HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 18-JUN-10 3NJY TITLE CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH 5-CARBOXY-8- TITLE 2 HYDROXYQUINOLINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28 BSA4 KEYWDS OXIDOREDUCTASE, CHROMATIN REGULATOR, TRANSCRIPTION REGULATION, KEYWDS 2 DOUBLE-STRANDED BETA HELIX, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.N.F.KING,I.J.CLIFTON,M.WANG,D.J.MALONEY,A.JADHAV,U.OPPERMANN, AUTHOR 2 T.D.HEIGHTMAN,A.SIMEONOV,M.A.MCDONOUGH,C.J.SCHOFIELD REVDAT 3 01-NOV-23 3NJY 1 REMARK SEQADV LINK REVDAT 2 15-DEC-10 3NJY 1 JRNL REVDAT 1 08-DEC-10 3NJY 0 JRNL AUTH O.N.F.KING,X.S.LI,M.SAKURAI,A.KAWAMURA,N.R.ROSE,S.S.NG, JRNL AUTH 2 A.M.QUINN,G.RAI,B.T.MOTT,P.BESWICK,R.J.KLOSE,U.OPPERMANN, JRNL AUTH 3 A.JADHAV,T.D.HEIGHTMAN,D.J.MALONEY,C.J.SCHOFIELD,A.SIMEONOV JRNL TITL QUANTITATIVE HIGH-THROUGHPUT SCREENING IDENTIFIES JRNL TITL 2 8-HYDROXYQUINOLINES AS CELL-ACTIVE HISTONE DEMETHYLASE JRNL TITL 3 INHIBITORS JRNL REF PLOS ONE V. 5 15535 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 21124847 JRNL DOI 10.1371/JOURNAL.PONE.0015535 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6_289 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 26687 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1342 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 37.6822 - 5.5960 0.97 2693 119 0.1705 0.2108 REMARK 3 2 5.5960 - 4.4440 0.99 2587 137 0.1383 0.1853 REMARK 3 3 4.4440 - 3.8829 0.99 2549 146 0.1403 0.1610 REMARK 3 4 3.8829 - 3.5282 0.99 2536 142 0.1642 0.2306 REMARK 3 5 3.5282 - 3.2754 0.99 2552 128 0.1770 0.2265 REMARK 3 6 3.2754 - 3.0824 1.00 2521 143 0.1978 0.2396 REMARK 3 7 3.0824 - 2.9281 0.99 2526 130 0.2152 0.3098 REMARK 3 8 2.9281 - 2.8007 0.99 2460 141 0.2319 0.2930 REMARK 3 9 2.8007 - 2.6929 0.98 2485 119 0.2349 0.2732 REMARK 3 10 2.6929 - 2.6000 0.96 2436 137 0.2483 0.3046 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 : 0.34 REMARK 3 B_SOL : 30.24 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 : 0.015 5839 REMARK 3 ANGLE : 1.097 7946 REMARK 3 CHIRALITY : 0.059 822 REMARK 3 PLANARITY : 0.006 1018 REMARK 3 DIHEDRAL : 15.346 2062 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 3NJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000059923. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97860 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA CCP4_3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26805 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 41.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.440 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : 0.11100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.4073 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.37 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2OQ6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRATE, 4MM NICL2, 20% PEG 3350, REMARK 280 PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z 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 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 50.27500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.27500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.49500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 VAL A -11 REMARK 465 ASP A -10 REMARK 465 LEU A -9 REMARK 465 GLY A -8 REMARK 465 THR A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 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 GLU A 6 REMARK 465 THR A 7 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 -21 REMARK 465 HIS B -20 REMARK 465 HIS B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 SER B -14 REMARK 465 SER B -13 REMARK 465 GLY B -12 REMARK 465 VAL B -11 REMARK 465 ASP B -10 REMARK 465 LEU B -9 REMARK 465 GLY B -8 REMARK 465 THR B -7 REMARK 465 GLU B -6 REMARK 465 ASN B -5 REMARK 465 LEU B -4 REMARK 465 TYR B -3 REMARK 465 PHE B -2 REMARK 465 GLN B -1 REMARK 465 SER B 0 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 GLU B 6 REMARK 465 THR B 7 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 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 ARG A 13 NE CZ NH1 NH2 REMARK 470 GLU A 22 CG CD OE1 OE2 REMARK 470 ARG A 25 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 29 CZ NH1 NH2 REMARK 470 LYS A 54 CD CE NZ REMARK 470 LYS A 90 CD CE NZ REMARK 470 ARG A 95 NE CZ NH1 NH2 REMARK 470 LYS A 99 CG CD CE NZ REMARK 470 ARG A 110 CD NE CZ NH1 NH2 REMARK 470 GLU A 113 CD OE1 OE2 REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 ARG A 154 NE CZ NH1 NH2 REMARK 470 LYS A 162 CD CE NZ REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 ARG A 221 CD NE CZ NH1 NH2 REMARK 470 LYS A 224 CD CE NZ REMARK 470 GLN A 232 CG CD OE1 NE2 REMARK 470 LYS A 310 CG CD CE NZ REMARK 470 ASP A 311 CG OD1 OD2 REMARK 470 LYS A 314 CG CD CE NZ REMARK 470 LYS A 330 CE NZ REMARK 470 LYS A 336 CD CE NZ REMARK 470 GLU B 22 CD OE1 OE2 REMARK 470 LYS B 51 CD CE NZ REMARK 470 LYS B 54 CD CE NZ REMARK 470 LYS B 89 CE NZ REMARK 470 LYS B 90 CG CD CE NZ REMARK 470 LYS B 99 CD CE NZ REMARK 470 ARG B 110 NE CZ NH1 NH2 REMARK 470 GLU B 113 CD OE1 OE2 REMARK 470 LYS B 123 CD CE NZ REMARK 470 LYS B 143 CD CE NZ REMARK 470 ARG B 154 NE CZ NH1 NH2 REMARK 470 GLU B 161 CD OE1 OE2 REMARK 470 LYS B 162 CG CD CE NZ REMARK 470 GLN B 232 CG CD OE1 NE2 REMARK 470 LYS B 310 CG CD CE NZ REMARK 470 ASP B 311 CG OD1 OD2 REMARK 470 LYS B 336 CD CE NZ 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 OD2 ASP B 258 O HOH B 494 2.14 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 TYR A 59 42.03 -98.62 REMARK 500 SER A 112 -77.37 -91.86 REMARK 500 LYS A 143 -30.07 -39.89 REMARK 500 ARG A 152 78.17 -152.93 REMARK 500 SER A 164 -11.70 -141.73 REMARK 500 VAL A 171 -61.83 -101.77 REMARK 500 LYS A 182 10.96 80.71 REMARK 500 MET A 192 17.10 59.86 REMARK 500 ALA B 91 159.63 -45.67 REMARK 500 GLN B 325 58.45 -142.74 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 501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 188 NE2 REMARK 620 2 GLU A 190 OE2 91.1 REMARK 620 3 GLU A 190 OE1 127.6 51.7 REMARK 620 4 8XQ A 360 OAC 87.1 80.8 115.8 REMARK 620 5 8XQ A 360 NAI 81.9 158.0 145.9 78.1 REMARK 620 6 HOH A 508 O 88.4 113.4 77.9 165.2 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 HIS A 240 NE2 108.4 REMARK 620 3 CYS A 306 SG 115.1 115.3 REMARK 620 4 CYS A 308 SG 111.8 90.1 113.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 GLU B 190 OE2 95.9 REMARK 620 3 8XQ B 360 OAC 89.9 77.0 REMARK 620 4 8XQ B 360 NAI 86.9 156.1 79.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 234 SG REMARK 620 2 HIS B 240 NE2 109.4 REMARK 620 3 CYS B 306 SG 119.1 116.1 REMARK 620 4 CYS B 308 SG 104.4 84.8 117.7 REMARK 620 N 1 2 3 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 8XQ A 360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 8XQ B 360 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WWJ RELATED DB: PDB REMARK 900 STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR 10A REMARK 900 RELATED ID: 2VD7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR PYRIDINE-2,4- REMARK 900 DICARBOXYLIC ACID REMARK 900 RELATED ID: 2GP5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CATALYTIC CORE DOMAIN OF JMJD2A COMPLEXED WITH REMARK 900 ALPHA-KETOGLUTARATE REMARK 900 RELATED ID: 2GP3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC CORE DOMAIN OF JMJD2A REMARK 900 RELATED ID: 2GFA RELATED DB: PDB REMARK 900 DOUBLE TUDOR DOMAIN COMPLEX STRUCTURE REMARK 900 RELATED ID: 2GF7 RELATED DB: PDB REMARK 900 DOUBLE TUDOR DOMAIN STRUCTURE DBREF 3NJY A 1 359 UNP O75164 KDM4A_HUMAN 1 359 DBREF 3NJY B 1 359 UNP O75164 KDM4A_HUMAN 1 359 SEQADV 3NJY MET A -21 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS A -20 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS A -19 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS A -18 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS A -17 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS A -16 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS A -15 UNP O75164 EXPRESSION TAG SEQADV 3NJY SER A -14 UNP O75164 EXPRESSION TAG SEQADV 3NJY SER A -13 UNP O75164 EXPRESSION TAG SEQADV 3NJY GLY A -12 UNP O75164 EXPRESSION TAG SEQADV 3NJY VAL A -11 UNP O75164 EXPRESSION TAG SEQADV 3NJY ASP A -10 UNP O75164 EXPRESSION TAG SEQADV 3NJY LEU A -9 UNP O75164 EXPRESSION TAG SEQADV 3NJY GLY A -8 UNP O75164 EXPRESSION TAG SEQADV 3NJY THR A -7 UNP O75164 EXPRESSION TAG SEQADV 3NJY GLU A -6 UNP O75164 EXPRESSION TAG SEQADV 3NJY ASN A -5 UNP O75164 EXPRESSION TAG SEQADV 3NJY LEU A -4 UNP O75164 EXPRESSION TAG SEQADV 3NJY TYR A -3 UNP O75164 EXPRESSION TAG SEQADV 3NJY PHE A -2 UNP O75164 EXPRESSION TAG SEQADV 3NJY GLN A -1 UNP O75164 EXPRESSION TAG SEQADV 3NJY SER A 0 UNP O75164 EXPRESSION TAG SEQADV 3NJY MET B -21 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS B -20 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS B -19 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS B -18 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS B -17 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS B -16 UNP O75164 EXPRESSION TAG SEQADV 3NJY HIS B -15 UNP O75164 EXPRESSION TAG SEQADV 3NJY SER B -14 UNP O75164 EXPRESSION TAG SEQADV 3NJY SER B -13 UNP O75164 EXPRESSION TAG SEQADV 3NJY GLY B -12 UNP O75164 EXPRESSION TAG SEQADV 3NJY VAL B -11 UNP O75164 EXPRESSION TAG SEQADV 3NJY ASP B -10 UNP O75164 EXPRESSION TAG SEQADV 3NJY LEU B -9 UNP O75164 EXPRESSION TAG SEQADV 3NJY GLY B -8 UNP O75164 EXPRESSION TAG SEQADV 3NJY THR B -7 UNP O75164 EXPRESSION TAG SEQADV 3NJY GLU B -6 UNP O75164 EXPRESSION TAG SEQADV 3NJY ASN B -5 UNP O75164 EXPRESSION TAG SEQADV 3NJY LEU B -4 UNP O75164 EXPRESSION TAG SEQADV 3NJY TYR B -3 UNP O75164 EXPRESSION TAG SEQADV 3NJY PHE B -2 UNP O75164 EXPRESSION TAG SEQADV 3NJY GLN B -1 UNP O75164 EXPRESSION TAG SEQADV 3NJY SER B 0 UNP O75164 EXPRESSION TAG SEQRES 1 A 381 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 381 GLY THR GLU ASN LEU TYR PHE GLN SER MET ALA SER GLU SEQRES 3 A 381 SER GLU THR LEU ASN PRO SER ALA ARG ILE MET THR PHE SEQRES 4 A 381 TYR PRO THR MET GLU GLU PHE ARG ASN PHE SER ARG TYR SEQRES 5 A 381 ILE ALA TYR ILE GLU SER GLN GLY ALA HIS ARG ALA GLY SEQRES 6 A 381 LEU ALA LYS VAL VAL PRO PRO LYS GLU TRP LYS PRO ARG SEQRES 7 A 381 ALA SER TYR ASP ASP ILE ASP ASP LEU VAL ILE PRO ALA SEQRES 8 A 381 PRO ILE GLN GLN LEU VAL THR GLY GLN SER GLY LEU PHE SEQRES 9 A 381 THR GLN TYR ASN ILE GLN LYS LYS ALA MET THR VAL ARG SEQRES 10 A 381 GLU PHE ARG LYS ILE ALA ASN SER ASP LYS TYR CYS THR SEQRES 11 A 381 PRO ARG TYR SER GLU PHE GLU GLU LEU GLU ARG LYS TYR SEQRES 12 A 381 TRP LYS ASN LEU THR PHE ASN PRO PRO ILE TYR GLY ALA SEQRES 13 A 381 ASP VAL ASN GLY THR LEU TYR GLU LYS HIS VAL ASP GLU SEQRES 14 A 381 TRP ASN ILE GLY ARG LEU ARG THR ILE LEU ASP LEU VAL SEQRES 15 A 381 GLU LYS GLU SER GLY ILE THR ILE GLU GLY VAL ASN THR SEQRES 16 A 381 PRO TYR LEU TYR PHE GLY MET TRP LYS THR SER PHE ALA SEQRES 17 A 381 TRP HIS THR GLU ASP MET ASP LEU TYR SER ILE ASN TYR SEQRES 18 A 381 LEU HIS PHE GLY GLU PRO LYS SER TRP TYR SER VAL PRO SEQRES 19 A 381 PRO GLU HIS GLY LYS ARG LEU GLU ARG LEU ALA LYS GLY SEQRES 20 A 381 PHE PHE PRO GLY SER ALA GLN SER CYS GLU ALA PHE LEU SEQRES 21 A 381 ARG HIS LYS MET THR LEU ILE SER PRO LEU MET LEU LYS SEQRES 22 A 381 LYS TYR GLY ILE PRO PHE ASP LYS VAL THR GLN GLU ALA SEQRES 23 A 381 GLY GLU PHE MET ILE THR PHE PRO TYR GLY TYR HIS ALA SEQRES 24 A 381 GLY PHE ASN HIS GLY PHE ASN CYS ALA GLU SER THR ASN SEQRES 25 A 381 PHE ALA THR ARG ARG TRP ILE GLU TYR GLY LYS GLN ALA SEQRES 26 A 381 VAL LEU CYS SER CYS ARG LYS ASP MET VAL LYS ILE SER SEQRES 27 A 381 MET ASP VAL PHE VAL ARG LYS PHE GLN PRO GLU ARG TYR SEQRES 28 A 381 LYS LEU TRP LYS ALA GLY LYS ASP ASN THR VAL ILE ASP SEQRES 29 A 381 HIS THR LEU PRO THR PRO GLU ALA ALA GLU PHE LEU LYS SEQRES 30 A 381 GLU SER GLU LEU SEQRES 1 B 381 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 B 381 GLY THR GLU ASN LEU TYR PHE GLN SER MET ALA SER GLU SEQRES 3 B 381 SER GLU THR LEU ASN PRO SER ALA ARG ILE MET THR PHE SEQRES 4 B 381 TYR PRO THR MET GLU GLU PHE ARG ASN PHE SER ARG TYR SEQRES 5 B 381 ILE ALA TYR ILE GLU SER GLN GLY ALA HIS ARG ALA GLY SEQRES 6 B 381 LEU ALA LYS VAL VAL PRO PRO LYS GLU TRP LYS PRO ARG SEQRES 7 B 381 ALA SER TYR ASP ASP ILE ASP ASP LEU VAL ILE PRO ALA SEQRES 8 B 381 PRO ILE GLN GLN LEU VAL THR GLY GLN SER GLY LEU PHE SEQRES 9 B 381 THR GLN TYR ASN ILE GLN LYS LYS ALA MET THR VAL ARG SEQRES 10 B 381 GLU PHE ARG LYS ILE ALA ASN SER ASP LYS TYR CYS THR SEQRES 11 B 381 PRO ARG TYR SER GLU PHE GLU GLU LEU GLU ARG LYS TYR SEQRES 12 B 381 TRP LYS ASN LEU THR PHE ASN PRO PRO ILE TYR GLY ALA SEQRES 13 B 381 ASP VAL ASN GLY THR LEU TYR GLU LYS HIS VAL ASP GLU SEQRES 14 B 381 TRP ASN ILE GLY ARG LEU ARG THR ILE LEU ASP LEU VAL SEQRES 15 B 381 GLU LYS GLU SER GLY ILE THR ILE GLU GLY VAL ASN THR SEQRES 16 B 381 PRO TYR LEU TYR PHE GLY MET TRP LYS THR SER PHE ALA SEQRES 17 B 381 TRP HIS THR GLU ASP MET ASP LEU TYR SER ILE ASN TYR SEQRES 18 B 381 LEU HIS PHE GLY GLU PRO LYS SER TRP TYR SER VAL PRO SEQRES 19 B 381 PRO GLU HIS GLY LYS ARG LEU GLU ARG LEU ALA LYS GLY SEQRES 20 B 381 PHE PHE PRO GLY SER ALA GLN SER CYS GLU ALA PHE LEU SEQRES 21 B 381 ARG HIS LYS MET THR LEU ILE SER PRO LEU MET LEU LYS SEQRES 22 B 381 LYS TYR GLY ILE PRO PHE ASP LYS VAL THR GLN GLU ALA SEQRES 23 B 381 GLY GLU PHE MET ILE THR PHE PRO TYR GLY TYR HIS ALA SEQRES 24 B 381 GLY PHE ASN HIS GLY PHE ASN CYS ALA GLU SER THR ASN SEQRES 25 B 381 PHE ALA THR ARG ARG TRP ILE GLU TYR GLY LYS GLN ALA SEQRES 26 B 381 VAL LEU CYS SER CYS ARG LYS ASP MET VAL LYS ILE SER SEQRES 27 B 381 MET ASP VAL PHE VAL ARG LYS PHE GLN PRO GLU ARG TYR SEQRES 28 B 381 LYS LEU TRP LYS ALA GLY LYS ASP ASN THR VAL ILE ASP SEQRES 29 B 381 HIS THR LEU PRO THR PRO GLU ALA ALA GLU PHE LEU LYS SEQRES 30 B 381 GLU SER GLU LEU HET NI A 501 1 HET ZN A 502 1 HET 8XQ A 360 14 HET NI B 501 1 HET ZN B 502 1 HET 8XQ B 360 14 HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION HETNAM 8XQ 8-HYDROXYQUINOLINE-5-CARBOXYLIC ACID FORMUL 3 NI 2(NI 2+) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 8XQ 2(C10 H7 N O3) FORMUL 9 HOH *284(H2 O) HELIX 1 1 THR A 20 ASN A 26 1 7 HELIX 2 2 ASN A 26 GLN A 37 1 12 HELIX 3 3 GLY A 38 ALA A 42 5 5 HELIX 4 4 VAL A 94 SER A 103 1 10 HELIX 5 5 GLU A 113 LEU A 125 1 13 HELIX 6 6 THR A 155 LEU A 157 5 3 HELIX 7 7 ASP A 158 GLY A 165 1 8 HELIX 8 8 GLU A 190 LEU A 194 5 5 HELIX 9 9 PRO A 212 GLU A 214 5 3 HELIX 10 10 HIS A 215 PHE A 227 1 13 HELIX 11 11 PHE A 227 CYS A 234 1 8 HELIX 12 12 ALA A 236 LYS A 241 5 6 HELIX 13 13 SER A 246 TYR A 253 1 8 HELIX 14 14 ARG A 295 ALA A 303 1 9 HELIX 15 15 MET A 317 GLN A 325 1 9 HELIX 16 16 ARG A 328 ALA A 334 1 7 HELIX 17 17 THR A 347 LEU A 354 5 8 HELIX 18 18 THR B 20 ARG B 25 1 6 HELIX 19 19 ASN B 26 GLN B 37 1 12 HELIX 20 20 GLY B 38 ALA B 42 5 5 HELIX 21 21 VAL B 94 SER B 103 1 10 HELIX 22 22 GLU B 113 LEU B 125 1 13 HELIX 23 23 THR B 155 LEU B 157 5 3 HELIX 24 24 ASP B 158 GLY B 165 1 8 HELIX 25 25 GLU B 190 LEU B 194 5 5 HELIX 26 26 PRO B 212 GLU B 214 5 3 HELIX 27 27 HIS B 215 PHE B 227 1 13 HELIX 28 28 PHE B 227 CYS B 234 1 8 HELIX 29 29 ALA B 236 LYS B 241 5 6 HELIX 30 30 SER B 246 TYR B 253 1 8 HELIX 31 31 ARG B 295 ALA B 303 1 9 HELIX 32 32 MET B 317 GLN B 325 1 9 HELIX 33 33 GLN B 325 GLY B 335 1 11 HELIX 34 34 THR B 347 LEU B 354 5 8 SHEET 1 A10 THR A 16 PHE A 17 0 SHEET 2 A10 LEU A 44 VAL A 47 1 O LYS A 46 N PHE A 17 SHEET 3 A10 PHE A 267 THR A 270 -1 O ILE A 269 N ALA A 45 SHEET 4 A10 TYR A 195 GLY A 203 -1 N ASN A 198 O MET A 268 SHEET 5 A10 ASN A 284 PHE A 291 -1 O GLU A 287 N TYR A 199 SHEET 6 A10 TYR A 175 GLY A 179 -1 N TYR A 177 O ALA A 286 SHEET 7 A10 ILE A 131 ASN A 137 -1 N GLY A 133 O PHE A 178 SHEET 8 A10 ILE A 71 GLN A 78 -1 N ILE A 71 O TYR A 132 SHEET 9 A10 LEU A 81 GLN A 88 -1 O TYR A 85 N LEU A 74 SHEET 10 A10 THR A 243 ILE A 245 -1 O LEU A 244 N PHE A 82 SHEET 1 B 2 VAL A 66 ILE A 67 0 SHEET 2 B 2 MET A 92 THR A 93 -1 O MET A 92 N ILE A 67 SHEET 1 C 4 SER A 184 HIS A 188 0 SHEET 2 C 4 TYR A 275 ASN A 280 -1 O HIS A 276 N HIS A 188 SHEET 3 C 4 LYS A 206 VAL A 211 -1 N TYR A 209 O ALA A 277 SHEET 4 C 4 ASP A 258 GLN A 262 -1 O GLN A 262 N LYS A 206 SHEET 1 D10 THR B 16 PHE B 17 0 SHEET 2 D10 LEU B 44 VAL B 47 1 O LYS B 46 N PHE B 17 SHEET 3 D10 PHE B 267 THR B 270 -1 O ILE B 269 N ALA B 45 SHEET 4 D10 TYR B 195 GLY B 203 -1 N ASN B 198 O MET B 268 SHEET 5 D10 ASN B 284 PHE B 291 -1 O GLU B 287 N TYR B 199 SHEET 6 D10 TYR B 175 GLY B 179 -1 N TYR B 177 O ALA B 286 SHEET 7 D10 ILE B 131 ASN B 137 -1 N GLY B 133 O PHE B 178 SHEET 8 D10 ILE B 71 GLN B 78 -1 N ILE B 71 O TYR B 132 SHEET 9 D10 LEU B 81 GLN B 88 -1 O TYR B 85 N LEU B 74 SHEET 10 D10 THR B 243 ILE B 245 -1 O LEU B 244 N PHE B 82 SHEET 1 E 2 VAL B 66 ILE B 67 0 SHEET 2 E 2 MET B 92 THR B 93 -1 O MET B 92 N ILE B 67 SHEET 1 F 4 SER B 184 HIS B 188 0 SHEET 2 F 4 TYR B 275 ASN B 280 -1 O GLY B 278 N PHE B 185 SHEET 3 F 4 LYS B 206 VAL B 211 -1 N TYR B 209 O ALA B 277 SHEET 4 F 4 ASP B 258 GLN B 262 -1 O VAL B 260 N TRP B 208 LINK NE2 HIS A 188 NI NI A 501 1555 1555 2.35 LINK OE2 GLU A 190 NI NI A 501 1555 1555 2.21 LINK OE1 GLU A 190 NI NI A 501 1555 1555 2.72 LINK SG CYS A 234 ZN ZN A 502 1555 1555 2.21 LINK NE2 HIS A 240 ZN ZN A 502 1555 1555 2.11 LINK SG CYS A 306 ZN ZN A 502 1555 1555 2.18 LINK SG CYS A 308 ZN ZN A 502 1555 1555 2.49 LINK OAC 8XQ A 360 NI NI A 501 1555 1555 2.18 LINK NAI 8XQ A 360 NI NI A 501 1555 1555 2.30 LINK NI NI A 501 O HOH A 508 1555 1555 2.35 LINK NE2 HIS B 188 NI NI B 501 1555 1555 2.15 LINK OE2 GLU B 190 NI NI B 501 1555 1555 2.21 LINK SG CYS B 234 ZN ZN B 502 1555 1555 2.29 LINK NE2 HIS B 240 ZN ZN B 502 1555 1555 2.11 LINK SG CYS B 306 ZN ZN B 502 1555 1555 2.31 LINK SG CYS B 308 ZN ZN B 502 1555 1555 2.17 LINK OAC 8XQ B 360 NI NI B 501 1555 1555 1.99 LINK NAI 8XQ B 360 NI NI B 501 1555 1555 2.39 SITE 1 AC1 5 HIS A 188 GLU A 190 HIS A 276 8XQ A 360 SITE 2 AC1 5 HOH A 508 SITE 1 AC2 4 CYS A 234 HIS A 240 CYS A 306 CYS A 308 SITE 1 AC3 12 TYR A 132 TYR A 177 PHE A 185 HIS A 188 SITE 2 AC3 12 GLU A 190 LYS A 206 TRP A 208 LYS A 241 SITE 3 AC3 12 HIS A 276 HOH A 440 HOH A 475 NI A 501 SITE 1 AC4 5 HIS B 188 GLU B 190 HIS B 276 8XQ B 360 SITE 2 AC4 5 HOH B 466 SITE 1 AC5 4 CYS B 234 HIS B 240 CYS B 306 CYS B 308 SITE 1 AC6 10 TYR B 132 TYR B 177 PHE B 185 HIS B 188 SITE 2 AC6 10 GLU B 190 LYS B 206 TRP B 208 HIS B 276 SITE 3 AC6 10 HOH B 488 NI B 501 CRYST1 100.550 148.990 56.910 90.00 90.00 90.00 P 21 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 0.009945 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006712 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017572 0.00000