HEADER OXIDOREDUCTASE 04-SEP-17 6AVS TITLE COMPLEX STRUCTURE OF JMJD5 AND SYMMETRIC MONOMETHYL-ARGININE (MMA) CAVEAT 6AVS NMM HAS A RSR OF 0.59 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING PROTEIN 5,JUMONJI DOMAIN-CONTAINING COMPND 5 PROTEIN 5; COMPND 6 EC: 1.14.11.27; COMPND 7 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: KDM8, JMJD5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS DEMETHYLASE, JUMONJI, HISTONE, ENDOPEPTIDASE, EXOPEPTIDASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LEE,H.LIU,Y.WANG,S.DAI,G.ZHANG REVDAT 3 04-OCT-23 6AVS 1 REMARK REVDAT 2 07-MAR-18 6AVS 1 JRNL REVDAT 1 28-FEB-18 6AVS 0 JRNL AUTH H.LIU,C.WANG,S.LEE,F.NING,Y.WANG,Q.ZHANG,Z.CHEN,J.ZANG, JRNL AUTH 2 J.NIX,S.DAI,P.MARRACK,J.HAGMAN,J.KAPPLER,G.ZHANG JRNL TITL SPECIFIC RECOGNITION OF ARGININE METHYLATED HISTONE TAILS BY JRNL TITL 2 JMJD5 AND JMJD7. JRNL REF SCI REP V. 8 3275 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 29459673 JRNL DOI 10.1038/S41598-018-21432-8 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 17149 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1716 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 50.0147 - 4.6174 1.00 1395 157 0.1982 0.2388 REMARK 3 2 4.6174 - 3.6653 1.00 1330 148 0.1708 0.2043 REMARK 3 3 3.6653 - 3.2021 1.00 1313 146 0.2196 0.2485 REMARK 3 4 3.2021 - 2.9094 1.00 1279 141 0.2523 0.2790 REMARK 3 5 2.9094 - 2.7009 1.00 1297 146 0.2689 0.2836 REMARK 3 6 2.7009 - 2.5416 1.00 1282 141 0.2588 0.2747 REMARK 3 7 2.5416 - 2.4143 1.00 1279 142 0.2585 0.2646 REMARK 3 8 2.4143 - 2.3093 1.00 1273 141 0.2580 0.2807 REMARK 3 9 2.3093 - 2.2204 0.98 1263 138 0.4364 0.5116 REMARK 3 10 2.2204 - 2.1437 0.99 1250 137 0.3793 0.3939 REMARK 3 11 2.1437 - 2.0767 0.99 1249 142 0.3299 0.3580 REMARK 3 12 2.0767 - 2.0173 0.96 1223 137 0.4185 0.4080 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.026 1889 REMARK 3 ANGLE : 1.917 2582 REMARK 3 CHIRALITY : 0.169 276 REMARK 3 PLANARITY : 0.013 334 REMARK 3 DIHEDRAL : 21.668 1012 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 6AVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000229910. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17227 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 49.999 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6400 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 FOR SHELL : NULL 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: 5FBJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.0 8% PEG 3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.84250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.06950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.53150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.06950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.84250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.53150 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: 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 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 ARG A 189 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 193 CB CG CD OE1 NE2 REMARK 470 ARG A 196 CZ NH1 NH2 REMARK 470 GLN A 198 CG CD OE1 NE2 REMARK 470 GLN A 219 CB CG CD OE1 NE2 REMARK 470 GLU A 224 CG CD OE1 OE2 REMARK 470 GLU A 228 CG CD OE1 OE2 REMARK 470 SER A 241 CB OG REMARK 470 GLU A 246 CG CD OE1 OE2 REMARK 470 GLU A 247 CB CG CD OE1 OE2 REMARK 470 GLN A 250 CG CD OE1 NE2 REMARK 470 GLU A 266 CG CD OE1 OE2 REMARK 470 ARG A 268 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 284 CG CD OE1 OE2 REMARK 470 LYS A 286 CG CD CE NZ REMARK 470 GLN A 287 CB CG CD OE1 NE2 REMARK 470 ASP A 293 CG OD1 OD2 REMARK 470 SER A 296 OG REMARK 470 ASP A 299 CG OD1 OD2 REMARK 470 GLU A 301 CB CG CD OE1 OE2 REMARK 470 GLU A 303 CB CG CD OE1 OE2 REMARK 470 GLU A 304 CG CD OE1 OE2 REMARK 470 MET A 333 CG SD CE REMARK 470 ASP A 353 CB CG OD1 OD2 REMARK 470 HIS A 355 CB CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 356 CG CD1 CD2 REMARK 470 HIS A 358 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 369 CG OD1 OD2 REMARK 470 GLU A 371 CG CD OE1 OE2 REMARK 470 LYS A 378 CB CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 204 CZ REMARK 480 CYS A 217 C REMARK 480 GLU A 238 CD REMARK 480 ASP A 245 CA REMARK 480 GLU A 302 OE1 OE2 REMARK 480 GLN A 344 CD REMARK 480 HIS A 355 C REMARK 480 LEU A 407 CD1 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 LYS A 372 O HOH A 601 1.81 REMARK 500 O ASP A 323 O HOH A 602 1.91 REMARK 500 C ASP A 323 O HOH A 602 1.94 REMARK 500 O HOH A 649 O HOH A 676 1.99 REMARK 500 NH1 ARG A 339 O HOH A 603 2.12 REMARK 500 NE2 HIS A 194 O HOH A 604 2.13 REMARK 500 OD1 ASP A 245 O HOH A 605 2.15 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 660 O HOH A 679 3555 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 416 C SER A 416 O 0.152 REMARK 500 SER A 416 C SER A 416 OXT 0.235 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 ARG A 339 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 SER A 416 CA - C - O ANGL. DEV. = -16.1 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 ARG A 189 65.14 30.52 REMARK 500 ILE A 263 -56.14 -124.62 REMARK 500 GLU A 266 70.29 20.70 REMARK 500 ASP A 299 42.43 -91.88 REMARK 500 HIS A 355 -52.35 93.27 REMARK 500 ASN A 367 69.31 -153.44 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 321 NE2 REMARK 620 2 ASP A 323 OD2 110.6 REMARK 620 3 HIS A 400 NE2 90.4 96.5 REMARK 620 4 NMM A 502 O 65.6 97.7 155.2 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NMM A 502 DBREF 6AVS A 183 416 UNP Q8N371 KDM8_HUMAN 221 454 SEQADV 6AVS GLY A 181 UNP Q8N371 EXPRESSION TAG SEQADV 6AVS GLY A 182 UNP Q8N371 EXPRESSION TAG SEQRES 1 A 236 GLY GLY THR VAL PRO ARG LEU HIS ARG PRO SER LEU GLN SEQRES 2 A 236 HIS PHE ARG GLU GLN PHE LEU VAL PRO GLY ARG PRO VAL SEQRES 3 A 236 ILE LEU LYS GLY VAL ALA ASP HIS TRP PRO CYS MET GLN SEQRES 4 A 236 LYS TRP SER LEU GLU TYR ILE GLN GLU ILE ALA GLY CYS SEQRES 5 A 236 ARG THR VAL PRO VAL GLU VAL GLY SER ARG TYR THR ASP SEQRES 6 A 236 GLU GLU TRP SER GLN THR LEU MET THR VAL ASN GLU PHE SEQRES 7 A 236 ILE SER LYS TYR ILE VAL ASN GLU PRO ARG ASP VAL GLY SEQRES 8 A 236 TYR LEU ALA GLN HIS GLN LEU PHE ASP GLN ILE PRO GLU SEQRES 9 A 236 LEU LYS GLN ASP ILE SER ILE PRO ASP TYR CYS SER LEU SEQRES 10 A 236 GLY ASP GLY GLU GLU GLU GLU ILE THR ILE ASN ALA TRP SEQRES 11 A 236 PHE GLY PRO GLN GLY THR ILE SER PRO LEU HIS GLN ASP SEQRES 12 A 236 PRO GLN GLN ASN PHE LEU VAL GLN VAL MET GLY ARG LYS SEQRES 13 A 236 TYR ILE ARG LEU TYR SER PRO GLN GLU SER GLY ALA LEU SEQRES 14 A 236 TYR PRO HIS ASP THR HIS LEU LEU HIS ASN THR SER GLN SEQRES 15 A 236 VAL ASP VAL GLU ASN PRO ASP LEU GLU LYS PHE PRO LYS SEQRES 16 A 236 PHE ALA LYS ALA PRO PHE LEU SER CYS ILE LEU SER PRO SEQRES 17 A 236 GLY GLU ILE LEU PHE ILE PRO VAL LYS TYR TRP HIS TYR SEQRES 18 A 236 VAL ARG ALA LEU ASP LEU SER PHE SER VAL SER PHE TRP SEQRES 19 A 236 TRP SER HET ZN A 501 1 HET NMM A 502 13 HETNAM ZN ZINC ION HETNAM NMM (2S)-2-AMINO-5-[(N-METHYLCARBAMIMIDOYL)AMINO]PENTANOIC HETNAM 2 NMM ACID HETSYN NMM L-NMMA FORMUL 2 ZN ZN 2+ FORMUL 3 NMM C7 H16 N4 O2 FORMUL 4 HOH *89(H2 O) HELIX 1 AA1 SER A 191 PHE A 199 1 9 HELIX 2 AA2 TRP A 215 TRP A 221 1 7 HELIX 3 AA3 SER A 222 GLY A 231 1 10 HELIX 4 AA4 VAL A 255 ILE A 263 1 9 HELIX 5 AA5 GLN A 277 ILE A 282 1 6 HELIX 6 AA6 GLU A 284 ILE A 289 5 6 HELIX 7 AA7 PRO A 292 GLY A 298 5 7 HELIX 8 AA8 GLU A 301 ILE A 305 5 5 HELIX 9 AA9 SER A 342 TYR A 350 5 9 HELIX 10 AB1 PHE A 373 ALA A 377 5 5 SHEET 1 AA1 9 ARG A 186 HIS A 188 0 SHEET 2 AA1 9 VAL A 206 LYS A 209 1 O LYS A 209 N LEU A 187 SHEET 3 AA1 9 ILE A 391 ILE A 394 -1 O ILE A 391 N LEU A 208 SHEET 4 AA1 9 GLN A 326 MET A 333 -1 N ASN A 327 O ILE A 394 SHEET 5 AA1 9 SER A 408 TRP A 415 -1 O VAL A 411 N VAL A 330 SHEET 6 AA1 9 THR A 306 GLY A 312 -1 N THR A 306 O TRP A 414 SHEET 7 AA1 9 GLY A 271 HIS A 276 -1 N LEU A 273 O PHE A 311 SHEET 8 AA1 9 THR A 234 VAL A 239 -1 N GLU A 238 O TYR A 272 SHEET 9 AA1 9 SER A 249 THR A 254 -1 O MET A 253 N VAL A 235 SHEET 1 AA2 4 ILE A 317 HIS A 321 0 SHEET 2 AA2 4 TRP A 399 ALA A 404 -1 O VAL A 402 N SER A 318 SHEET 3 AA2 4 LYS A 336 TYR A 341 -1 N TYR A 341 O TRP A 399 SHEET 4 AA2 4 LEU A 382 LEU A 386 -1 O LEU A 382 N LEU A 340 LINK NE2 HIS A 321 ZN ZN A 501 1555 1555 1.97 LINK OD2 ASP A 323 ZN ZN A 501 1555 1555 2.20 LINK NE2 HIS A 400 ZN ZN A 501 1555 1555 1.96 LINK ZN ZN A 501 O NMM A 502 1555 1555 2.41 SITE 1 AC1 4 HIS A 321 ASP A 323 HIS A 400 NMM A 502 SITE 1 AC2 9 GLU A 238 TYR A 243 TYR A 272 GLN A 275 SITE 2 AC2 9 TRP A 310 SER A 318 HIS A 321 ASP A 323 SITE 3 AC2 9 ZN A 501 CRYST1 49.685 65.063 78.139 90.00 90.00 90.00 P 21 21 21 4 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 0.020127 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015370 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012798 0.00000