HEADER OXIDOREDUCTASE 09-NOV-16 5TVS TITLE JMJD2A IN COMPLEX WITH NI(II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-159; COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, COMPND 6 JUMONJI DOMAIN-CONTAINING PROTEIN 2A; COMPND 7 EC: 1.14.11.-; COMPND 8 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: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE DEMETHYLASE MONOOXYGENASE EPIGENETICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.CASCELLA,S.G.LEE,J.M.JEZ REVDAT 7 04-OCT-23 5TVS 1 REMARK REVDAT 6 27-NOV-19 5TVS 1 REMARK REVDAT 5 10-APR-19 5TVS 1 REMARK REVDAT 4 13-SEP-17 5TVS 1 REMARK REVDAT 3 22-FEB-17 5TVS 1 JRNL REMARK REVDAT 2 15-FEB-17 5TVS 1 JRNL REVDAT 1 01-FEB-17 5TVS 0 JRNL AUTH B.CASCELLA,S.G.LEE,S.SINGH,J.M.JEZ,L.M.MIRICA JRNL TITL THE SMALL MOLECULE JIB-04 DISRUPTS O2 BINDING IN THE JRNL TITL 2 FE-DEPENDENT HISTONE DEMETHYLASE KDM4A/JMJD2A. JRNL REF CHEM. COMMUN. (CAMB.) V. 53 2174 2017 JRNL REFN ESSN 1364-548X JRNL PMID 28144654 JRNL DOI 10.1039/C6CC09882G REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 23003 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1150 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 41.8366 - 5.4858 1.00 2907 152 0.1886 0.2299 REMARK 3 2 5.4858 - 4.3557 1.00 2767 146 0.1699 0.2104 REMARK 3 3 4.3557 - 3.8056 1.00 2747 145 0.1835 0.2320 REMARK 3 4 3.8056 - 3.4578 1.00 2735 144 0.2137 0.3137 REMARK 3 5 3.4578 - 3.2101 1.00 2709 143 0.2450 0.3513 REMARK 3 6 3.2101 - 3.0209 1.00 2713 142 0.2505 0.3748 REMARK 3 7 3.0209 - 2.8696 1.00 2676 141 0.2659 0.3788 REMARK 3 8 2.8696 - 2.7447 0.96 2599 137 0.2869 0.3590 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.011 5928 REMARK 3 ANGLE : 1.439 8036 REMARK 3 CHIRALITY : 0.056 826 REMARK 3 PLANARITY : 0.007 1032 REMARK 3 DIHEDRAL : 16.264 2202 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 5TVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1000224783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK HIGH-RESOLUTION REMARK 200 DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23062 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.745 REMARK 200 RESOLUTION RANGE LOW (A) : 41.832 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 35.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5TVR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17.5% PEG-3350 AND 0.1 M CITRATE PH REMARK 280 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.57000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.44700 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.57000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.44700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 SER A 5 REMARK 465 LEU A 354 REMARK 465 LYS A 355 REMARK 465 GLU A 356 REMARK 465 SER A 357 REMARK 465 GLU A 358 REMARK 465 LEU A 359 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 SER B 5 REMARK 465 LEU B 354 REMARK 465 LYS B 355 REMARK 465 GLU B 356 REMARK 465 SER B 357 REMARK 465 GLU B 358 REMARK 465 LEU B 359 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG B 29 OE2 GLU B 352 1.02 REMARK 500 NH2 ARG A 29 OE1 GLU A 352 1.15 REMARK 500 SG CYS A 234 SG CYS A 308 1.41 REMARK 500 CZ ARG A 29 OE1 GLU A 352 1.65 REMARK 500 OE2 GLU A 190 NI NI A 401 1.68 REMARK 500 NE2 HIS B 240 ZN ZN B 402 1.69 REMARK 500 CZ ARG B 29 OE2 GLU B 352 1.72 REMARK 500 NE ARG B 29 OE2 GLU B 352 2.05 REMARK 500 O PHE A 127 NZ LYS A 182 2.11 REMARK 500 NH1 ARG A 29 OE1 GLU A 352 2.12 REMARK 500 OE2 GLU A 190 NE2 HIS A 276 2.13 REMARK 500 NH2 ARG B 29 CD GLU B 352 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 190 CB GLU A 190 CG 0.127 REMARK 500 CYS B 306 CB CYS B 306 SG 0.105 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 ARG A 154 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 CYS A 234 CA - CB - SG ANGL. DEV. = 15.8 DEGREES REMARK 500 LYS B 162 N - CA - C ANGL. DEV. = 16.6 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 ALA A 91 160.70 -47.91 REMARK 500 SER A 112 -87.37 -102.17 REMARK 500 LYS A 143 -37.01 -33.03 REMARK 500 ARG A 154 52.41 74.92 REMARK 500 LYS A 162 -83.85 -65.40 REMARK 500 HIS A 188 140.02 -173.54 REMARK 500 MET A 192 15.59 57.29 REMARK 500 CYS A 306 99.19 -58.25 REMARK 500 MET A 312 126.92 -27.61 REMARK 500 SER A 316 106.12 -56.59 REMARK 500 SER B 112 -76.98 -99.35 REMARK 500 ASN B 128 63.73 37.87 REMARK 500 PRO B 129 109.26 -45.92 REMARK 500 ARG B 152 60.39 -154.84 REMARK 500 LEU B 159 38.96 -75.66 REMARK 500 LYS B 162 -83.31 41.92 REMARK 500 GLU B 163 -35.07 -164.71 REMARK 500 MET B 192 17.66 59.69 REMARK 500 GLU B 214 6.59 -67.66 REMARK 500 ALA B 236 61.25 -110.20 REMARK 500 VAL B 260 143.03 -173.84 REMARK 500 ARG B 309 -156.47 -115.04 REMARK 500 LYS B 310 -50.10 -147.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 309 LYS A 310 142.39 REMARK 500 GLU B 161 LYS B 162 133.56 REMARK 500 LYS B 162 GLU B 163 -127.12 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 A 401 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 188 NE2 REMARK 620 2 HIS A 276 NE2 68.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 240 NE2 REMARK 620 2 CYS A 308 SG 61.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 401 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 GLU B 190 OE2 81.2 REMARK 620 3 HIS B 276 NE2 59.6 57.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 234 SG REMARK 620 2 CYS B 306 SG 94.9 REMARK 620 3 CYS B 308 SG 108.8 98.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TVR RELATED DB: PDB DBREF 5TVS A 1 359 UNP O75164 KDM4A_HUMAN 1 359 DBREF 5TVS B 1 359 UNP O75164 KDM4A_HUMAN 1 359 SEQRES 1 A 359 MET ALA SER GLU SER GLU THR LEU ASN PRO SER ALA ARG SEQRES 2 A 359 ILE MET THR PHE TYR PRO THR MET GLU GLU PHE ARG ASN SEQRES 3 A 359 PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN GLY ALA SEQRES 4 A 359 HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO LYS GLU SEQRES 5 A 359 TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP ASP LEU SEQRES 6 A 359 VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR GLY GLN SEQRES 7 A 359 SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS LYS ALA SEQRES 8 A 359 MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SER ASP SEQRES 9 A 359 LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU GLU LEU SEQRES 10 A 359 GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN PRO PRO SEQRES 11 A 359 ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR GLU LYS SEQRES 12 A 359 HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG THR ILE SEQRES 13 A 359 LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR ILE GLU SEQRES 14 A 359 GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS SEQRES 15 A 359 THR SER PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR SEQRES 16 A 359 SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SER TRP SEQRES 17 A 359 TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU GLU ARG SEQRES 18 A 359 LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SER CYS SEQRES 19 A 359 GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SER PRO SEQRES 20 A 359 LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP LYS VAL SEQRES 21 A 359 THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE PRO TYR SEQRES 22 A 359 GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA SEQRES 23 A 359 GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE GLU TYR SEQRES 24 A 359 GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS ASP MET SEQRES 25 A 359 VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS PHE GLN SEQRES 26 A 359 PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS ASP ASN SEQRES 27 A 359 THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU ALA ALA SEQRES 28 A 359 GLU PHE LEU LYS GLU SER GLU LEU SEQRES 1 B 359 MET ALA SER GLU SER GLU THR LEU ASN PRO SER ALA ARG SEQRES 2 B 359 ILE MET THR PHE TYR PRO THR MET GLU GLU PHE ARG ASN SEQRES 3 B 359 PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN GLY ALA SEQRES 4 B 359 HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO LYS GLU SEQRES 5 B 359 TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP ASP LEU SEQRES 6 B 359 VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR GLY GLN SEQRES 7 B 359 SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS LYS ALA SEQRES 8 B 359 MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SER ASP SEQRES 9 B 359 LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU GLU LEU SEQRES 10 B 359 GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN PRO PRO SEQRES 11 B 359 ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR GLU LYS SEQRES 12 B 359 HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG THR ILE SEQRES 13 B 359 LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR ILE GLU SEQRES 14 B 359 GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS SEQRES 15 B 359 THR SER PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR SEQRES 16 B 359 SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SER TRP SEQRES 17 B 359 TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU GLU ARG SEQRES 18 B 359 LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SER CYS SEQRES 19 B 359 GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SER PRO SEQRES 20 B 359 LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP LYS VAL SEQRES 21 B 359 THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE PRO TYR SEQRES 22 B 359 GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA SEQRES 23 B 359 GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE GLU TYR SEQRES 24 B 359 GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS ASP MET SEQRES 25 B 359 VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS PHE GLN SEQRES 26 B 359 PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS ASP ASN SEQRES 27 B 359 THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU ALA ALA SEQRES 28 B 359 GLU PHE LEU LYS GLU SER GLU LEU HET NI A 401 1 HET ZN A 402 1 HET NI B 401 1 HET ZN B 402 1 HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION FORMUL 3 NI 2(NI 2+) FORMUL 4 ZN 2(ZN 2+) HELIX 1 AA1 THR A 20 ARG A 25 1 6 HELIX 2 AA2 ASN A 26 GLN A 37 1 12 HELIX 3 AA3 GLY A 38 ALA A 42 5 5 HELIX 4 AA4 VAL A 94 SER A 103 1 10 HELIX 5 AA5 GLU A 113 LEU A 125 1 13 HELIX 6 AA6 THR A 155 VAL A 160 5 6 HELIX 7 AA7 GLU A 190 LEU A 194 5 5 HELIX 8 AA8 PRO A 212 GLU A 214 5 3 HELIX 9 AA9 HIS A 215 PHE A 227 1 13 HELIX 10 AB1 PHE A 227 CYS A 234 1 8 HELIX 11 AB2 ALA A 236 LYS A 241 5 6 HELIX 12 AB3 SER A 246 TYR A 253 1 8 HELIX 13 AB4 ARG A 295 ALA A 303 1 9 HELIX 14 AB5 MET A 317 GLN A 325 1 9 HELIX 15 AB6 ARG A 328 ALA A 334 1 7 HELIX 16 AB7 THR A 347 GLU A 352 5 6 HELIX 17 AB8 THR B 20 ASN B 26 1 7 HELIX 18 AB9 ASN B 26 SER B 36 1 11 HELIX 19 AC1 GLN B 37 ALA B 42 5 6 HELIX 20 AC2 VAL B 94 SER B 103 1 10 HELIX 21 AC3 GLU B 113 LEU B 125 1 13 HELIX 22 AC4 THR B 155 LEU B 159 5 5 HELIX 23 AC5 GLU B 190 LEU B 194 5 5 HELIX 24 AC6 PRO B 212 PHE B 227 1 16 HELIX 25 AC7 PHE B 227 CYS B 234 1 8 HELIX 26 AC8 ALA B 236 LYS B 241 5 6 HELIX 27 AC9 SER B 246 TYR B 253 1 8 HELIX 28 AD1 ARG B 295 ALA B 303 1 9 HELIX 29 AD2 MET B 317 GLN B 325 1 9 HELIX 30 AD3 ARG B 328 ALA B 334 1 7 HELIX 31 AD4 THR B 347 PHE B 353 5 7 SHEET 1 AA110 MET A 15 PHE A 17 0 SHEET 2 AA110 LEU A 44 VAL A 47 1 O LYS A 46 N MET A 15 SHEET 3 AA110 PHE A 267 THR A 270 -1 O PHE A 267 N VAL A 47 SHEET 4 AA110 TYR A 195 GLY A 203 -1 N ASN A 198 O MET A 268 SHEET 5 AA110 ASN A 284 PHE A 291 -1 O GLU A 287 N TYR A 199 SHEET 6 AA110 TYR A 175 GLY A 179 -1 N TYR A 177 O ALA A 286 SHEET 7 AA110 ILE A 131 ASN A 137 -1 N VAL A 136 O LEU A 176 SHEET 8 AA110 ILE A 71 GLN A 78 -1 N ILE A 71 O TYR A 132 SHEET 9 AA110 LEU A 81 GLN A 88 -1 O ILE A 87 N GLN A 72 SHEET 10 AA110 THR A 243 ILE A 245 -1 O LEU A 244 N PHE A 82 SHEET 1 AA2 2 VAL A 66 ILE A 67 0 SHEET 2 AA2 2 MET A 92 THR A 93 -1 O MET A 92 N ILE A 67 SHEET 1 AA3 4 SER A 184 HIS A 188 0 SHEET 2 AA3 4 TYR A 275 ASN A 280 -1 O GLY A 278 N PHE A 185 SHEET 3 AA3 4 LYS A 206 VAL A 211 -1 N TYR A 209 O ALA A 277 SHEET 4 AA3 4 ASP A 258 GLN A 262 -1 O VAL A 260 N TRP A 208 SHEET 1 AA410 MET B 15 PHE B 17 0 SHEET 2 AA410 LEU B 44 VAL B 47 1 O LYS B 46 N MET B 15 SHEET 3 AA410 PHE B 267 THR B 270 -1 O ILE B 269 N ALA B 45 SHEET 4 AA410 TYR B 195 GLY B 203 -1 N ASN B 198 O MET B 268 SHEET 5 AA410 ASN B 284 PHE B 291 -1 O GLU B 287 N TYR B 199 SHEET 6 AA410 TYR B 175 GLY B 179 -1 N TYR B 177 O ALA B 286 SHEET 7 AA410 ILE B 131 ASN B 137 -1 N VAL B 136 O LEU B 176 SHEET 8 AA410 ILE B 71 GLN B 78 -1 N ILE B 71 O TYR B 132 SHEET 9 AA410 LEU B 81 GLN B 88 -1 O ILE B 87 N GLN B 72 SHEET 10 AA410 THR B 243 ILE B 245 -1 O LEU B 244 N PHE B 82 SHEET 1 AA5 2 VAL B 66 ILE B 67 0 SHEET 2 AA5 2 MET B 92 THR B 93 -1 O MET B 92 N ILE B 67 SHEET 1 AA6 4 SER B 184 HIS B 188 0 SHEET 2 AA6 4 TYR B 275 ASN B 280 -1 O GLY B 278 N PHE B 185 SHEET 3 AA6 4 LYS B 206 VAL B 211 -1 N TYR B 209 O ALA B 277 SHEET 4 AA6 4 ASP B 258 GLN B 262 -1 O VAL B 260 N TRP B 208 SSBOND 1 CYS A 306 CYS A 308 1555 1555 2.93 SSBOND 2 CYS B 234 CYS B 306 1555 1555 2.99 LINK NE2 HIS A 188 NI NI A 401 1555 1555 2.40 LINK NE2 HIS A 240 ZN ZN A 402 1555 1555 1.97 LINK NE2 HIS A 276 NI NI A 401 1555 1555 2.13 LINK SG CYS A 308 ZN ZN A 402 1555 1555 2.38 LINK NE2 HIS B 188 NI NI B 401 1555 1555 2.42 LINK OE2 GLU B 190 NI NI B 401 1555 1555 2.29 LINK SG CYS B 234 ZN ZN B 402 1555 1555 1.93 LINK NE2 HIS B 276 NI NI B 401 1555 1555 2.52 LINK SG CYS B 306 ZN ZN B 402 1555 1555 2.13 LINK SG CYS B 308 ZN ZN B 402 1555 1555 1.99 SITE 1 AC1 3 HIS A 188 GLU A 190 HIS A 276 SITE 1 AC2 5 CYS A 234 ALA A 236 PHE A 237 HIS A 240 SITE 2 AC2 5 CYS A 308 SITE 1 AC3 3 HIS B 188 GLU B 190 HIS B 276 SITE 1 AC4 4 CYS B 234 HIS B 240 CYS B 306 CYS B 308 CRYST1 56.689 101.140 148.894 90.00 90.00 90.00 P 2 21 21 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 0.017640 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006716 0.00000