HEADER METAL BINDING PROTEIN 14-MAR-07 2P5B TITLE THE COMPLEX STRUCTURE OF JMJD2A AND TRIMETHYLATED H3K36 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC CORE; COMPND 5 SYNONYM: JUMONJI DOMAIN-CONTAINING PROTEIN 2A; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE H3; COMPND 10 CHAIN: I, J; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: JMJD2A, JHDM3A, JMJD2, KIAA0677; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX 4T2; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS JMJD2A, JMJC DOMAIN, HISTONE DEMETHYLASE, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.ZHANG,Z.CHEN,J.ZANG,X.HONG,Y.SHI REVDAT 4 27-NOV-13 2P5B 1 FORMUL HET HETATM HETNAM REVDAT 4 2 1 LINK SITE VERSN REVDAT 3 17-NOV-09 2P5B 1 JRNL REVDAT 2 24-FEB-09 2P5B 1 VERSN REVDAT 1 12-JUN-07 2P5B 0 JRNL AUTH Z.CHEN,J.ZANG,J.KAPPLER,X.HONG,F.CRAWFORD,Q.WANG,F.LAN, JRNL AUTH 2 C.JIANG,J.WHETSTINE,S.DAI,K.HANSEN,Y.SHI,G.ZHANG JRNL TITL STRUCTURAL BASIS OF THE RECOGNITION OF A METHYLATED HISTONE JRNL TITL 2 TAIL BY JMJD2A. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 10818 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17567753 JRNL DOI 10.1073/PNAS.0704525104 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 84582.594 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.0 REMARK 3 NUMBER OF REFLECTIONS : 49265 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1466 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.11 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 27.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2715 REMARK 3 BIN R VALUE (WORKING SET) : 0.4190 REMARK 3 BIN FREE R VALUE : 0.4400 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 2.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 77 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5850 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 284 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.39000 REMARK 3 B22 (A**2) : 6.03000 REMARK 3 B33 (A**2) : -0.64000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.41 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.38 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.80 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 40.33 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : O2_CNS_PAR.TXT REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NOG_CNS_PAR.TXT REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : O2_CNS_TOP.TXT REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NOG_CNS_TOP.TXT REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2P5B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-07. REMARK 100 THE RCSB ID CODE IS RCSB041984. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52214 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: EVAPORATION 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 50.45750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.42200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.45750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 75.42200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, I 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, J 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 -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU A 349 REMARK 465 ALA A 350 REMARK 465 GLY 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 LEU B 8 REMARK 465 ASN B 9 REMARK 465 THR B 347 REMARK 465 PRO B 348 REMARK 465 GLU B 349 REMARK 465 ALA B 350 REMARK 465 ARG I 0 REMARK 465 GLY I 18 REMARK 465 THR I 19 REMARK 465 VAL I 20 REMARK 465 LEU I 21 REMARK 465 ARG J 0 REMARK 465 TYR J 15 REMARK 465 ARG J 16 REMARK 465 PRO J 17 REMARK 465 GLY J 18 REMARK 465 THR J 19 REMARK 465 VAL J 20 REMARK 465 LEU J 21 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 I 1 CG CD CE NZ REMARK 470 SER I 2 OG REMARK 470 LYS J 1 CG CD CE NZ REMARK 470 SER J 2 OG 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 GLU A 4 -21.36 56.98 REMARK 500 ASP A 60 30.35 -99.56 REMARK 500 ASP A 61 29.97 -144.13 REMARK 500 SER A 112 -68.30 -95.92 REMARK 500 LYS A 143 -39.16 -39.94 REMARK 500 ARG A 152 80.89 -158.23 REMARK 500 VAL A 171 -61.02 -97.30 REMARK 500 MET A 192 19.17 59.92 REMARK 500 CYS A 234 107.35 -168.21 REMARK 500 ALA A 236 46.06 -93.70 REMARK 500 ASP A 311 0.27 160.83 REMARK 500 ASN A 338 44.90 -107.31 REMARK 500 PRO A 346 -123.25 -84.10 REMARK 500 SER B 11 36.38 -82.72 REMARK 500 ASP B 61 32.01 -145.65 REMARK 500 SER B 112 -66.70 -96.52 REMARK 500 ASN B 128 67.85 38.76 REMARK 500 LYS B 143 -39.67 -38.80 REMARK 500 ARG B 152 80.56 -154.93 REMARK 500 VAL B 171 -63.13 -94.73 REMARK 500 MET B 192 16.45 57.51 REMARK 500 CYS B 234 110.27 -167.79 REMARK 500 ALA B 236 48.48 -95.05 REMARK 500 ASP B 311 -1.25 162.29 REMARK 500 HIS B 343 1.92 -61.20 REMARK 500 LEU B 345 -80.44 -13.61 REMARK 500 SER I 2 5.69 -177.44 REMARK 500 PRO I 12 -165.62 -62.19 REMARK 500 ALA J 3 155.75 63.94 REMARK 500 PRO J 12 -137.91 -76.64 REMARK 500 HIS J 13 94.78 -37.11 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 FE2 A 352 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 188 NE2 REMARK 620 2 GLU A 190 OE1 105.3 REMARK 620 3 HIS A 276 NE2 93.3 85.3 REMARK 620 4 OGA A 401 O2 164.8 87.3 96.1 REMARK 620 5 OGA A 401 O2' 92.9 158.8 104.8 73.3 REMARK 620 6 OXY A 502 O2 95.4 84.9 168.4 77.1 82.5 REMARK 620 7 OXY A 502 O1 71.6 95.8 164.6 99.2 79.4 24.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 351 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 240 NE2 REMARK 620 2 CYS A 234 SG 105.1 REMARK 620 3 CYS A 306 SG 116.5 114.3 REMARK 620 4 CYS A 308 SG 93.0 114.0 112.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 352 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 GLU B 190 OE1 104.8 REMARK 620 3 HIS B 276 NE2 91.3 87.3 REMARK 620 4 OXY B 503 O1 75.6 100.7 166.0 REMARK 620 5 OXY B 503 O2 95.9 82.4 168.6 24.5 REMARK 620 6 OGA B 402 O2' 90.5 161.2 103.4 72.3 85.4 REMARK 620 7 OGA B 402 O2 165.0 89.2 94.7 96.8 80.5 74.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 351 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 240 NE2 REMARK 620 2 CYS B 234 SG 105.7 REMARK 620 3 CYS B 306 SG 115.6 120.7 REMARK 620 4 CYS B 308 SG 87.5 110.6 111.8 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 ZN A 351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 352 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 B 352 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY B 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GP3 RELATED DB: PDB REMARK 900 THE STRUCTURE OF CATALYTIC CORE OF JMJD2A REMARK 900 RELATED ID: 2GP5 RELATED DB: PDB DBREF 2P5B A 2 350 UNP O75164 JHD3A_HUMAN 2 350 DBREF 2P5B B 2 350 UNP O75164 JHD3A_HUMAN 2 350 DBREF 2P5B I 0 20 UNP P84239 H3_URECA 27 47 DBREF 2P5B J 0 20 UNP P84239 H3_URECA 27 47 SEQADV 2P5B GLY A -1 UNP O75164 CLONING ARTIFACT SEQADV 2P5B SER A 0 UNP O75164 CLONING ARTIFACT SEQADV 2P5B MET A 1 UNP O75164 CLONING ARTIFACT SEQADV 2P5B GLY B -1 UNP O75164 CLONING ARTIFACT SEQADV 2P5B SER B 0 UNP O75164 CLONING ARTIFACT SEQADV 2P5B MET B 1 UNP O75164 CLONING ARTIFACT SEQADV 2P5B M3L I 10 UNP P84239 LYS 37 MODIFIED RESIDUE SEQADV 2P5B LEU I 21 UNP P84239 CLONING ARTIFACT SEQADV 2P5B M3L J 10 UNP P84239 LYS 37 MODIFIED RESIDUE SEQADV 2P5B LEU J 21 UNP P84239 CLONING ARTIFACT SEQRES 1 A 352 GLY SER MET ALA SER GLU SER GLU THR LEU ASN PRO SER SEQRES 2 A 352 ALA ARG ILE MET THR PHE TYR PRO THR MET GLU GLU PHE SEQRES 3 A 352 ARG ASN PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN SEQRES 4 A 352 GLY ALA HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO SEQRES 5 A 352 LYS GLU TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP SEQRES 6 A 352 ASP LEU VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR SEQRES 7 A 352 GLY GLN SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS SEQRES 8 A 352 LYS ALA MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SEQRES 9 A 352 SER ASP LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU SEQRES 10 A 352 GLU LEU GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN SEQRES 11 A 352 PRO PRO ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR SEQRES 12 A 352 GLU LYS HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG SEQRES 13 A 352 THR ILE LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR SEQRES 14 A 352 ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET SEQRES 15 A 352 TRP LYS THR SER PHE ALA TRP HIS THR GLU ASP MET ASP SEQRES 16 A 352 LEU TYR SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SEQRES 17 A 352 SER TRP TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU SEQRES 18 A 352 GLU ARG LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SEQRES 19 A 352 SER CYS GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SEQRES 20 A 352 SER PRO LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP SEQRES 21 A 352 LYS VAL THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE SEQRES 22 A 352 PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN SEQRES 23 A 352 CYS ALA GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE SEQRES 24 A 352 GLU TYR GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS SEQRES 25 A 352 ASP MET VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS SEQRES 26 A 352 PHE GLN PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS SEQRES 27 A 352 ASP ASN THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU SEQRES 28 A 352 ALA SEQRES 1 B 352 GLY SER MET ALA SER GLU SER GLU THR LEU ASN PRO SER SEQRES 2 B 352 ALA ARG ILE MET THR PHE TYR PRO THR MET GLU GLU PHE SEQRES 3 B 352 ARG ASN PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN SEQRES 4 B 352 GLY ALA HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO SEQRES 5 B 352 LYS GLU TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP SEQRES 6 B 352 ASP LEU VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR SEQRES 7 B 352 GLY GLN SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS SEQRES 8 B 352 LYS ALA MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SEQRES 9 B 352 SER ASP LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU SEQRES 10 B 352 GLU LEU GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN SEQRES 11 B 352 PRO PRO ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR SEQRES 12 B 352 GLU LYS HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG SEQRES 13 B 352 THR ILE LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR SEQRES 14 B 352 ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET SEQRES 15 B 352 TRP LYS THR SER PHE ALA TRP HIS THR GLU ASP MET ASP SEQRES 16 B 352 LEU TYR SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SEQRES 17 B 352 SER TRP TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU SEQRES 18 B 352 GLU ARG LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SEQRES 19 B 352 SER CYS GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SEQRES 20 B 352 SER PRO LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP SEQRES 21 B 352 LYS VAL THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE SEQRES 22 B 352 PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN SEQRES 23 B 352 CYS ALA GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE SEQRES 24 B 352 GLU TYR GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS SEQRES 25 B 352 ASP MET VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS SEQRES 26 B 352 PHE GLN PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS SEQRES 27 B 352 ASP ASN THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU SEQRES 28 B 352 ALA SEQRES 1 I 22 ARG LYS SER ALA PRO ALA THR GLY GLY VAL M3L LYS PRO SEQRES 2 I 22 HIS ARG TYR ARG PRO GLY THR VAL LEU SEQRES 1 J 22 ARG LYS SER ALA PRO ALA THR GLY GLY VAL M3L LYS PRO SEQRES 2 J 22 HIS ARG TYR ARG PRO GLY THR VAL LEU MODRES 2P5B M3L I 10 LYS N-TRIMETHYLLYSINE MODRES 2P5B M3L J 10 LYS N-TRIMETHYLLYSINE HET M3L I 10 12 HET M3L J 10 12 HET ZN A 351 1 HET ZN B 351 1 HET FE2 A 352 1 HET FE2 B 352 1 HET OGA A 401 10 HET OGA B 402 10 HET OXY A 501 2 HET OXY A 502 2 HET OXY B 503 2 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION HETNAM FE2 FE (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM OXY OXYGEN MOLECULE FORMUL 3 M3L 2(C9 H21 N2 O2 1+) FORMUL 5 ZN 2(ZN 2+) FORMUL 7 FE2 2(FE 2+) FORMUL 9 OGA 2(C4 H5 N O5) FORMUL 11 OXY 3(O2) FORMUL 14 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 GLN A 325 ALA A 334 1 10 HELIX 17 17 THR B 20 ASN B 26 1 7 HELIX 18 18 ASN B 26 GLN B 37 1 12 HELIX 19 19 GLY B 38 ALA B 42 5 5 HELIX 20 20 VAL B 94 SER B 103 1 10 HELIX 21 21 GLU B 113 LEU B 125 1 13 HELIX 22 22 THR B 155 LEU B 157 5 3 HELIX 23 23 ASP B 158 GLY B 165 1 8 HELIX 24 24 GLU B 190 LEU B 194 5 5 HELIX 25 25 PRO B 212 GLU B 214 5 3 HELIX 26 26 HIS B 215 PHE B 227 1 13 HELIX 27 27 PHE B 227 CYS B 234 1 8 HELIX 28 28 ALA B 236 LYS B 241 5 6 HELIX 29 29 SER B 246 TYR B 253 1 8 HELIX 30 30 ARG B 295 ALA B 303 1 9 HELIX 31 31 MET B 317 GLN B 325 1 9 HELIX 32 32 GLN B 325 GLY B 335 1 11 SHEET 1 A10 MET A 15 PHE A 17 0 SHEET 2 A10 LEU A 44 VAL A 47 1 O LYS A 46 N MET A 15 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 VAL A 260 N TRP A 208 SHEET 1 D10 MET B 15 PHE B 17 0 SHEET 2 D10 LEU B 44 VAL B 47 1 O LYS B 46 N MET B 15 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 HIS B 276 N HIS B 188 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 FE FE2 A 352 1555 1555 2.22 LINK OE1 GLU A 190 FE FE2 A 352 1555 1555 2.06 LINK NE2 HIS A 240 ZN ZN A 351 1555 1555 2.12 LINK NE2 HIS A 276 FE FE2 A 352 1555 1555 2.11 LINK NE2 HIS B 188 FE FE2 B 352 1555 1555 2.24 LINK OE1 GLU B 190 FE FE2 B 352 1555 1555 2.06 LINK NE2 HIS B 240 ZN ZN B 351 1555 1555 2.23 LINK NE2 HIS B 276 FE FE2 B 352 1555 1555 2.09 LINK FE FE2 A 352 O2 OGA A 401 1555 1555 2.41 LINK FE FE2 A 352 O2' OGA A 401 1555 1555 2.25 LINK FE FE2 A 352 O2 OXY A 502 1555 1555 2.42 LINK FE FE2 A 352 O1 OXY A 502 1555 1555 2.41 LINK FE FE2 B 352 O1 OXY B 503 1555 1555 2.43 LINK FE FE2 B 352 O2 OXY B 503 1555 1555 2.39 LINK FE FE2 B 352 O2' OGA B 402 1555 1555 2.34 LINK FE FE2 B 352 O2 OGA B 402 1555 1555 2.24 LINK SG CYS A 234 ZN ZN A 351 1555 1555 2.32 LINK SG CYS A 306 ZN ZN A 351 1555 1555 2.23 LINK SG CYS A 308 ZN ZN A 351 1555 1555 2.41 LINK SG CYS B 234 ZN ZN B 351 1555 1555 2.33 LINK SG CYS B 306 ZN ZN B 351 1555 1555 2.32 LINK SG CYS B 308 ZN ZN B 351 1555 1555 2.45 LINK C VAL I 9 N M3L I 10 1555 1555 1.33 LINK C M3L I 10 N LYS I 11 1555 1555 1.33 LINK C VAL J 9 N M3L J 10 1555 1555 1.33 LINK C M3L J 10 N LYS J 11 1555 1555 1.33 SITE 1 AC1 4 CYS A 234 HIS A 240 CYS A 306 CYS A 308 SITE 1 AC2 4 CYS B 234 HIS B 240 CYS B 306 CYS B 308 SITE 1 AC3 5 HIS A 188 GLU A 190 HIS A 276 OGA A 401 SITE 2 AC3 5 OXY A 502 SITE 1 AC4 5 HIS B 188 GLU B 190 HIS B 276 OGA B 402 SITE 2 AC4 5 OXY B 503 SITE 1 AC5 11 TYR A 132 PHE A 185 HIS A 188 GLU A 190 SITE 2 AC5 11 SER A 196 ASN A 198 LYS A 206 TRP A 208 SITE 3 AC5 11 HIS A 276 FE2 A 352 OXY A 502 SITE 1 AC6 12 TYR B 132 PHE B 185 HIS B 188 GLU B 190 SITE 2 AC6 12 SER B 196 ASN B 198 LYS B 206 TRP B 208 SITE 3 AC6 12 HIS B 276 FE2 B 352 OXY B 503 HOH B 604 SITE 1 AC7 7 HIS A 188 GLU A 190 ASP A 191 LYS A 241 SITE 2 AC7 7 OXY A 502 HOH A 578 M3L I 10 SITE 1 AC8 7 HIS A 188 GLU A 190 LYS A 241 FE2 A 352 SITE 2 AC8 7 OGA A 401 OXY A 501 M3L I 10 SITE 1 AC9 7 HIS B 188 GLU B 190 LYS B 241 FE2 B 352 SITE 2 AC9 7 OGA B 402 HOH B 593 M3L J 10 CRYST1 100.915 150.844 57.346 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 0.009909 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006629 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017438 0.00000