HEADER OXIDOREDUCTASE 14-MAR-17 5NFO TITLE HUMAN JMJD7 IN COMPLEX WITH MN AND 2OG IN THE P21212 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING PROTEIN 7; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: JUMONJI DOMAIN-CONTAINING PROTEIN 7; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: JMJD7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS OXIDOREDUCTASE, NON-HEME, IRON, 2-OXOGLUTARATE, DIOXYGENASE, KEYWDS 2 OXYGENASE, JMJC, JMJC DOMAIN, JMJC DOMAIN-CONTAINING PROTEIN 7, KEYWDS 3 JMJD7, JMJC HYDROXYLASE, JMJC DEMETHYLASE, KDMS, POST-TRANSLATIONAL KEYWDS 4 MODIFICATIONS, PTM, HYDROXYLATION, LYSYL HYDROXYLATION, KEYWDS 5 DIMERISATION, TRANSLATION FACTOR, DEVELOPMENTALLY REGULATED GTP KEYWDS 6 BINDING PROTEINS, DRG1, DRG2, TRAFAC GTPASE, HYPOXIA, NUCLEIC ACID- KEYWDS 7 BINDING, METAL-BINDING, TRANSLATION, HELIX-LOOP-HELIX-BETA, DSBH, KEYWDS 8 FACIAL TRIAD, DEVELOPMENT, CANCER, RIBOSOME BIOGENESIS EXPDTA X-RAY DIFFRACTION AUTHOR R.CHOWDHURY,S.MARKOLOVIC,C.J.SCHOFIELD REVDAT 3 17-JAN-24 5NFO 1 LINK REVDAT 2 12-JUN-19 5NFO 1 AUTHOR REVDAT 1 14-MAR-18 5NFO 0 JRNL AUTH S.MARKOLOVIC,Q.ZHUANG,S.E.WILKINS,C.EATON,M.J.KATZ, JRNL AUTH 2 H.E.SMITH,R.K.LESNIAK,C.HALL,W.B.STRUWE,R.KONIETZNY,S.DAVIS, JRNL AUTH 3 M.YANG,W.GE,J.L.BENESCH,B.M.KESSLER,P.J.RATCLIFFE, JRNL AUTH 4 M.E.COCKMAN,R.FISCHER,P.WAPPNER,R.CHOWDHURY,M.L.COLEMAN, JRNL AUTH 5 C.J.SCHOFIELD JRNL TITL (3S)-LYSYL HYDROXYLATION OF TRAFAC GTPASES IS CATALYZED BY JRNL TITL 2 THE HUMAN JUMONJI-C OXYGENASE JMJD7. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 38901 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1919 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 49.7893 - 5.2347 1.00 2836 139 0.1885 0.2373 REMARK 3 2 5.2347 - 4.1556 1.00 2711 130 0.1218 0.1559 REMARK 3 3 4.1556 - 3.6305 1.00 2669 141 0.1301 0.1722 REMARK 3 4 3.6305 - 3.2986 1.00 2642 157 0.1479 0.1718 REMARK 3 5 3.2986 - 3.0622 1.00 2620 135 0.1583 0.2105 REMARK 3 6 3.0622 - 2.8817 1.00 2647 137 0.1755 0.1769 REMARK 3 7 2.8817 - 2.7374 1.00 2658 100 0.1794 0.2251 REMARK 3 8 2.7374 - 2.6182 1.00 2590 154 0.1957 0.2275 REMARK 3 9 2.6182 - 2.5174 1.00 2639 113 0.2130 0.2723 REMARK 3 10 2.5174 - 2.4306 1.00 2603 156 0.2228 0.2638 REMARK 3 11 2.4306 - 2.3546 1.00 2578 134 0.2249 0.2466 REMARK 3 12 2.3546 - 2.2873 1.00 2604 141 0.2442 0.2436 REMARK 3 13 2.2873 - 2.2271 1.00 2596 140 0.2495 0.2822 REMARK 3 14 2.2271 - 2.1727 1.00 2589 142 0.2694 0.3162 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 : 0.38 REMARK 3 B_SOL : 45.20 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.87000 REMARK 3 B22 (A**2) : 11.57000 REMARK 3 B33 (A**2) : -10.70000 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 : 0.010 5309 REMARK 3 ANGLE : 1.210 7275 REMARK 3 CHIRALITY : 0.048 775 REMARK 3 PLANARITY : 0.005 951 REMARK 3 DIHEDRAL : 13.966 3150 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 5NFO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200004034. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 706E REMARK 200 DATA SCALING SOFTWARE : HKL-2000 706E REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38951 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.170 REMARK 200 RESOLUTION RANGE LOW (A) : 49.776 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2857 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 1.17600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.750 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: 5NFN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26 MG/ML HIS6-JMJD7-R260C, 2 MM MNCL2, REMARK 280 4 MM 2OG, 1.5 M SODIUM NITRATE, 0.1 M SODIUM ACETATE PH 4.6 AND REMARK 280 ADDITIVES (0.25% BETA-NADP, 0.25% ATP, 0.25% N-ACETYL-D- REMARK 280 GALACTOSAMINE, 0.25% GENTAMICIN SULFATE, 0.02 M HEPES-NA PH 6.8), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 68.65750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 68.65750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.51000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 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 HIS A 0 CG ND1 CD2 CE1 NE2 REMARK 470 MET A 1 CG SD CE REMARK 470 GLU A 3 CG CD OE1 OE2 REMARK 470 ARG A 55 CZ NH1 NH2 REMARK 470 GLN A 217 CG CD OE1 NE2 REMARK 470 GLU A 220 CG CD OE1 OE2 REMARK 470 GLU A 221 CD OE1 OE2 REMARK 470 LYS A 225 CG CD CE NZ REMARK 470 GLU A 230 CD OE1 OE2 REMARK 470 GLU A 233 CG CD OE1 OE2 REMARK 470 SER B -1 OG REMARK 470 HIS B 0 ND1 CD2 CE1 NE2 REMARK 470 GLU B 3 CG CD OE1 OE2 REMARK 470 GLU B 22 CG CD OE1 OE2 REMARK 470 LYS B 34 CD CE NZ REMARK 470 GLN B 65 CG CD OE1 NE2 REMARK 470 GLU B 220 CG CD OE1 OE2 REMARK 470 ARG B 249 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 129 27.51 -149.67 REMARK 500 GLN A 131 -143.22 63.92 REMARK 500 HIS A 181 43.04 -90.47 REMARK 500 ALA A 231 44.84 -85.80 REMARK 500 LEU A 274 -0.96 76.17 REMARK 500 ASP A 297 -159.23 -122.09 REMARK 500 TRP B 45 -48.27 -130.28 REMARK 500 VAL B 76 22.65 -140.49 REMARK 500 GLN B 131 -143.03 63.58 REMARK 500 HIS B 181 33.68 -88.95 REMARK 500 LEU B 274 -2.18 71.36 REMARK 500 ASP B 297 -155.17 -118.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 178 NE2 REMARK 620 2 ASP A 180 OD2 103.6 REMARK 620 3 HIS A 277 NE2 91.3 92.2 REMARK 620 4 AKG A 502 O2 168.7 84.0 96.9 REMARK 620 5 AKG A 502 O5 92.4 164.0 88.6 80.1 REMARK 620 6 HOH A 680 O 90.9 85.6 177.2 81.2 93.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 178 NE2 REMARK 620 2 ASP B 180 OD2 106.9 REMARK 620 3 HIS B 277 NE2 87.9 85.8 REMARK 620 4 AKG B 502 O2 166.5 82.0 103.1 REMARK 620 5 AKG B 502 O5 93.4 159.3 91.1 78.8 REMARK 620 6 HOH B 680 O 86.4 90.1 171.6 83.4 95.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 B 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5NFN RELATED DB: PDB DBREF 5NFO A 1 316 UNP P0C870 JMJD7_HUMAN 1 316 DBREF 5NFO B 1 316 UNP P0C870 JMJD7_HUMAN 1 316 SEQADV 5NFO GLY A -18 UNP P0C870 EXPRESSION TAG SEQADV 5NFO SER A -17 UNP P0C870 EXPRESSION TAG SEQADV 5NFO SER A -16 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS A -15 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS A -14 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS A -13 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS A -12 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS A -11 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS A -10 UNP P0C870 EXPRESSION TAG SEQADV 5NFO SER A -9 UNP P0C870 EXPRESSION TAG SEQADV 5NFO SER A -8 UNP P0C870 EXPRESSION TAG SEQADV 5NFO GLY A -7 UNP P0C870 EXPRESSION TAG SEQADV 5NFO LEU A -6 UNP P0C870 EXPRESSION TAG SEQADV 5NFO VAL A -5 UNP P0C870 EXPRESSION TAG SEQADV 5NFO PRO A -4 UNP P0C870 EXPRESSION TAG SEQADV 5NFO ARG A -3 UNP P0C870 EXPRESSION TAG SEQADV 5NFO GLY A -2 UNP P0C870 EXPRESSION TAG SEQADV 5NFO SER A -1 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS A 0 UNP P0C870 EXPRESSION TAG SEQADV 5NFO CYS A 260 UNP P0C870 ARG 260 ENGINEERED MUTATION SEQADV 5NFO GLY B -18 UNP P0C870 EXPRESSION TAG SEQADV 5NFO SER B -17 UNP P0C870 EXPRESSION TAG SEQADV 5NFO SER B -16 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS B -15 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS B -14 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS B -13 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS B -12 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS B -11 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS B -10 UNP P0C870 EXPRESSION TAG SEQADV 5NFO SER B -9 UNP P0C870 EXPRESSION TAG SEQADV 5NFO SER B -8 UNP P0C870 EXPRESSION TAG SEQADV 5NFO GLY B -7 UNP P0C870 EXPRESSION TAG SEQADV 5NFO LEU B -6 UNP P0C870 EXPRESSION TAG SEQADV 5NFO VAL B -5 UNP P0C870 EXPRESSION TAG SEQADV 5NFO PRO B -4 UNP P0C870 EXPRESSION TAG SEQADV 5NFO ARG B -3 UNP P0C870 EXPRESSION TAG SEQADV 5NFO GLY B -2 UNP P0C870 EXPRESSION TAG SEQADV 5NFO SER B -1 UNP P0C870 EXPRESSION TAG SEQADV 5NFO HIS B 0 UNP P0C870 EXPRESSION TAG SEQADV 5NFO CYS B 260 UNP P0C870 ARG 260 ENGINEERED MUTATION SEQRES 1 A 335 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 A 335 VAL PRO ARG GLY SER HIS MET ALA GLU ALA ALA LEU GLU SEQRES 3 A 335 ALA VAL ARG SER GLU LEU ARG GLU PHE PRO ALA ALA ALA SEQRES 4 A 335 ARG GLU LEU CYS VAL PRO LEU ALA VAL PRO TYR LEU ASP SEQRES 5 A 335 LYS PRO PRO THR PRO LEU HIS PHE TYR ARG ASP TRP VAL SEQRES 6 A 335 CYS PRO ASN ARG PRO CYS ILE ILE ARG ASN ALA LEU GLN SEQRES 7 A 335 HIS TRP PRO ALA LEU GLN LYS TRP SER LEU PRO TYR PHE SEQRES 8 A 335 ARG ALA THR VAL GLY SER THR GLU VAL SER VAL ALA VAL SEQRES 9 A 335 THR PRO ASP GLY TYR ALA ASP ALA VAL ARG GLY ASP ARG SEQRES 10 A 335 PHE MET MET PRO ALA GLU ARG ARG LEU PRO LEU SER PHE SEQRES 11 A 335 VAL LEU ASP VAL LEU GLU GLY ARG ALA GLN HIS PRO GLY SEQRES 12 A 335 VAL LEU TYR VAL GLN LYS GLN CYS SER ASN LEU PRO SER SEQRES 13 A 335 GLU LEU PRO GLN LEU LEU PRO ASP LEU GLU SER HIS VAL SEQRES 14 A 335 PRO TRP ALA SER GLU ALA LEU GLY LYS MET PRO ASP ALA SEQRES 15 A 335 VAL ASN PHE TRP LEU GLY GLU ALA ALA ALA VAL THR SER SEQRES 16 A 335 LEU HIS LYS ASP HIS TYR GLU ASN LEU TYR CYS VAL VAL SEQRES 17 A 335 SER GLY GLU LYS HIS PHE LEU PHE HIS PRO PRO SER ASP SEQRES 18 A 335 ARG PRO PHE ILE PRO TYR GLU LEU TYR THR PRO ALA THR SEQRES 19 A 335 TYR GLN LEU THR GLU GLU GLY THR PHE LYS VAL VAL ASP SEQRES 20 A 335 GLU GLU ALA MET GLU LYS VAL PRO TRP ILE PRO LEU ASP SEQRES 21 A 335 PRO LEU ALA PRO ASP LEU ALA ARG TYR PRO SER TYR SER SEQRES 22 A 335 GLN ALA GLN ALA LEU CYS CYS THR VAL ARG ALA GLY GLU SEQRES 23 A 335 MET LEU TYR LEU PRO ALA LEU TRP PHE HIS HIS VAL GLN SEQRES 24 A 335 GLN SER GLN GLY CYS ILE ALA VAL ASN PHE TRP TYR ASP SEQRES 25 A 335 MET GLU TYR ASP LEU LYS TYR SER TYR PHE GLN LEU LEU SEQRES 26 A 335 ASP SER LEU THR LYS ALA SER GLY LEU ASP SEQRES 1 B 335 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 B 335 VAL PRO ARG GLY SER HIS MET ALA GLU ALA ALA LEU GLU SEQRES 3 B 335 ALA VAL ARG SER GLU LEU ARG GLU PHE PRO ALA ALA ALA SEQRES 4 B 335 ARG GLU LEU CYS VAL PRO LEU ALA VAL PRO TYR LEU ASP SEQRES 5 B 335 LYS PRO PRO THR PRO LEU HIS PHE TYR ARG ASP TRP VAL SEQRES 6 B 335 CYS PRO ASN ARG PRO CYS ILE ILE ARG ASN ALA LEU GLN SEQRES 7 B 335 HIS TRP PRO ALA LEU GLN LYS TRP SER LEU PRO TYR PHE SEQRES 8 B 335 ARG ALA THR VAL GLY SER THR GLU VAL SER VAL ALA VAL SEQRES 9 B 335 THR PRO ASP GLY TYR ALA ASP ALA VAL ARG GLY ASP ARG SEQRES 10 B 335 PHE MET MET PRO ALA GLU ARG ARG LEU PRO LEU SER PHE SEQRES 11 B 335 VAL LEU ASP VAL LEU GLU GLY ARG ALA GLN HIS PRO GLY SEQRES 12 B 335 VAL LEU TYR VAL GLN LYS GLN CYS SER ASN LEU PRO SER SEQRES 13 B 335 GLU LEU PRO GLN LEU LEU PRO ASP LEU GLU SER HIS VAL SEQRES 14 B 335 PRO TRP ALA SER GLU ALA LEU GLY LYS MET PRO ASP ALA SEQRES 15 B 335 VAL ASN PHE TRP LEU GLY GLU ALA ALA ALA VAL THR SER SEQRES 16 B 335 LEU HIS LYS ASP HIS TYR GLU ASN LEU TYR CYS VAL VAL SEQRES 17 B 335 SER GLY GLU LYS HIS PHE LEU PHE HIS PRO PRO SER ASP SEQRES 18 B 335 ARG PRO PHE ILE PRO TYR GLU LEU TYR THR PRO ALA THR SEQRES 19 B 335 TYR GLN LEU THR GLU GLU GLY THR PHE LYS VAL VAL ASP SEQRES 20 B 335 GLU GLU ALA MET GLU LYS VAL PRO TRP ILE PRO LEU ASP SEQRES 21 B 335 PRO LEU ALA PRO ASP LEU ALA ARG TYR PRO SER TYR SER SEQRES 22 B 335 GLN ALA GLN ALA LEU CYS CYS THR VAL ARG ALA GLY GLU SEQRES 23 B 335 MET LEU TYR LEU PRO ALA LEU TRP PHE HIS HIS VAL GLN SEQRES 24 B 335 GLN SER GLN GLY CYS ILE ALA VAL ASN PHE TRP TYR ASP SEQRES 25 B 335 MET GLU TYR ASP LEU LYS TYR SER TYR PHE GLN LEU LEU SEQRES 26 B 335 ASP SER LEU THR LYS ALA SER GLY LEU ASP HET MN A 501 1 HET AKG A 502 10 HET GOL A 503 6 HET GOL A 504 6 HET GOL A 505 6 HET NO3 A 506 4 HET MN B 501 1 HET AKG B 502 10 HET GOL B 503 6 HET GOL B 504 6 HET GOL B 505 6 HET NO3 B 506 4 HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM GOL GLYCEROL HETNAM NO3 NITRATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MN 2(MN 2+) FORMUL 4 AKG 2(C5 H6 O5) FORMUL 5 GOL 6(C3 H8 O3) FORMUL 8 NO3 2(N O3 1-) FORMUL 15 HOH *308(H2 O) HELIX 1 AA1 HIS A 0 VAL A 25 1 26 HELIX 2 AA2 THR A 37 TRP A 45 1 9 HELIX 3 AA3 TRP A 61 TRP A 67 1 7 HELIX 4 AA4 SER A 68 GLY A 77 1 10 HELIX 5 AA5 LEU A 109 GLU A 117 1 9 HELIX 6 AA6 SER A 133 LEU A 139 1 7 HELIX 7 AA7 PRO A 140 LEU A 146 5 7 HELIX 8 AA8 VAL A 150 GLY A 158 1 9 HELIX 9 AA9 PRO A 199 ILE A 206 5 8 HELIX 10 AB1 TYR A 250 ALA A 256 5 7 HELIX 11 AB2 ASP A 297 SER A 313 1 17 HELIX 12 AB3 HIS B 0 VAL B 25 1 26 HELIX 13 AB4 THR B 37 TRP B 45 1 9 HELIX 14 AB5 PRO B 62 TRP B 67 1 6 HELIX 15 AB6 SER B 68 GLY B 77 1 10 HELIX 16 AB7 LEU B 109 GLU B 117 1 9 HELIX 17 AB8 SER B 133 LEU B 139 1 7 HELIX 18 AB9 PRO B 140 LEU B 146 5 7 HELIX 19 AC1 VAL B 150 GLY B 158 1 9 HELIX 20 AC2 PRO B 199 ILE B 206 5 8 HELIX 21 AC3 TYR B 250 ALA B 256 5 7 HELIX 22 AC4 ASP B 297 SER B 313 1 17 SHEET 1 AA1 9 TYR A 31 LEU A 32 0 SHEET 2 AA1 9 CYS A 52 ILE A 54 1 O ILE A 53 N LEU A 32 SHEET 3 AA1 9 MET A 268 LEU A 271 -1 O MET A 268 N ILE A 54 SHEET 4 AA1 9 TYR A 182 SER A 190 -1 N TYR A 186 O LEU A 269 SHEET 5 AA1 9 ILE A 286 ASP A 293 -1 O VAL A 288 N CYS A 187 SHEET 6 AA1 9 ALA A 163 GLY A 169 -1 N TRP A 167 O ALA A 287 SHEET 7 AA1 9 VAL A 125 VAL A 128 -1 N VAL A 128 O LEU A 168 SHEET 8 AA1 9 GLU A 80 THR A 86 -1 N THR A 86 O VAL A 125 SHEET 9 AA1 9 ALA A 103 PRO A 108 -1 O ALA A 103 N VAL A 85 SHEET 1 AA2 5 TYR A 90 ALA A 91 0 SHEET 2 AA2 5 VAL A 174 HIS A 178 1 O SER A 176 N ALA A 91 SHEET 3 AA2 5 PHE A 276 GLN A 281 -1 O HIS A 277 N HIS A 178 SHEET 4 AA2 5 GLU A 192 HIS A 198 -1 N HIS A 194 O GLN A 280 SHEET 5 AA2 5 LEU A 259 ARG A 264 -1 O LEU A 259 N PHE A 197 SHEET 1 AA3 4 ALA A 93 ARG A 95 0 SHEET 2 AA3 4 ARG A 98 MET A 101 -1 O MET A 100 N ALA A 93 SHEET 3 AA3 4 GLU A 209 LEU A 218 1 O ALA A 214 N MET A 101 SHEET 4 AA3 4 PHE A 224 ASP A 228 -1 O VAL A 227 N THR A 215 SHEET 1 AA4 4 ALA A 93 ARG A 95 0 SHEET 2 AA4 4 ARG A 98 MET A 101 -1 O MET A 100 N ALA A 93 SHEET 3 AA4 4 GLU A 209 LEU A 218 1 O ALA A 214 N MET A 101 SHEET 4 AA4 4 VAL A 235 TRP A 237 -1 O TRP A 237 N GLU A 209 SHEET 1 AA5 9 TYR B 31 LEU B 32 0 SHEET 2 AA5 9 CYS B 52 ILE B 54 1 O ILE B 53 N LEU B 32 SHEET 3 AA5 9 MET B 268 LEU B 271 -1 O MET B 268 N ILE B 54 SHEET 4 AA5 9 TYR B 182 SER B 190 -1 N TYR B 186 O LEU B 269 SHEET 5 AA5 9 CYS B 285 ASP B 293 -1 O VAL B 288 N CYS B 187 SHEET 6 AA5 9 ALA B 163 GLY B 169 -1 N TRP B 167 O ALA B 287 SHEET 7 AA5 9 VAL B 125 VAL B 128 -1 N VAL B 128 O LEU B 168 SHEET 8 AA5 9 GLU B 80 THR B 86 -1 N THR B 86 O VAL B 125 SHEET 9 AA5 9 ALA B 103 PRO B 108 -1 O ARG B 105 N VAL B 83 SHEET 1 AA6 5 TYR B 90 ALA B 91 0 SHEET 2 AA6 5 VAL B 174 HIS B 178 1 N VAL B 174 O ALA B 91 SHEET 3 AA6 5 PHE B 276 GLN B 281 -1 O VAL B 279 N THR B 175 SHEET 4 AA6 5 GLU B 192 HIS B 198 -1 N HIS B 194 O GLN B 280 SHEET 5 AA6 5 LEU B 259 ARG B 264 -1 O LEU B 259 N PHE B 197 SHEET 1 AA7 4 ALA B 93 ARG B 95 0 SHEET 2 AA7 4 ARG B 98 MET B 101 -1 O ARG B 98 N ARG B 95 SHEET 3 AA7 4 GLU B 209 LEU B 218 1 O ALA B 214 N MET B 101 SHEET 4 AA7 4 PHE B 224 ASP B 228 -1 O LYS B 225 N GLN B 217 SHEET 1 AA8 4 ALA B 93 ARG B 95 0 SHEET 2 AA8 4 ARG B 98 MET B 101 -1 O ARG B 98 N ARG B 95 SHEET 3 AA8 4 GLU B 209 LEU B 218 1 O ALA B 214 N MET B 101 SHEET 4 AA8 4 VAL B 235 TRP B 237 -1 O VAL B 235 N TYR B 211 SSBOND 1 CYS A 47 CYS B 47 1555 1555 2.04 LINK NE2 HIS A 178 MN MN A 501 1555 1555 2.03 LINK OD2 ASP A 180 MN MN A 501 1555 1555 2.13 LINK NE2 HIS A 277 MN MN A 501 1555 1555 2.08 LINK MN MN A 501 O2 AKG A 502 1555 1555 2.08 LINK MN MN A 501 O5 AKG A 502 1555 1555 2.10 LINK MN MN A 501 O HOH A 680 1555 1555 2.48 LINK NE2 HIS B 178 MN MN B 501 1555 1555 2.20 LINK OD2 ASP B 180 MN MN B 501 1555 1555 2.14 LINK NE2 HIS B 277 MN MN B 501 1555 1555 2.23 LINK MN MN B 501 O2 AKG B 502 1555 1555 2.07 LINK MN MN B 501 O5 AKG B 502 1555 1555 2.06 LINK MN MN B 501 O HOH B 680 1555 1555 2.33 SITE 1 AC1 5 HIS A 178 ASP A 180 HIS A 277 AKG A 502 SITE 2 AC1 5 HOH A 680 SITE 1 AC2 14 TYR A 127 THR A 175 HIS A 178 ASP A 180 SITE 2 AC2 14 ASN A 184 TYR A 186 LYS A 193 HIS A 277 SITE 3 AC2 14 VAL A 279 ASN A 289 TRP A 291 MN A 501 SITE 4 AC2 14 HOH A 656 HOH A 680 SITE 1 AC3 8 ALA A 93 VAL A 94 ARG A 95 GLY A 118 SITE 2 AC3 8 SER A 176 ILE A 238 PRO A 239 HOH A 661 SITE 1 AC4 7 LYS A 179 ARG A 203 TYR A 208 PRO A 236 SITE 2 AC4 7 ASP A 307 LYS A 311 HOH A 718 SITE 1 AC5 3 TYR A 300 HOH A 666 SER B -1 SITE 1 AC6 5 SER A 254 GLN A 255 ALA A 256 GLN A 257 SITE 2 AC6 5 HOH A 606 SITE 1 AC7 5 HIS B 178 ASP B 180 HIS B 277 AKG B 502 SITE 2 AC7 5 HOH B 680 SITE 1 AC8 14 TYR B 127 THR B 175 HIS B 178 ASP B 180 SITE 2 AC8 14 ASN B 184 TYR B 186 LYS B 193 HIS B 277 SITE 3 AC8 14 VAL B 279 ASN B 289 TRP B 291 MN B 501 SITE 4 AC8 14 HOH B 645 HOH B 680 SITE 1 AC9 9 CYS A 47 TYR B 42 GLU B 183 MET B 294 SITE 2 AC9 9 GLU B 295 ASP B 297 LYS B 299 HOH B 618 SITE 3 AC9 9 HOH B 632 SITE 1 AD1 5 ARG B 203 TYR B 208 PRO B 236 ASP B 307 SITE 2 AD1 5 LYS B 311 SITE 1 AD2 8 ALA B 93 VAL B 94 ARG B 95 SER B 176 SITE 2 AD2 8 ILE B 238 PRO B 239 ASP B 241 HOH B 656 SITE 1 AD3 4 GLU B 104 ARG B 105 GLN B 217 LEU B 218 CRYST1 137.315 61.020 86.055 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 0.007283 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011620 0.00000