HEADER METAL BINDING PROTEIN 16-APR-06 2GP5 TITLE CRYSTAL STRUCTURE OF CATALYTIC CORE DOMAIN OF JMJD2A COMPLEXED WITH TITLE 2 ALPHA-KETOGLUTARATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: JUMONJI DOMAIN-CONTAINING PROTEIN 2A; COMPND 3 CHAIN: A, B; COMPND 4 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; 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 KEYWDS BETA BARREL, ZINC FINGER, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.CHEN,J.ZANG,J.WHETSTINE,X.HONG,F.DAVRAZOU,T.G.KUTATELADZE, AUTHOR 2 M.SIMPSON,S.DAI,J.HAGMAN,Y.SHI,G.ZHANG REVDAT 5 14-FEB-24 2GP5 1 REMARK LINK REVDAT 4 27-NOV-13 2GP5 1 FORMUL HET HETATM HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 13-JUL-11 2GP5 1 VERSN REVDAT 2 20-MAY-08 2GP5 1 JRNL VERSN REVDAT 1 23-MAY-06 2GP5 0 JRNL AUTH Z.CHEN,J.ZANG,J.WHETSTINE,X.HONG,F.DAVRAZOU,T.G.KUTATELADZE, JRNL AUTH 2 M.SIMPSON,Q.MAO,C.H.PAN,S.DAI,J.HAGMAN,K.HANSEN,Y.SHI, JRNL AUTH 3 G.ZHANG JRNL TITL STRUCTURAL INSIGHTS INTO HISTONE DEMETHYLATION BY JMJD2 JRNL TITL 2 FAMILY MEMBERS JRNL REF CELL(CAMBRIDGE,MASS.) V. 125 691 2006 JRNL REFN ISSN 0092-8674 JRNL PMID 16677698 JRNL DOI 10.1016/J.CELL.2006.04.024 REMARK 2 REMARK 2 RESOLUTION. 2.28 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 70123.850 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.9 REMARK 3 NUMBER OF REFLECTIONS : 32572 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) : 0.236 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1132 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 24.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1545 REMARK 3 BIN R VALUE (WORKING SET) : 0.3370 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 53 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.052 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5624 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.40000 REMARK 3 B22 (A**2) : -0.57000 REMARK 3 B33 (A**2) : 1.97000 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) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.38 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) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.920 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 : 0.41 REMARK 3 BSOL : 59.73 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 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : AKG.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : AKG.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GP5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32572 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 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 (%) : 80.9 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: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 100 MM MGCL2, 100 TRIS, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 50.55350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.76200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.55350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.76200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 349 REMARK 465 ALA A 350 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 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 ASN A 9 N SER A 11 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 10 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 LEU B 345 N - CA - C ANGL. DEV. = 22.5 DEGREES REMARK 500 PRO B 346 C - N - CA ANGL. DEV. = -12.6 DEGREES 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 SER A 3 92.74 42.86 REMARK 500 GLU A 4 -17.62 -41.73 REMARK 500 GLU A 6 46.35 -60.96 REMARK 500 ASN A 9 87.28 -11.01 REMARK 500 PRO A 10 28.66 3.83 REMARK 500 ALA A 12 47.20 33.33 REMARK 500 GLU A 52 36.32 -80.82 REMARK 500 TYR A 59 42.46 -101.78 REMARK 500 ASP A 61 58.25 -90.81 REMARK 500 ILE A 62 -4.78 -146.65 REMARK 500 SER A 79 58.37 38.75 REMARK 500 LYS A 89 -131.32 -82.68 REMARK 500 ALA A 91 148.11 -26.92 REMARK 500 SER A 112 -74.36 -108.00 REMARK 500 LYS A 143 -39.48 -37.54 REMARK 500 VAL A 145 108.85 -58.98 REMARK 500 VAL A 171 -69.35 -90.41 REMARK 500 MET A 192 16.24 58.83 REMARK 500 ALA A 236 63.02 -112.47 REMARK 500 LYS A 310 62.50 -103.29 REMARK 500 ASP A 311 14.35 -172.69 REMARK 500 ASN A 338 55.67 -101.24 REMARK 500 ALA B 12 35.46 -94.83 REMARK 500 GLU B 52 37.90 -82.06 REMARK 500 TYR B 59 43.34 -103.45 REMARK 500 ILE B 62 -2.71 -151.61 REMARK 500 SER B 79 57.28 38.78 REMARK 500 LYS B 89 -131.16 -82.85 REMARK 500 ALA B 91 148.66 -29.19 REMARK 500 SER B 112 -72.51 -108.65 REMARK 500 LYS B 143 -37.06 -36.74 REMARK 500 VAL B 145 108.15 -59.07 REMARK 500 VAL B 171 -72.69 -90.24 REMARK 500 MET B 192 16.23 57.00 REMARK 500 ALA B 236 66.45 -113.10 REMARK 500 LYS B 310 63.61 -102.99 REMARK 500 ASP B 311 13.88 -173.38 REMARK 500 HIS B 343 27.55 -56.45 REMARK 500 THR B 344 21.60 -142.79 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 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 188 NE2 REMARK 620 2 GLU A 190 OE1 100.1 REMARK 620 3 HIS A 276 NE2 94.3 84.8 REMARK 620 4 AKG A 403 O2 160.8 93.3 100.5 REMARK 620 5 AKG A 403 O5 95.8 152.7 116.1 66.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 HIS A 240 NE2 102.8 REMARK 620 3 CYS A 306 SG 110.9 125.8 REMARK 620 4 CYS A 308 SG 110.3 87.9 116.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 GLU B 190 OE1 101.6 REMARK 620 3 HIS B 276 NE2 91.0 82.5 REMARK 620 4 AKG B 403 O2 172.4 85.6 92.4 REMARK 620 5 AKG B 403 O5 103.8 154.2 101.7 68.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 234 SG REMARK 620 2 HIS B 240 NE2 99.2 REMARK 620 3 CYS B 306 SG 118.6 129.9 REMARK 620 4 CYS B 308 SG 100.8 82.3 117.8 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GP3 RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITHOUT ALPHA-KETOGLUTARATE DBREF 2GP5 A 2 350 UNP O75164 JHD3A_HUMAN 2 350 DBREF 2GP5 B 2 350 UNP O75164 JHD3A_HUMAN 2 350 SEQRES 1 A 349 ALA SER GLU SER GLU THR LEU ASN PRO SER ALA ARG ILE SEQRES 2 A 349 MET THR PHE TYR PRO THR MET GLU GLU PHE ARG ASN PHE SEQRES 3 A 349 SER ARG TYR ILE ALA TYR ILE GLU SER GLN GLY ALA HIS SEQRES 4 A 349 ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO LYS GLU TRP SEQRES 5 A 349 LYS PRO ARG ALA SER TYR ASP ASP ILE ASP ASP LEU VAL SEQRES 6 A 349 ILE PRO ALA PRO ILE GLN GLN LEU VAL THR GLY GLN SER SEQRES 7 A 349 GLY LEU PHE THR GLN TYR ASN ILE GLN LYS LYS ALA MET SEQRES 8 A 349 THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SER ASP LYS SEQRES 9 A 349 TYR CYS THR PRO ARG TYR SER GLU PHE GLU GLU LEU GLU SEQRES 10 A 349 ARG LYS TYR TRP LYS ASN LEU THR PHE ASN PRO PRO ILE SEQRES 11 A 349 TYR GLY ALA ASP VAL ASN GLY THR LEU TYR GLU LYS HIS SEQRES 12 A 349 VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG THR ILE LEU SEQRES 13 A 349 ASP LEU VAL GLU LYS GLU SER GLY ILE THR ILE GLU GLY SEQRES 14 A 349 VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS THR SEQRES 15 A 349 SER PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR SER SEQRES 16 A 349 ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SER TRP TYR SEQRES 17 A 349 SER VAL PRO PRO GLU HIS GLY LYS ARG LEU GLU ARG LEU SEQRES 18 A 349 ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SER CYS GLU SEQRES 19 A 349 ALA PHE LEU ARG HIS LYS MET THR LEU ILE SER PRO LEU SEQRES 20 A 349 MET LEU LYS LYS TYR GLY ILE PRO PHE ASP LYS VAL THR SEQRES 21 A 349 GLN GLU ALA GLY GLU PHE MET ILE THR PHE PRO TYR GLY SEQRES 22 A 349 TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA GLU SEQRES 23 A 349 SER THR ASN PHE ALA THR ARG ARG TRP ILE GLU TYR GLY SEQRES 24 A 349 LYS GLN ALA VAL LEU CYS SER CYS ARG LYS ASP MET VAL SEQRES 25 A 349 LYS ILE SER MET ASP VAL PHE VAL ARG LYS PHE GLN PRO SEQRES 26 A 349 GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS ASP ASN THR SEQRES 27 A 349 VAL ILE ASP HIS THR LEU PRO THR PRO GLU ALA SEQRES 1 B 349 ALA SER GLU SER GLU THR LEU ASN PRO SER ALA ARG ILE SEQRES 2 B 349 MET THR PHE TYR PRO THR MET GLU GLU PHE ARG ASN PHE SEQRES 3 B 349 SER ARG TYR ILE ALA TYR ILE GLU SER GLN GLY ALA HIS SEQRES 4 B 349 ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO LYS GLU TRP SEQRES 5 B 349 LYS PRO ARG ALA SER TYR ASP ASP ILE ASP ASP LEU VAL SEQRES 6 B 349 ILE PRO ALA PRO ILE GLN GLN LEU VAL THR GLY GLN SER SEQRES 7 B 349 GLY LEU PHE THR GLN TYR ASN ILE GLN LYS LYS ALA MET SEQRES 8 B 349 THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SER ASP LYS SEQRES 9 B 349 TYR CYS THR PRO ARG TYR SER GLU PHE GLU GLU LEU GLU SEQRES 10 B 349 ARG LYS TYR TRP LYS ASN LEU THR PHE ASN PRO PRO ILE SEQRES 11 B 349 TYR GLY ALA ASP VAL ASN GLY THR LEU TYR GLU LYS HIS SEQRES 12 B 349 VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG THR ILE LEU SEQRES 13 B 349 ASP LEU VAL GLU LYS GLU SER GLY ILE THR ILE GLU GLY SEQRES 14 B 349 VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS THR SEQRES 15 B 349 SER PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR SER SEQRES 16 B 349 ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SER TRP TYR SEQRES 17 B 349 SER VAL PRO PRO GLU HIS GLY LYS ARG LEU GLU ARG LEU SEQRES 18 B 349 ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SER CYS GLU SEQRES 19 B 349 ALA PHE LEU ARG HIS LYS MET THR LEU ILE SER PRO LEU SEQRES 20 B 349 MET LEU LYS LYS TYR GLY ILE PRO PHE ASP LYS VAL THR SEQRES 21 B 349 GLN GLU ALA GLY GLU PHE MET ILE THR PHE PRO TYR GLY SEQRES 22 B 349 TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA GLU SEQRES 23 B 349 SER THR ASN PHE ALA THR ARG ARG TRP ILE GLU TYR GLY SEQRES 24 B 349 LYS GLN ALA VAL LEU CYS SER CYS ARG LYS ASP MET VAL SEQRES 25 B 349 LYS ILE SER MET ASP VAL PHE VAL ARG LYS PHE GLN PRO SEQRES 26 B 349 GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS ASP ASN THR SEQRES 27 B 349 VAL ILE ASP HIS THR LEU PRO THR PRO GLU ALA HET ZN A 401 1 HET FE2 A 402 1 HET AKG A 403 10 HET ZN B 401 1 HET FE2 B 402 1 HET AKG B 403 10 HETNAM ZN ZINC ION HETNAM FE2 FE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 3 ZN 2(ZN 2+) FORMUL 4 FE2 2(FE 2+) FORMUL 5 AKG 2(C5 H6 O5) FORMUL 9 HOH *125(H2 O) HELIX 1 1 THR A 20 ARG A 25 1 6 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 ARG B 25 1 6 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 ALA B 334 1 10 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 PHE A 17 SHEET 3 A10 PHE A 267 THR A 270 -1 O PHE A 267 N VAL A 47 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 GLY A 278 N PHE A 185 SHEET 3 C 4 LYS A 206 VAL A 211 -1 N TYR A 209 O ALA A 277 SHEET 4 C 4 ASP A 258 GLN A 262 -1 O GLN A 262 N LYS A 206 SHEET 1 D10 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 PHE B 267 N VAL B 47 SHEET 4 D10 TYR B 195 GLY B 203 -1 N SER B 196 O THR B 270 SHEET 5 D10 ASN B 284 PHE B 291 -1 O GLU B 287 N TYR B 199 SHEET 6 D10 TYR B 175 GLY B 179 -1 N TYR B 177 O ALA B 286 SHEET 7 D10 ILE B 131 ASN B 137 -1 N GLY B 133 O PHE B 178 SHEET 8 D10 ILE B 71 GLN B 78 -1 N ILE B 71 O TYR B 132 SHEET 9 D10 LEU B 81 GLN B 88 -1 O TYR B 85 N LEU B 74 SHEET 10 D10 THR B 243 ILE B 245 -1 O LEU B 244 N PHE B 82 SHEET 1 E 2 VAL B 66 ILE B 67 0 SHEET 2 E 2 MET B 92 THR B 93 -1 O MET B 92 N ILE B 67 SHEET 1 F 4 SER B 184 HIS B 188 0 SHEET 2 F 4 TYR B 275 ASN B 280 -1 O GLY B 278 N PHE B 185 SHEET 3 F 4 LYS B 206 VAL B 211 -1 N TYR B 209 O ALA B 277 SHEET 4 F 4 ASP B 258 GLN B 262 -1 O VAL B 260 N TRP B 208 LINK NE2 HIS A 188 FE FE2 A 402 1555 1555 2.30 LINK OE1 GLU A 190 FE FE2 A 402 1555 1555 2.10 LINK SG CYS A 234 ZN ZN A 401 1555 1555 2.35 LINK NE2 HIS A 240 ZN ZN A 401 1555 1555 2.28 LINK NE2 HIS A 276 FE FE2 A 402 1555 1555 2.18 LINK SG CYS A 306 ZN ZN A 401 1555 1555 2.43 LINK SG CYS A 308 ZN ZN A 401 1555 1555 2.58 LINK FE FE2 A 402 O2 AKG A 403 1555 1555 2.43 LINK FE FE2 A 402 O5 AKG A 403 1555 1555 2.56 LINK NE2 HIS B 188 FE FE2 B 402 1555 1555 2.23 LINK OE1 GLU B 190 FE FE2 B 402 1555 1555 2.14 LINK SG CYS B 234 ZN ZN B 401 1555 1555 2.34 LINK NE2 HIS B 240 ZN ZN B 401 1555 1555 2.38 LINK NE2 HIS B 276 FE FE2 B 402 1555 1555 2.27 LINK SG CYS B 306 ZN ZN B 401 1555 1555 2.34 LINK SG CYS B 308 ZN ZN B 401 1555 1555 2.74 LINK FE FE2 B 402 O2 AKG B 403 1555 1555 2.33 LINK FE FE2 B 402 O5 AKG B 403 1555 1555 2.52 SITE 1 AC1 4 CYS A 234 HIS A 240 CYS A 306 CYS A 308 SITE 1 AC2 4 HIS A 188 GLU A 190 HIS A 276 AKG A 403 SITE 1 AC3 10 TYR A 132 PHE A 185 HIS A 188 GLU A 190 SITE 2 AC3 10 SER A 196 ASN A 198 LYS A 206 TRP A 208 SITE 3 AC3 10 HIS A 276 FE2 A 402 SITE 1 AC4 4 CYS B 234 HIS B 240 CYS B 306 CYS B 308 SITE 1 AC5 4 HIS B 188 GLU B 190 HIS B 276 AKG B 403 SITE 1 AC6 11 TYR B 132 PHE B 185 HIS B 188 GLU B 190 SITE 2 AC6 11 SER B 196 ASN B 198 LYS B 206 TRP B 208 SITE 3 AC6 11 HIS B 276 SER B 288 FE2 B 402 CRYST1 101.107 149.524 57.028 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 0.009891 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017535 0.00000