLE CRYSTAL STRUCTURE OF HUMAN ALKBH5 IN COMPLEX WITH PYRIDINE-2,4- TITLE 2 DICARBOXYLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA DEMETHYLASE ALKBH5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 66-292; COMPND 5 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 5, ALPHA- COMPND 6 KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 5; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: ABH5, ALKBH5, OFOXD1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS ALKBH5, 6-METHYL ADENOSINE, PROTEIN/DNA INTERACTION, HUMAN KEYWDS 2 DIOXYGENASE, METAL-BINDING, NUCLEUS, DEMETHYLATION, RNA REPAIR, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.FENG,Z.CHEN,Y.LIU REVDAT 3 08-NOV-23 4NRQ 1 REMARK SEQADV LINK REVDAT 2 21-OCT-15 4NRQ 1 JRNL REVDAT 1 19-MAR-14 4NRQ 0 JRNL AUTH C.FENG,Y.LIU,G.WANG,Z.DENG,Q.ZHANG,W.WU,Y.TONG,C.CHENG, JRNL AUTH 2 Z.CHEN JRNL TITL CRYSTAL STRUCTURES OF THE HUMAN RNA DEMETHYLASE ALKBH5 JRNL TITL 2 REVEAL BASIS FOR SUBSTRATE RECOGNITION JRNL REF J.BIOL.CHEM. V. 289 11571 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24616105 JRNL DOI 10.1074/JBC.M113.546168 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 8215 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 477 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) : 2.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 510 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.4010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1608 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : 0.44000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.283 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.200 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.573 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.923 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1656 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2250 ; 1.000 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 208 ; 5.404 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 71 ;27.361 ;23.380 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 262 ;15.481 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;21.185 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 254 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1268 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 1656 ; 1.578 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 1 ;28.251 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1624 ; 9.094 ; 5.000 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4NRQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 130 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8721 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 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) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 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: BALBES REMARK 200 STARTING MODEL: 4NRM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4K, 100MM CH3CO2NH4, 100MM NA REMARK 280 -CITRATE , PH 5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.35300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.38350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.38350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 108.52950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.38350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.38350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.17650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.38350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.38350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 108.52950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.38350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.38350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.17650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.35300 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLY A 63 REMARK 465 HIS A 64 REMARK 465 MET A 65 REMARK 465 PRO A 66 REMARK 465 GLU A 67 REMARK 465 ARG A 68 REMARK 465 SER A 69 REMARK 465 ASP A 70 REMARK 465 TYR A 71 REMARK 465 GLU A 72 REMARK 465 TYR A 141 REMARK 465 GLY A 142 REMARK 465 ALA A 143 REMARK 465 GLN A 144 REMARK 465 LEU A 145 REMARK 465 GLN A 146 REMARK 465 LYS A 147 REMARK 465 ARG A 148 REMARK 465 GLY A 149 REMARK 465 PRO A 150 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 GLU A 73 CG CD OE1 OE2 REMARK 470 GLN A 74 CG CD OE1 NE2 REMARK 470 GLN A 75 CG CD OE1 NE2 REMARK 470 GLN A 77 CG CD OE1 NE2 REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 GLU A 80 CG CD OE1 OE2 REMARK 470 ARG A 83 NE CZ NH1 NH2 REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 93 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 97 CD OE1 NE2 REMARK 470 LYS A 102 CG CD CE NZ REMARK 470 LEU A 129 CG CD1 CD2 REMARK 470 GLU A 163 CD OE1 OE2 REMARK 470 GLN A 170 CG CD OE1 NE2 REMARK 470 ARG A 180 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 LYS A 235 CE NZ REMARK 470 ARG A 238 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 249 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 291 CD NE CZ NH1 NH2 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 GLN A 152 56.50 -115.39 REMARK 500 SER A 203 125.07 -35.38 REMARK 500 PHE A 220 -73.69 -123.00 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 MN A 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 204 NE2 REMARK 620 2 ASP A 206 OD1 89.0 REMARK 620 3 HIS A 266 NE2 86.9 99.2 REMARK 620 4 PD2 A 301 O21 72.7 103.3 149.1 REMARK 620 5 PD2 A 301 N1 110.0 159.6 89.4 76.8 REMARK 620 6 HOH A 401 O 171.9 92.9 100.6 99.2 67.2 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 PD2 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NRM RELATED DB: PDB REMARK 900 RELATED ID: 4NRO RELATED DB: PDB REMARK 900 RELATED ID: 4NRP RELATED DB: PDB DBREF 4NRQ A 66 292 UNP Q6P6C2 ALKB5_HUMAN 66 292 SEQADV 4NRQ GLY A 63 UNP Q6P6C2 EXPRESSION TAG SEQADV 4NRQ HIS A 64 UNP Q6P6C2 EXPRESSION TAG SEQADV 4NRQ MET A 65 UNP Q6P6C2 EXPRESSION TAG SEQRES 1 A 230 GLY HIS MET PRO GLU ARG SER ASP TYR GLU GLU GLN GLN SEQRES 2 A 230 LEU GLN LYS GLU GLU GLU ALA ARG LYS VAL LYS SER GLY SEQRES 3 A 230 ILE ARG GLN MET ARG LEU PHE SER GLN ASP GLU CYS ALA SEQRES 4 A 230 LYS ILE GLU ALA ARG ILE ASP GLU VAL VAL SER ARG ALA SEQRES 5 A 230 GLU LYS GLY LEU TYR ASN GLU HIS THR VAL ASP ARG ALA SEQRES 6 A 230 PRO LEU ARG ASN LYS TYR PHE PHE GLY GLU GLY TYR THR SEQRES 7 A 230 TYR GLY ALA GLN LEU GLN LYS ARG GLY PRO GLY GLN GLU SEQRES 8 A 230 ARG LEU TYR PRO PRO GLY ASP VAL ASP GLU ILE PRO GLU SEQRES 9 A 230 TRP VAL HIS GLN LEU VAL ILE GLN LYS LEU VAL GLU HIS SEQRES 10 A 230 ARG VAL ILE PRO GLU GLY PHE VAL ASN SER ALA VAL ILE SEQRES 11 A 230 ASN ASP TYR GLN PRO GLY GLY CYS ILE VAL SER HIS VAL SEQRES 12 A 230 ASP PRO ILE HIS ILE PHE GLU ARG PRO ILE VAL SER VAL SEQRES 13 A 230 SER PHE PHE SER ASP SER ALA LEU CYS PHE GLY CYS LYS SEQRES 14 A 230 PHE GLN PHE LYS PRO ILE ARG VAL SER GLU PRO VAL LEU SEQRES 15 A 230 SER LEU PRO VAL ARG ARG GLY SER VAL THR VAL LEU SER SEQRES 16 A 230 GLY TYR ALA ALA ASP GLU ILE THR HIS CYS ILE ARG PRO SEQRES 17 A 230 GLN ASP ILE LYS GLU ARG ARG ALA VAL ILE ILE LEU ARG SEQRES 18 A 230 LYS THR ARG LEU ASP ALA PRO ARG LEU HET PD2 A 301 12 HET MN A 302 1 HETNAM PD2 PYRIDINE-2,4-DICARBOXYLIC ACID HETNAM MN MANGANESE (II) ION FORMUL 2 PD2 C7 H5 N O4 FORMUL 3 MN MN 2+ FORMUL 4 HOH *4(H2 O) HELIX 1 1 GLU A 73 SER A 87 1 15 HELIX 2 2 SER A 96 LYS A 116 1 21 HELIX 3 3 ASN A 120 HIS A 122 5 3 HELIX 4 4 PRO A 165 VAL A 172 1 8 HELIX 5 5 VAL A 172 HIS A 179 1 8 HELIX 6 6 CYS A 230 PHE A 234 5 5 HELIX 7 7 SER A 257 GLU A 263 1 7 HELIX 8 8 ARG A 269 ILE A 273 5 5 SHEET 1 A 7 ILE A 89 ARG A 93 0 SHEET 2 A 7 SER A 252 LEU A 256 -1 O VAL A 253 N MET A 92 SHEET 3 A 7 ILE A 215 SER A 219 -1 N SER A 217 O THR A 254 SHEET 4 A 7 ARG A 277 ARG A 283 -1 O LEU A 282 N VAL A 216 SHEET 5 A 7 SER A 189 TYR A 195 -1 N TYR A 195 O ARG A 277 SHEET 6 A 7 ARG A 130 PHE A 135 -1 N ASN A 131 O ASP A 194 SHEET 7 A 7 VAL A 124 ALA A 127 -1 N ASP A 125 O LYS A 132 SHEET 1 B 4 ILE A 201 HIS A 204 0 SHEET 2 B 4 HIS A 266 ILE A 268 -1 O HIS A 266 N HIS A 204 SHEET 3 B 4 SER A 224 PHE A 228 -1 N CYS A 227 O CYS A 267 SHEET 4 B 4 LEU A 244 VAL A 248 -1 O LEU A 244 N PHE A 228 SSBOND 1 CYS A 230 CYS A 267 1555 1555 2.01 LINK NE2 HIS A 204 MN MN A 302 1555 1555 2.53 LINK OD1 ASP A 206 MN MN A 302 1555 1555 2.19 LINK NE2 HIS A 266 MN MN A 302 1555 1555 2.08 LINK O21 PD2 A 301 MN MN A 302 1555 1555 2.13 LINK N1 PD2 A 301 MN MN A 302 1555 1555 2.25 LINK MN MN A 302 O HOH A 401 1555 1555 2.73 CISPEP 1 ARG A 213 PRO A 214 0 4.22 SITE 1 AC1 13 LYS A 132 ASN A 193 TYR A 195 ILE A 201 SITE 2 AC1 13 HIS A 204 ASP A 206 HIS A 266 ILE A 268 SITE 3 AC1 13 ARG A 277 VAL A 279 ILE A 281 MN A 302 SITE 4 AC1 13 HOH A 401 SITE 1 AC2 5 HIS A 204 ASP A 206 HIS A 266 PD2 A 301 SITE 2 AC2 5 HOH A 401 CRYST1 56.767 56.767 144.706 90.00 90.00 90.00 P 43 21 2 8 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 0.017616 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017616 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006911 0.00000