HEADER OXIDOREDUCTASE 15-FEB-16 5FWE TITLE JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3ME2S PEPTIDE 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, JUMONJI DOMAIN CONTAINING COMPND 7 PROTEIN 2A; COMPND 8 EC: 1.14.11.-; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: SYNTHETIC PEPTIDE; COMPND 12 CHAIN: C, D; COMPND 13 FRAGMENT: HISTONE H4(1-15)R3ME2S PEPTIDE, UNP RESIDUES 2-16; COMPND 14 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: R3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS JMJD2A, OXIDOREDUCTASE, NON-HEME, IRON, 2-OXOGLUTARATE, DIOXYGENASE, KEYWDS 2 OXYGENASE, DOUBLE-STRANDED BETA HELIX, DSBH, FACIAL TRIAD, KEYWDS 3 DEMETHYLASE, HISTONE, JMJC DOMAIN, METAL BINDING PROTEIN, EPIGENETIC KEYWDS 4 AND TRANSCRIPTION REGULATION, CHROMATIN REGULATOR, HYDROXYLATION EXPDTA X-RAY DIFFRACTION AUTHOR R.CHOWDHURY,L.J.WALPORT,C.J.SCHOFIELD REVDAT 6 23-OCT-24 5FWE 1 REMARK REVDAT 5 10-JAN-24 5FWE 1 REMARK LINK REVDAT 4 08-MAY-19 5FWE 1 REMARK REVDAT 3 06-MAR-19 5FWE 1 REMARK LINK REVDAT 2 06-JUL-16 5FWE 1 JRNL REVDAT 1 06-APR-16 5FWE 0 JRNL AUTH L.J.WALPORT,R.J.HOPKINSON,R.CHOWDHURY,R.SCHILLER,W.GE, JRNL AUTH 2 A.KAWAMURA,C.J.SCHOFIELD JRNL TITL ARGININE DEMETHYLATION IS CATALYSED BY A SUBSET OF JMJC JRNL TITL 2 HISTONE LYSINE DEMETHYLASES. JRNL REF NAT.COMMUN. V. 7 11974 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27337104 JRNL DOI 10.1038/NCOMMS11974 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 54928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2709 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 49.8687 - 5.4669 1.00 2978 155 0.1870 0.2019 REMARK 3 2 5.4669 - 4.3400 0.98 2778 138 0.1449 0.1464 REMARK 3 3 4.3400 - 3.7916 1.00 2805 147 0.1587 0.1755 REMARK 3 4 3.7916 - 3.4451 1.00 2802 136 0.1806 0.2177 REMARK 3 5 3.4451 - 3.1982 1.00 2758 137 0.1883 0.2266 REMARK 3 6 3.1982 - 3.0097 1.00 2788 134 0.1940 0.1942 REMARK 3 7 3.0097 - 2.8589 1.00 2753 138 0.2100 0.2561 REMARK 3 8 2.8589 - 2.7345 1.00 2747 132 0.2153 0.2617 REMARK 3 9 2.7345 - 2.6292 0.98 2699 142 0.2173 0.2510 REMARK 3 10 2.6292 - 2.5385 1.00 2739 157 0.2310 0.2721 REMARK 3 11 2.5385 - 2.4591 1.00 2709 156 0.2235 0.2808 REMARK 3 12 2.4591 - 2.3889 1.00 2733 133 0.2306 0.2733 REMARK 3 13 2.3889 - 2.3260 1.00 2735 147 0.2418 0.3080 REMARK 3 14 2.3260 - 2.2692 1.00 2716 150 0.2424 0.3094 REMARK 3 15 2.2692 - 2.2176 1.00 2746 124 0.2480 0.2729 REMARK 3 16 2.2176 - 2.1704 1.00 2712 160 0.2672 0.2869 REMARK 3 17 2.1704 - 2.1270 1.00 2687 154 0.2734 0.3359 REMARK 3 18 2.1270 - 2.0869 1.00 2736 149 0.2814 0.3450 REMARK 3 19 2.0869 - 2.0496 0.96 2598 120 0.2924 0.2928 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 : 0.33 REMARK 3 B_SOL : 44.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.74000 REMARK 3 B22 (A**2) : -1.51000 REMARK 3 B33 (A**2) : 2.25000 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 : 0.006 5988 REMARK 3 ANGLE : 0.779 8132 REMARK 3 CHIRALITY : 0.044 843 REMARK 3 PLANARITY : 0.004 1059 REMARK 3 DIHEDRAL : 14.121 3542 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 5FWE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1290066235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91741 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54997 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 49.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 2OX0 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SITTING DROPS, 277 K, 0.15 M POTASSIUM REMARK 280 BROMIDE, 30 % W/V PEG 2000 MME, PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP 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 50.36950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.36950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.70000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 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 GLU B 356 REMARK 465 SER B 357 REMARK 465 GLU B 358 REMARK 465 LEU B 359 REMARK 465 SER C 1 REMARK 465 GLY C 4 REMARK 465 LYS C 5 REMARK 465 GLY C 6 REMARK 465 GLY C 7 REMARK 465 LYS C 8 REMARK 465 GLY C 9 REMARK 465 LEU C 10 REMARK 465 GLY C 11 REMARK 465 LYS C 12 REMARK 465 GLY C 13 REMARK 465 GLY C 14 REMARK 465 ALA C 15 REMARK 465 GLY D 4 REMARK 465 LYS D 5 REMARK 465 GLY D 6 REMARK 465 GLY D 7 REMARK 465 LYS D 8 REMARK 465 GLY D 9 REMARK 465 LEU D 10 REMARK 465 GLY D 11 REMARK 465 LYS D 12 REMARK 465 GLY D 13 REMARK 465 GLY D 14 REMARK 465 ALA D 15 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 THR A 7 OG1 CG2 REMARK 470 GLU A 22 CD OE1 OE2 REMARK 470 LYS A 51 CD CE NZ REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 LYS A 90 CG CD CE NZ REMARK 470 ARG A 98 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 99 CE NZ REMARK 470 ARG A 110 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 ARG A 154 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 162 CG CD CE NZ REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 LYS A 251 CE NZ REMARK 470 LYS A 310 CG CD CE NZ REMARK 470 ASP A 311 CG OD1 OD2 REMARK 470 MET A 312 CE REMARK 470 LYS A 336 CE NZ REMARK 470 SER B 3 OG REMARK 470 GLU B 4 CG CD OE1 OE2 REMARK 470 GLU B 6 CG CD OE1 OE2 REMARK 470 GLU B 22 CG CD OE1 OE2 REMARK 470 ARG B 25 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 51 NZ REMARK 470 GLU B 52 CD OE1 OE2 REMARK 470 LYS B 54 CG CD CE NZ REMARK 470 ASP B 63 CG OD1 OD2 REMARK 470 LYS B 89 NZ REMARK 470 LYS B 90 CG CD CE NZ REMARK 470 ARG B 95 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 99 CG CD CE NZ REMARK 470 ARG B 110 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 113 CD OE1 OE2 REMARK 470 GLU B 115 CD OE1 OE2 REMARK 470 LYS B 120 CD CE NZ REMARK 470 LYS B 143 CG CD CE NZ REMARK 470 ARG B 154 CD NE CZ NH1 NH2 REMARK 470 LYS B 162 CG CD CE NZ REMARK 470 ARG B 221 CD NE CZ NH1 NH2 REMARK 470 LYS B 224 CD CE NZ REMARK 470 LYS B 310 CD CE NZ REMARK 470 MET B 312 CG SD CE REMARK 470 LYS B 330 CD CE NZ REMARK 470 LYS B 336 CE NZ REMARK 470 LEU B 354 CG CD1 CD2 REMARK 470 LYS B 355 CG 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 OD1 ASP A 318 O HOH A 2174 2.05 REMARK 500 OD1 ASP B 318 NH1 ARG B 322 2.10 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 ARG A 152 65.32 -157.68 REMARK 500 MET A 192 19.60 56.01 REMARK 500 ALA A 236 47.38 -97.83 REMARK 500 ASN A 338 32.73 -97.21 REMARK 500 ARG B 152 69.61 -159.03 REMARK 500 LYS B 182 -0.66 78.66 REMARK 500 MET B 192 19.32 55.49 REMARK 500 ALA B 236 59.31 -104.73 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 A1355 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 188 NE2 REMARK 620 2 GLU A 190 OE2 106.2 REMARK 620 3 HIS A 276 NE2 86.8 86.8 REMARK 620 4 OGA A1358 O2 163.6 87.0 84.2 REMARK 620 5 OGA A1358 O2' 90.2 163.1 98.7 77.6 REMARK 620 6 HOH A2102 O 101.0 86.3 170.7 89.3 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1356 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 HIS A 240 NE2 111.0 REMARK 620 3 CYS A 306 SG 115.9 106.9 REMARK 620 4 CYS A 308 SG 117.6 90.1 111.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1356 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 GLU B 190 OE2 100.5 REMARK 620 3 HIS B 276 NE2 89.4 89.1 REMARK 620 4 OGA B1359 O2 167.3 92.2 90.9 REMARK 620 5 OGA B1359 O2' 89.9 164.4 102.8 77.6 REMARK 620 6 HOH B2112 O 84.0 79.8 165.8 98.4 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1357 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 234 SG REMARK 620 2 HIS B 240 NE2 111.2 REMARK 620 3 CYS B 306 SG 110.8 113.8 REMARK 620 4 CYS B 308 SG 114.2 94.1 111.9 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 1355 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1356 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1357 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 1358 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1356 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1357 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1358 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA B 1359 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1360 DBREF 5FWE A 1 359 UNP O75164 KDM4A_HUMAN 1 359 DBREF 5FWE B 1 359 UNP O75164 KDM4A_HUMAN 1 359 DBREF 5FWE C 1 15 UNP P62805 H4_HUMAN 2 16 DBREF 5FWE D 1 15 UNP P62805 H4_HUMAN 2 16 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 SEQRES 1 C 15 SER GLY 2MR GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 C 15 GLY ALA SEQRES 1 D 15 SER GLY 2MR GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 D 15 GLY ALA MODRES 5FWE 2MR C 3 ARG N3, N4-DIMETHYLARGININE MODRES 5FWE 2MR D 3 ARG N3, N4-DIMETHYLARGININE HET 2MR C 3 13 HET 2MR D 3 22 HET NI A1355 1 HET ZN A1356 1 HET CL A1357 1 HET OGA A1358 10 HET NI B1356 1 HET ZN B1357 1 HET CL B1358 1 HET OGA B1359 10 HET GOL B1360 6 HETNAM 2MR N3, N4-DIMETHYLARGININE HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM OGA N-OXALYLGLYCINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 2MR 2(C8 H18 N4 O2) FORMUL 5 NI 2(NI 2+) FORMUL 6 ZN 2(ZN 2+) FORMUL 7 CL 2(CL 1-) FORMUL 8 OGA 2(C4 H5 N O5) FORMUL 13 GOL C3 H8 O3 FORMUL 14 HOH *391(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 TYR A 59 ASP A 63 5 5 HELIX 5 5 VAL A 94 ASN A 102 1 9 HELIX 6 6 GLU A 113 LEU A 125 1 13 HELIX 7 7 THR A 155 LEU A 157 5 3 HELIX 8 8 ASP A 158 GLU A 163 1 6 HELIX 9 9 GLU A 190 LEU A 194 5 5 HELIX 10 10 PRO A 212 GLU A 214 5 3 HELIX 11 11 HIS A 215 PHE A 227 1 13 HELIX 12 12 PHE A 227 CYS A 234 1 8 HELIX 13 13 ALA A 236 LYS A 241 5 6 HELIX 14 14 SER A 246 TYR A 253 1 8 HELIX 15 15 ARG A 295 ALA A 303 1 9 HELIX 16 16 MET A 317 GLN A 325 1 9 HELIX 17 17 GLN A 325 ALA A 334 1 10 HELIX 18 18 THR A 347 ALA A 351 5 5 HELIX 19 19 SER B 3 LEU B 8 1 6 HELIX 20 20 THR B 20 ARG B 25 1 6 HELIX 21 21 ASN B 26 GLN B 37 1 12 HELIX 22 22 GLY B 38 ALA B 42 5 5 HELIX 23 23 ASP B 61 ASP B 64 5 4 HELIX 24 24 VAL B 94 SER B 103 1 10 HELIX 25 25 GLU B 113 LEU B 125 1 13 HELIX 26 26 THR B 155 LEU B 157 5 3 HELIX 27 27 ASP B 158 GLY B 165 1 8 HELIX 28 28 GLU B 190 LEU B 194 5 5 HELIX 29 29 PRO B 212 GLU B 214 5 3 HELIX 30 30 HIS B 215 PHE B 227 1 13 HELIX 31 31 PHE B 227 CYS B 234 1 8 HELIX 32 32 ALA B 236 LYS B 241 5 6 HELIX 33 33 SER B 246 TYR B 253 1 8 HELIX 34 34 ARG B 295 ALA B 303 1 9 HELIX 35 35 MET B 317 GLN B 325 1 9 HELIX 36 36 ARG B 328 ALA B 334 1 7 HELIX 37 37 THR B 347 GLU B 349 5 3 HELIX 38 38 ALA B 350 LYS B 355 1 6 SHEET 1 AA10 MET A 15 PHE A 17 0 SHEET 2 AA10 LEU A 44 VAL A 47 1 O LEU A 44 N MET A 15 SHEET 3 AA10 PHE A 267 THR A 270 -1 O PHE A 267 N VAL A 47 SHEET 4 AA10 TYR A 195 GLY A 203 -1 O SER A 196 N THR A 270 SHEET 5 AA10 ASN A 284 PHE A 291 -1 O CYS A 285 N HIS A 201 SHEET 6 AA10 TYR A 175 GLY A 179 -1 O TYR A 175 N SER A 288 SHEET 7 AA10 ILE A 131 ASN A 137 -1 O GLY A 133 N PHE A 178 SHEET 8 AA10 ILE A 71 GLN A 78 -1 O ILE A 71 N TYR A 132 SHEET 9 AA10 LEU A 81 GLN A 88 -1 O LEU A 81 N GLN A 78 SHEET 10 AA10 THR A 243 ILE A 245 -1 O LEU A 244 N PHE A 82 SHEET 1 AB 2 VAL A 66 ILE A 67 0 SHEET 2 AB 2 MET A 92 THR A 93 -1 O MET A 92 N ILE A 67 SHEET 1 AC 4 SER A 184 HIS A 188 0 SHEET 2 AC 4 TYR A 275 ASN A 280 -1 O HIS A 276 N HIS A 188 SHEET 3 AC 4 LYS A 206 VAL A 211 -1 O SER A 207 N PHE A 279 SHEET 4 AC 4 ASP A 258 GLN A 262 -1 O ASP A 258 N SER A 210 SHEET 1 BA10 MET B 15 PHE B 17 0 SHEET 2 BA10 LEU B 44 VAL B 47 1 O LEU B 44 N MET B 15 SHEET 3 BA10 PHE B 267 THR B 270 -1 O PHE B 267 N VAL B 47 SHEET 4 BA10 TYR B 195 GLY B 203 -1 O SER B 196 N THR B 270 SHEET 5 BA10 ASN B 284 PHE B 291 -1 O CYS B 285 N HIS B 201 SHEET 6 BA10 TYR B 175 GLY B 179 -1 O TYR B 175 N SER B 288 SHEET 7 BA10 ILE B 131 ASN B 137 -1 O GLY B 133 N PHE B 178 SHEET 8 BA10 ILE B 71 GLN B 78 -1 O ILE B 71 N TYR B 132 SHEET 9 BA10 LEU B 81 GLN B 88 -1 O LEU B 81 N GLN B 78 SHEET 10 BA10 THR B 243 ILE B 245 -1 O LEU B 244 N PHE B 82 SHEET 1 BB 2 VAL B 66 ILE B 67 0 SHEET 2 BB 2 MET B 92 THR B 93 -1 O MET B 92 N ILE B 67 SHEET 1 BC 4 SER B 184 HIS B 188 0 SHEET 2 BC 4 TYR B 275 ASN B 280 -1 O HIS B 276 N HIS B 188 SHEET 3 BC 4 LYS B 206 VAL B 211 -1 O SER B 207 N PHE B 279 SHEET 4 BC 4 ASP B 258 GLN B 262 -1 O ASP B 258 N SER B 210 LINK C GLY C 2 N 2MR C 3 1555 1555 1.33 LINK C GLY D 2 N 2MR D 3 1555 1555 1.33 LINK NE2 HIS A 188 NI NI A1355 1555 1555 2.13 LINK OE2 GLU A 190 NI NI A1355 1555 1555 2.02 LINK SG CYS A 234 ZN ZN A1356 1555 1555 2.28 LINK NE2 HIS A 240 ZN ZN A1356 1555 1555 2.20 LINK NE2 HIS A 276 NI NI A1355 1555 1555 2.30 LINK SG CYS A 306 ZN ZN A1356 1555 1555 2.19 LINK SG CYS A 308 ZN ZN A1356 1555 1555 2.31 LINK NI NI A1355 O2 OGA A1358 1555 1555 2.25 LINK NI NI A1355 O2' OGA A1358 1555 1555 2.16 LINK NI NI A1355 O HOH A2102 1555 1555 2.29 LINK NE2 HIS B 188 NI NI B1356 1555 1555 2.19 LINK OE2 GLU B 190 NI NI B1356 1555 1555 2.01 LINK SG CYS B 234 ZN ZN B1357 1555 1555 2.34 LINK NE2 HIS B 240 ZN ZN B1357 1555 1555 2.04 LINK NE2 HIS B 276 NI NI B1356 1555 1555 2.03 LINK SG CYS B 306 ZN ZN B1357 1555 1555 2.25 LINK SG CYS B 308 ZN ZN B1357 1555 1555 2.38 LINK NI NI B1356 O2 OGA B1359 1555 1555 2.22 LINK NI NI B1356 O2' OGA B1359 1555 1555 2.20 LINK NI NI B1356 O HOH B2112 1555 1555 2.21 SITE 1 AC1 5 HIS A 188 GLU A 190 HIS A 276 OGA A1358 SITE 2 AC1 5 HOH A2102 SITE 1 AC2 4 CYS A 234 HIS A 240 CYS A 306 CYS A 308 SITE 1 AC3 3 PHE A 227 GLY A 229 SER A 230 SITE 1 AC4 13 TYR A 132 PHE A 185 HIS A 188 GLU A 190 SITE 2 AC4 13 SER A 196 ASN A 198 LYS A 206 TRP A 208 SITE 3 AC4 13 THR A 270 HIS A 276 NI A1355 HOH A2102 SITE 4 AC4 13 HOH A2189 SITE 1 AC5 5 HIS B 188 GLU B 190 HIS B 276 OGA B1359 SITE 2 AC5 5 HOH B2112 SITE 1 AC6 4 CYS B 234 HIS B 240 CYS B 306 CYS B 308 SITE 1 AC7 3 PHE B 227 PRO B 228 GLY B 229 SITE 1 AC8 13 TYR B 132 PHE B 185 HIS B 188 GLU B 190 SITE 2 AC8 13 SER B 196 ASN B 198 LYS B 206 TRP B 208 SITE 3 AC8 13 THR B 270 HIS B 276 NI B1356 HOH B2202 SITE 4 AC8 13 2MR D 3 SITE 1 AC9 2 TYR B 59 ARG B 98 CRYST1 100.739 149.400 57.372 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 0.009927 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006693 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017430 0.00000