HEADER TRANSCRIPTION 14-NOV-14 4D6S TITLE CRYSTAL STRUCTURE OF HUMAN JMJD2D IN COMPLEX WITH N-OXALYLGLYCINE AND TITLE 2 BOUND 5,6-DIMETHYLBENZIMIDAZOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JUMONJI DOMAIN, RESIDUES 1-342; COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, COMPND 6 JUMONJI DOMAIN-CONTAINING PROTEIN 2D, JMJD2D; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: 2,4-PYRIDINECARBOXYLIC ACID IS BOUND TO ACTIVE SITE NI COMPND 9 ATOM 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 KEYWDS TRANSCRIPTION, KDM4D, FLJ10251, MGC141909, DEMETHYLASE/2OG, JUMONJI KEYWDS 2 DOMAIN CONTAINING 2D EXPDTA X-RAY DIFFRACTION AUTHOR T.KROJER,M.VOLLMAR,A.BRADLEY,L.CRAWLEY,A.SZYKOWSKA,N.BURGESS-BROWN, AUTHOR 2 C.GILEADI,C.JOHANSSON,U.OPPERMANN,C.BOUNTRA,C.H.ARROWSMITH, AUTHOR 3 A.EDWARDS,F.VON DELFT REVDAT 2 24-JAN-18 4D6S 1 JRNL REVDAT 1 24-DEC-14 4D6S 0 JRNL AUTH T.KROJER,M.VOLLMAR,A.BRADLEY,L.CRAWLEY,A.SZYKOWSKA, JRNL AUTH 2 N.BURGESS-BROWN,C.GILEADI,C.JOHANSSON,U.OPPERMANN,C.BOUNTRA, JRNL AUTH 3 C.H.ARROWSMITH,A.EDWARDS,F.VON DELFT JRNL TITL CRYSTAL STRUCTURE OF HUMAN JMJD2D IN COMPLEX WITH JRNL TITL 2 N-OXALYLGLYCINE AND BOUND 5,6- DIMETHYLBENZIMIDAZOLE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 76558 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3833 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 29.3309 - 4.1961 1.00 2984 136 0.1718 0.2036 REMARK 3 2 4.1961 - 3.3321 1.00 2833 136 0.1431 0.1637 REMARK 3 3 3.3321 - 2.9113 1.00 2756 167 0.1491 0.1733 REMARK 3 4 2.9113 - 2.6453 1.00 2727 156 0.1514 0.1713 REMARK 3 5 2.6453 - 2.4558 1.00 2744 135 0.1469 0.1433 REMARK 3 6 2.4558 - 2.3111 1.00 2685 186 0.1420 0.1512 REMARK 3 7 2.3111 - 2.1954 1.00 2743 120 0.1403 0.1641 REMARK 3 8 2.1954 - 2.0998 1.00 2709 117 0.1291 0.1490 REMARK 3 9 2.0998 - 2.0190 1.00 2722 144 0.1323 0.1542 REMARK 3 10 2.0190 - 1.9494 1.00 2700 142 0.1233 0.1505 REMARK 3 11 1.9494 - 1.8884 1.00 2679 153 0.1208 0.1490 REMARK 3 12 1.8884 - 1.8345 1.00 2661 149 0.1245 0.1451 REMARK 3 13 1.8345 - 1.7862 1.00 2713 127 0.1246 0.1417 REMARK 3 14 1.7862 - 1.7426 1.00 2655 161 0.1244 0.1584 REMARK 3 15 1.7426 - 1.7030 1.00 2666 153 0.1245 0.1582 REMARK 3 16 1.7030 - 1.6667 1.00 2695 124 0.1169 0.1587 REMARK 3 17 1.6667 - 1.6334 1.00 2677 130 0.1191 0.1502 REMARK 3 18 1.6334 - 1.6026 1.00 2667 150 0.1131 0.1654 REMARK 3 19 1.6026 - 1.5740 1.00 2658 116 0.1140 0.1534 REMARK 3 20 1.5740 - 1.5473 1.00 2669 139 0.1107 0.1561 REMARK 3 21 1.5473 - 1.5223 1.00 2669 148 0.1157 0.1686 REMARK 3 22 1.5223 - 1.4989 1.00 2649 147 0.1161 0.1654 REMARK 3 23 1.4989 - 1.4769 1.00 2668 131 0.1168 0.1538 REMARK 3 24 1.4769 - 1.4561 0.99 2630 135 0.1213 0.1614 REMARK 3 25 1.4561 - 1.4364 0.98 2623 149 0.1275 0.1601 REMARK 3 26 1.4364 - 1.4177 0.98 2585 143 0.1360 0.1763 REMARK 3 27 1.4177 - 1.4000 0.97 2558 139 0.1439 0.1834 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.53 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 : 0.006 2993 REMARK 3 ANGLE : 1.084 4076 REMARK 3 CHIRALITY : 0.046 404 REMARK 3 PLANARITY : 0.006 556 REMARK 3 DIHEDRAL : 12.702 1094 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 4D6S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1290062321. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97630 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PIXEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76648 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG3350, 0.1M HEPES PH 7.0, 0.25M REMARK 280 AMMONIUM SULFATE 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 75.10400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.61250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.61250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.65600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.61250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.61250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.55200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.61250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.61250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.65600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.61250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.61250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.55200 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 75.10400 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2015 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2212 LIES ON A SPECIAL POSITION. 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 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 MET A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 LYS A 7 REMARK 465 ALA A 8 REMARK 465 ASN A 9 REMARK 465 CYS A 10 REMARK 465 ARG A 338 REMARK 465 GLY A 339 REMARK 465 GLN A 340 REMARK 465 ASP A 341 REMARK 465 ARG A 342 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 LYS A 58 CG CD CE NZ REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 LYS A 92 NZ REMARK 470 ARG A 225 NE CZ NH1 NH2 REMARK 470 LYS A 255 CD CE NZ REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 337 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 O HOH A 2125 O HOH A 2127 2.12 REMARK 500 O HOH A 2119 O HOH A 2241 2.13 REMARK 500 O HOH A 2118 O HOH A 2243 2.15 REMARK 500 O HOH A 2116 O HOH A 2122 2.17 REMARK 500 OD1 ASN A 202 O HOH A 2283 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2013 O HOH A 2340 7555 2.12 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 LYS A 186 -5.56 74.85 REMARK 500 ALA A 240 50.16 -143.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2055 DISTANCE = 5.87 ANGSTROMS 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 ZN A1338 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 238 SG REMARK 620 2 HIS A 244 NE2 108.2 REMARK 620 3 CYS A 310 SG 116.1 111.9 REMARK 620 4 CYS A 312 SG 115.2 98.5 105.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1339 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 280 NE2 REMARK 620 2 GLU A 194 OE2 91.5 REMARK 620 3 HIS A 192 NE2 85.1 98.7 REMARK 620 4 HOH A2273 O 173.8 86.2 89.6 REMARK 620 5 OGA A1341 O1 95.4 92.0 169.2 90.4 REMARK 620 6 OGA A1341 C2 102.5 145.5 113.6 82.5 55.7 REMARK 620 7 OGA A1341 O2' 94.7 170.1 89.6 88.3 79.7 24.9 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1338 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMD A 1340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 1341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1346 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1347 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1348 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1349 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1350 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1351 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1352 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1353 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D6Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2D IN COMPLEX WITH 2, 4-PDCA REMARK 900 RELATED ID: 4D6R RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2D IN COMPLEX WITH N- OXALYLGLYCINE REMARK 900 AND BOUND O-TOLUENESULFONAMIDE DBREF 4D6S A 1 342 UNP Q6B0I6 KDM4D_HUMAN 1 342 SEQADV 4D6S SER A 0 UNP Q6B0I6 EXPRESSION TAG SEQRES 1 A 343 SER MET GLU THR MET LYS SER LYS ALA ASN CYS ALA GLN SEQRES 2 A 343 ASN PRO ASN CYS ASN ILE MET ILE PHE HIS PRO THR LYS SEQRES 3 A 343 GLU GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA TYR MET SEQRES 4 A 343 GLU SER GLN GLY ALA HIS ARG ALA GLY LEU ALA LYS ILE SEQRES 5 A 343 ILE PRO PRO LYS GLU TRP LYS ALA ARG GLU THR TYR ASP SEQRES 6 A 343 ASN ILE SER GLU ILE LEU ILE ALA THR PRO LEU GLN GLN SEQRES 7 A 343 VAL ALA SER GLY ARG ALA GLY VAL PHE THR GLN TYR HIS SEQRES 8 A 343 LYS LYS LYS LYS ALA MET THR VAL GLY GLU TYR ARG HIS SEQRES 9 A 343 LEU ALA ASN SER LYS LYS TYR GLN THR PRO PRO HIS GLN SEQRES 10 A 343 ASN PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN ARG SEQRES 11 A 343 ILE TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SER GLY SEQRES 12 A 343 SER LEU PHE ASP GLU ASN THR LYS GLN TRP ASN LEU GLY SEQRES 13 A 343 HIS LEU GLY THR ILE GLN ASP LEU LEU GLU LYS GLU CYS SEQRES 14 A 343 GLY VAL VAL ILE GLU GLY VAL ASN THR PRO TYR LEU TYR SEQRES 15 A 343 PHE GLY MET TRP LYS THR THR PHE ALA TRP HIS THR GLU SEQRES 16 A 343 ASP MET ASP LEU TYR SER ILE ASN TYR LEU HIS LEU GLY SEQRES 17 A 343 GLU PRO LYS THR TRP TYR VAL VAL PRO PRO GLU HIS GLY SEQRES 18 A 343 GLN ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE PRO GLY SEQRES 19 A 343 SER SER ARG GLY CYS GLY ALA PHE LEU ARG HIS LYS VAL SEQRES 20 A 343 ALA LEU ILE SER PRO THR VAL LEU LYS GLU ASN GLY ILE SEQRES 21 A 343 PRO PHE ASN ARG ILE THR GLN GLU ALA GLY GLU PHE MET SEQRES 22 A 343 VAL THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS SEQRES 23 A 343 GLY PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA THR PRO SEQRES 24 A 343 ARG TRP ILE ASP TYR GLY LYS MET ALA SER GLN CYS SER SEQRES 25 A 343 CYS GLY GLU ALA ARG VAL THR PHE SER MET ASP ALA PHE SEQRES 26 A 343 VAL ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU TRP LYS SEQRES 27 A 343 ARG GLY GLN ASP ARG HET ZN A1338 1 HET NI A1339 1 HET DMD A1340 11 HET OGA A1341 10 HET EDO A1342 4 HET EDO A1343 4 HET EDO A1344 4 HET EDO A1345 4 HET EDO A1346 4 HET EDO A1347 4 HET EDO A1348 4 HET EDO A1349 4 HET EDO A1350 4 HET EDO A1351 4 HET DMS A1352 4 HET SO4 A1353 5 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM DMD 5,6-DIMETHYLBENZIMIDAZOLE HETNAM OGA N-OXALYLGLYCINE HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 NI NI 2+ FORMUL 4 DMD C9 H10 N2 FORMUL 5 OGA C4 H5 N O5 FORMUL 6 EDO 10(C2 H6 O2) FORMUL 16 DMS C2 H6 O S FORMUL 17 SO4 O4 S 2- FORMUL 18 HOH *390(H2 O) HELIX 1 1 ASP A 30 GLN A 41 1 12 HELIX 2 2 GLY A 42 ALA A 46 5 5 HELIX 3 3 VAL A 98 ASN A 106 1 9 HELIX 4 4 ASN A 117 ARG A 129 1 13 HELIX 5 5 ILE A 130 ASN A 132 5 3 HELIX 6 6 THR A 159 GLY A 169 1 11 HELIX 7 7 GLU A 194 LEU A 198 5 5 HELIX 8 8 PRO A 216 GLU A 218 5 3 HELIX 9 9 HIS A 219 PHE A 231 1 13 HELIX 10 10 PHE A 231 CYS A 238 1 8 HELIX 11 11 ALA A 240 LYS A 245 5 6 HELIX 12 12 SER A 250 ASN A 257 1 8 HELIX 13 13 ARG A 299 ALA A 307 1 9 HELIX 14 14 THR A 318 GLN A 329 1 12 HELIX 15 15 GLN A 329 LYS A 337 1 9 SHEET 1 AA10 MET A 19 PHE A 21 0 SHEET 2 AA10 LEU A 48 ILE A 51 1 O LEU A 48 N MET A 19 SHEET 3 AA10 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51 SHEET 4 AA10 TYR A 199 GLY A 207 -1 O SER A 200 N THR A 274 SHEET 5 AA10 ASN A 288 PHE A 295 -1 O CYS A 289 N HIS A 205 SHEET 6 AA10 TYR A 179 GLY A 183 -1 O TYR A 179 N ALA A 292 SHEET 7 AA10 ILE A 135 SER A 141 -1 O GLY A 137 N PHE A 182 SHEET 8 AA10 LEU A 75 ARG A 82 -1 O LEU A 75 N TYR A 136 SHEET 9 AA10 VAL A 85 LYS A 92 -1 O VAL A 85 N ARG A 82 SHEET 10 AA10 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86 SHEET 1 AB 2 LEU A 70 ILE A 71 0 SHEET 2 AB 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71 SHEET 1 AC 4 THR A 188 HIS A 192 0 SHEET 2 AC 4 HIS A 280 ASN A 284 -1 O HIS A 280 N HIS A 192 SHEET 3 AC 4 LYS A 210 VAL A 214 -1 O THR A 211 N PHE A 283 SHEET 4 AC 4 ASN A 262 GLN A 266 -1 O ASN A 262 N VAL A 214 LINK ZN ZN A1338 SG CYS A 238 1555 1555 2.23 LINK ZN ZN A1338 NE2 HIS A 244 1555 1555 2.08 LINK ZN ZN A1338 SG CYS A 310 1555 1555 2.27 LINK ZN ZN A1338 SG CYS A 312 1555 1555 2.31 LINK NI NI A1339 NE2 HIS A 280 1555 1555 2.15 LINK NI NI A1339 OE2 GLU A 194 1555 1555 2.00 LINK NI NI A1339 NE2 HIS A 192 1555 1555 2.24 LINK NI NI A1339 O HOH A2273 1555 1555 2.13 LINK NI NI A1339 O1 OGA A1341 1555 1555 2.16 LINK NI NI A1339 C2 OGA A1341 1555 1555 2.75 LINK NI NI A1339 O2' OGA A1341 1555 1555 2.09 SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC2 5 HIS A 192 GLU A 194 HIS A 280 OGA A1341 SITE 2 AC2 5 HOH A2273 SITE 1 AC3 4 TYR A 277 MET A 306 HOH A2282 HOH A2304 SITE 1 AC4 13 TYR A 136 PHE A 189 HIS A 192 GLU A 194 SITE 2 AC4 13 SER A 200 ASN A 202 LYS A 210 HIS A 280 SITE 3 AC4 13 ALA A 292 NI A1339 EDO A1343 HOH A2273 SITE 4 AC4 13 HOH A2384 SITE 1 AC5 2 ASN A 106 HOH A2108 SITE 1 AC6 7 TYR A 179 TYR A 181 GLU A 194 ALA A 292 SITE 2 AC6 7 ASN A 294 OGA A1341 HOH A2273 SITE 1 AC7 7 LYS A 150 GLN A 151 TRP A 152 ASN A 153 SITE 2 AC7 7 HIS A 156 HOH A2049 HOH A2050 SITE 1 AC8 6 GLU A 39 THR A 297 PRO A 298 ARG A 299 SITE 2 AC8 6 HOH A2061 HOH A2385 SITE 1 AC9 6 SER A 80 THR A 87 PHE A 231 LYS A 305 SITE 2 AC9 6 HOH A2265 HOH A2314 SITE 1 BC1 4 MET A 19 ILE A 20 HOH A2021 HOH A2386 SITE 1 BC2 8 SER A 143 THR A 159 GLN A 161 ASP A 162 SITE 2 BC2 8 GLY A 174 VAL A 175 EDO A1350 HOH A2233 SITE 1 BC3 6 GLY A 84 TRP A 126 SER A 250 HOH A2218 SITE 2 BC3 6 HOH A2333 HOH A2388 SITE 1 BC4 8 PHE A 145 ASP A 146 GLU A 147 ASN A 153 SITE 2 BC4 8 HIS A 156 ASP A 162 EDO A1348 HOH A2257 SITE 1 BC5 6 PHE A 118 GLU A 122 ARG A 263 ILE A 264 SITE 2 BC5 6 THR A 265 HOH A2389 SITE 1 BC6 5 PRO A 113 LYS A 124 ASN A 128 TRP A 185 SITE 2 BC6 5 LYS A 186 SITE 1 BC7 3 LYS A 124 LYS A 127 ASN A 128 CRYST1 71.225 71.225 150.208 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 0.014040 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006657 0.00000