PDB Short entry for 3PUA HEADER PROTEIN BINDING 03-DEC-10 3PUA TITLE PHF2 JUMONJI-NOG-NI(II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD FINGER PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JUMONJI DOMAIN (UNP RESIDUES 60-451); COMPND 5 SYNONYM: GRC5; COMPND 6 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: PHF2, KIAA0662; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PXC870 KEYWDS ALPHA-KETOGLUTARATE-FE2+ DEPENDENT DIOXYGENASES, HISTONE TAIL BINDING KEYWDS 2 PROTEIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,A.K.UPADHYAY,H.HASHIMOTO,X.ZHANG,X.CHENG REVDAT 4 06-SEP-23 3PUA 1 REMARK LINK REVDAT 3 29-FEB-12 3PUA 1 JRNL REVDAT 2 02-NOV-11 3PUA 1 VERSN REVDAT 1 26-JAN-11 3PUA 0 JRNL AUTH J.R.HORTON,A.K.UPADHYAY,H.HASHIMOTO,X.ZHANG,X.CHENG JRNL TITL STRUCTURAL BASIS FOR HUMAN PHF2 JUMONJI DOMAIN INTERACTION JRNL TITL 2 WITH METAL IONS. JRNL REF J.MOL.BIOL. V. 406 1 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21167174 JRNL DOI 10.1016/J.JMB.2010.12.013 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 31464 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1575 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 32.8885 - 4.0599 0.93 3388 169 0.1524 0.2076 REMARK 3 2 4.0599 - 3.2233 0.95 3401 171 0.1467 0.1853 REMARK 3 3 3.2233 - 2.8161 0.93 3355 168 0.1679 0.1954 REMARK 3 4 2.8161 - 2.5588 0.91 3199 162 0.1690 0.2168 REMARK 3 5 2.5588 - 2.3754 0.88 3107 162 0.1660 0.2157 REMARK 3 6 2.3754 - 2.2354 0.85 3011 155 0.1614 0.2163 REMARK 3 7 2.2354 - 2.1235 0.81 2884 149 0.1669 0.1985 REMARK 3 8 2.1235 - 2.0311 0.78 2760 149 0.1783 0.2375 REMARK 3 9 2.0311 - 1.9529 0.73 2546 145 0.1899 0.2067 REMARK 3 10 1.9529 - 1.8855 0.64 2238 145 0.2211 0.3048 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 : 0.35 REMARK 3 B_SOL : 47.59 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.86450 REMARK 3 B22 (A**2) : -5.81130 REMARK 3 B33 (A**2) : -7.05310 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.15060 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 3019 REMARK 3 ANGLE : 0.982 4075 REMARK 3 CHIRALITY : 0.068 441 REMARK 3 PLANARITY : 0.005 520 REMARK 3 DIHEDRAL : 13.744 1095 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 80:200) REMARK 3 ORIGIN FOR THE GROUP (A): 24.7602 15.9289 24.4989 REMARK 3 T TENSOR REMARK 3 T11: 0.3582 T22: 0.2049 REMARK 3 T33: 0.1200 T12: -0.0145 REMARK 3 T13: 0.0069 T23: 0.0193 REMARK 3 L TENSOR REMARK 3 L11: 1.2177 L22: 1.3929 REMARK 3 L33: 1.6349 L12: 0.0908 REMARK 3 L13: 0.1668 L23: -0.3855 REMARK 3 S TENSOR REMARK 3 S11: 0.0362 S12: -0.1964 S13: -0.0650 REMARK 3 S21: 0.4284 S22: -0.1438 S23: -0.0661 REMARK 3 S31: 0.2734 S32: 0.1471 S33: 0.0836 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 201:356) REMARK 3 ORIGIN FOR THE GROUP (A): 25.2065 20.0459 14.8712 REMARK 3 T TENSOR REMARK 3 T11: 0.1466 T22: 0.1147 REMARK 3 T33: 0.1025 T12: 0.0038 REMARK 3 T13: -0.0157 T23: 0.0258 REMARK 3 L TENSOR REMARK 3 L11: 0.6990 L22: 1.5893 REMARK 3 L33: 1.4226 L12: 0.1764 REMARK 3 L13: 0.0271 L23: 0.4178 REMARK 3 S TENSOR REMARK 3 S11: 0.0198 S12: -0.0116 S13: -0.0486 REMARK 3 S21: 0.2290 S22: -0.0873 S23: -0.1151 REMARK 3 S31: 0.1842 S32: 0.1581 S33: 0.0594 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 357:444) REMARK 3 ORIGIN FOR THE GROUP (A): 17.1510 18.3735 -8.2103 REMARK 3 T TENSOR REMARK 3 T11: 0.2289 T22: 0.2257 REMARK 3 T33: 0.1979 T12: 0.0355 REMARK 3 T13: -0.0132 T23: 0.0032 REMARK 3 L TENSOR REMARK 3 L11: 0.9747 L22: 1.0222 REMARK 3 L33: 0.6335 L12: 0.5390 REMARK 3 L13: 0.2448 L23: 0.4648 REMARK 3 S TENSOR REMARK 3 S11: -0.0966 S12: 0.1993 S13: 0.0855 REMARK 3 S21: -0.1921 S22: 0.0335 S23: 0.0142 REMARK 3 S31: -0.1003 S32: 0.0697 S33: 0.0540 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 3PUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34150 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 32.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.56300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: PDB ENTRY 3KV4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18-30% POLYETHYLENE GLYCOL 3350 AND REMARK 280 100 MM NACITRATE, PH 5.2-6.0, VAPOR DIFFUSION, PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 54.78750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.88350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.78750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.88350 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 60 REMARK 465 THR A 61 REMARK 465 LEU A 62 REMARK 465 LYS A 63 REMARK 465 LYS A 64 REMARK 465 LYS A 65 REMARK 465 ARG A 66 REMARK 465 THR A 67 REMARK 465 TRP A 68 REMARK 465 HIS A 69 REMARK 465 LYS A 70 REMARK 465 HIS A 71 REMARK 465 GLY A 72 REMARK 465 PRO A 73 REMARK 465 GLY A 74 REMARK 465 GLN A 75 REMARK 465 ALA A 76 REMARK 465 PRO A 77 REMARK 465 ASP A 78 REMARK 465 VAL A 79 REMARK 465 ALA A 445 REMARK 465 SER A 446 REMARK 465 LYS A 447 REMARK 465 ALA A 448 REMARK 465 VAL A 449 REMARK 465 ARG A 450 REMARK 465 PRO A 451 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 GLN A 83 CG CD OE1 NE2 REMARK 470 GLN A 87 CG CD OE1 NE2 REMARK 470 LEU A 88 CG CD1 CD2 REMARK 470 LYS A 91 CG CD CE NZ REMARK 470 GLU A 120 CG CD OE1 OE2 REMARK 470 LYS A 175 CG CD CE NZ REMARK 470 GLU A 176 CG CD OE1 OE2 REMARK 470 ASN A 185 CG OD1 ND2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 SER A 359 OG REMARK 470 LEU A 360 CG CD1 CD2 REMARK 470 THR A 361 OG1 CG2 REMARK 470 GLN A 362 CG CD OE1 NE2 REMARK 470 LYS A 389 CG CD CE NZ REMARK 470 LYS A 411 CG CD CE NZ REMARK 470 LYS A 412 CG CD CE NZ REMARK 470 GLN A 413 CG CD OE1 NE2 REMARK 470 GLU A 417 CG CD OE1 OE2 REMARK 470 LYS A 433 CG CD CE NZ 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 VAL A 233 18.19 -140.59 REMARK 500 ASP A 243 7.54 82.12 REMARK 500 PRO A 273 46.91 -81.15 REMARK 500 LEU A 360 -27.13 67.60 REMARK 500 ALA A 414 35.20 -69.00 REMARK 500 LEU A 415 -165.77 65.64 REMARK 500 ALA A 416 -0.72 -142.84 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 NI A 2 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 249 NE2 REMARK 620 2 ASP A 251 OD1 92.5 REMARK 620 3 TYR A 321 OH 97.7 87.8 REMARK 620 4 OGA A 454 O2' 91.9 175.1 89.4 REMARK 620 5 OGA A 454 O2 171.5 95.7 84.6 80.0 REMARK 620 6 HOH A 462 O 93.3 90.9 169.0 91.1 84.6 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 NI A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 452 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 453 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 454 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PTR RELATED DB: PDB REMARK 900 PHF2 JUMONJI DOMAIN REMARK 900 RELATED ID: 3PU3 RELATED DB: PDB REMARK 900 PHF2 JUMONJI-NOG REMARK 900 RELATED ID: 3PU8 RELATED DB: PDB REMARK 900 PHF2 JUMONJI-NOG-F2(II) REMARK 900 RELATED ID: 3PUA RELATED DB: PDB DBREF 3PUA A 60 451 UNP O75151 PHF2_HUMAN 60 451 SEQRES 1 A 392 SER THR LEU LYS LYS LYS ARG THR TRP HIS LYS HIS GLY SEQRES 2 A 392 PRO GLY GLN ALA PRO ASP VAL LYS PRO VAL GLN ASN GLY SEQRES 3 A 392 SER GLN LEU PHE ILE LYS GLU LEU ARG SER ARG THR PHE SEQRES 4 A 392 PRO SER ALA GLU ASP VAL VAL ALA ARG VAL PRO GLY SER SEQRES 5 A 392 GLN LEU THR LEU GLY TYR MET GLU GLU HIS GLY PHE THR SEQRES 6 A 392 GLU PRO ILE LEU VAL PRO LYS LYS ASP GLY LEU GLY LEU SEQRES 7 A 392 ALA VAL PRO ALA PRO THR PHE TYR VAL SER ASP VAL GLU SEQRES 8 A 392 ASN TYR VAL GLY PRO GLU ARG SER VAL ASP VAL THR ASP SEQRES 9 A 392 VAL THR LYS GLN LYS ASP CYS LYS MET LYS LEU LYS GLU SEQRES 10 A 392 PHE VAL ASP TYR TYR TYR SER THR ASN ARG LYS ARG VAL SEQRES 11 A 392 LEU ASN VAL THR ASN LEU GLU PHE SER ASP THR ARG MET SEQRES 12 A 392 SER SER PHE VAL GLU PRO PRO ASP ILE VAL LYS LYS LEU SEQRES 13 A 392 SER TRP VAL GLU ASN TYR TRP PRO ASP ASP ALA LEU LEU SEQRES 14 A 392 ALA LYS PRO LYS VAL THR LYS TYR CYS LEU ILE CYS VAL SEQRES 15 A 392 LYS ASP SER TYR THR ASP PHE HIS ILE ASP SER GLY GLY SEQRES 16 A 392 ALA SER ALA TRP TYR HIS VAL LEU LYS GLY GLU LYS THR SEQRES 17 A 392 PHE TYR LEU ILE ARG PRO ALA SER ALA ASN ILE SER LEU SEQRES 18 A 392 TYR GLU ARG TRP ARG SER ALA SER ASN HIS SER GLU MET SEQRES 19 A 392 PHE PHE ALA ASP GLN VAL ASP LYS CYS TYR LYS CYS ILE SEQRES 20 A 392 VAL LYS GLN GLY GLN THR LEU PHE ILE PRO SER GLY TRP SEQRES 21 A 392 ILE TYR ALA THR LEU THR PRO VAL ASP CYS LEU ALA PHE SEQRES 22 A 392 ALA GLY HIS PHE LEU HIS SER LEU SER VAL GLU MET GLN SEQRES 23 A 392 MET ARG ALA TYR GLU VAL GLU ARG ARG LEU LYS LEU GLY SEQRES 24 A 392 SER LEU THR GLN PHE PRO ASN PHE GLU THR ALA CYS TRP SEQRES 25 A 392 TYR MET GLY LYS HIS LEU LEU GLU ALA PHE LYS GLY SER SEQRES 26 A 392 HIS LYS SER GLY LYS GLN LEU PRO PRO HIS LEU VAL GLN SEQRES 27 A 392 GLY ALA LYS ILE LEU ASN GLY ALA PHE ARG SER TRP THR SEQRES 28 A 392 LYS LYS GLN ALA LEU ALA GLU HIS GLU ASP GLU LEU PRO SEQRES 29 A 392 GLU HIS PHE LYS PRO SER GLN LEU ILE LYS ASP LEU ALA SEQRES 30 A 392 LYS GLU ILE ARG LEU SER GLU ASN ALA SER LYS ALA VAL SEQRES 31 A 392 ARG PRO HET NI A 2 1 HET EDO A 1 4 HET EDO A 452 4 HET EDO A 3 4 HET EDO A 4 4 HET EDO A 5 4 HET EDO A 6 4 HET EDO A 7 4 HET EDO A 8 4 HET EDO A 9 4 HET EDO A 10 4 HET EDO A 11 4 HET CL A 453 1 HET OGA A 454 10 HETNAM NI NICKEL (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETNAM OGA N-OXALYLGLYCINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NI NI 2+ FORMUL 3 EDO 11(C2 H6 O2) FORMUL 14 CL CL 1- FORMUL 15 OGA C4 H5 N O5 FORMUL 16 HOH *227(H2 O) HELIX 1 1 SER A 86 ARG A 96 1 11 HELIX 2 2 SER A 100 VAL A 104 5 5 HELIX 3 3 PRO A 109 LEU A 113 5 5 HELIX 4 4 THR A 114 GLY A 122 1 9 HELIX 5 5 TYR A 145 GLY A 154 1 10 HELIX 6 6 LEU A 174 TYR A 182 1 9 HELIX 7 7 THR A 200 VAL A 206 5 7 HELIX 8 8 PRO A 209 SER A 216 1 8 HELIX 9 9 SER A 216 TRP A 222 1 7 HELIX 10 10 ASP A 251 ALA A 255 5 5 HELIX 11 11 ALA A 274 ALA A 287 1 14 HELIX 12 12 ASN A 289 MET A 293 5 5 HELIX 13 13 PHE A 294 VAL A 299 5 6 HELIX 14 14 SER A 341 LYS A 356 1 16 HELIX 15 15 ASN A 365 GLY A 388 1 24 HELIX 16 16 PRO A 392 THR A 410 1 19 HELIX 17 17 HIS A 418 LEU A 422 5 5 HELIX 18 18 LYS A 427 ASN A 444 1 18 SHEET 1 A 6 ALA A 106 ARG A 107 0 SHEET 2 A 6 ILE A 127 VAL A 129 1 O LEU A 128 N ALA A 106 SHEET 3 A 6 THR A 312 ILE A 315 -1 O THR A 312 N VAL A 129 SHEET 4 A 6 SER A 256 ILE A 271 -1 N TYR A 259 O LEU A 313 SHEET 5 A 6 ILE A 320 PHE A 336 -1 O PHE A 332 N HIS A 260 SHEET 6 A 6 TYR A 245 HIS A 249 -1 N THR A 246 O THR A 323 SHEET 1 B 7 ASP A 169 LYS A 173 0 SHEET 2 B 7 SER A 158 ASP A 163 -1 N VAL A 161 O CYS A 170 SHEET 3 B 7 LEU A 190 GLU A 196 -1 O ASN A 191 N THR A 162 SHEET 4 B 7 TYR A 236 CYS A 240 -1 O ILE A 239 N VAL A 192 SHEET 5 B 7 ILE A 320 PHE A 336 -1 O ALA A 333 N TYR A 236 SHEET 6 B 7 SER A 256 ILE A 271 -1 N HIS A 260 O PHE A 332 SHEET 7 B 7 TYR A 303 LYS A 308 -1 O CYS A 305 N PHE A 268 LINK NI NI A 2 NE2 HIS A 249 1555 1555 2.17 LINK NI NI A 2 OD1 ASP A 251 1555 1555 2.10 LINK NI NI A 2 OH TYR A 321 1555 1555 2.12 LINK NI NI A 2 O2' OGA A 454 1555 1555 2.15 LINK NI NI A 2 O2 OGA A 454 1555 1555 2.20 LINK NI NI A 2 O HOH A 462 1555 1555 2.21 SITE 1 AC1 5 HIS A 249 ASP A 251 TYR A 321 OGA A 454 SITE 2 AC1 5 HOH A 462 SITE 1 AC2 6 PHE A 426 LYS A 427 LEU A 431 HOH A 573 SITE 2 AC2 6 HOH A 596 HOH A 631 SITE 1 AC3 1 HIS A 290 SITE 1 AC4 4 ARG A 272 ALA A 416 ASP A 420 HOH A 563 SITE 1 AC5 3 SER A 275 ARG A 347 HOH A 533 SITE 1 AC6 5 ARG A 107 PRO A 109 PRO A 130 ASP A 179 SITE 2 AC6 5 TYR A 182 SITE 1 AC7 4 HOH A 45 SER A 111 GLY A 134 HIS A 385 SITE 1 AC8 4 TYR A 221 TYR A 372 GLU A 379 HOH A 612 SITE 1 AC9 6 EDO A 9 TYR A 236 HIS A 335 THR A 361 SITE 2 AC9 6 PHE A 363 HOH A 496 SITE 1 BC1 5 EDO A 8 THR A 193 TYR A 236 HIS A 335 SITE 2 BC1 5 OGA A 454 SITE 1 BC2 3 THR A 184 ASN A 185 ARG A 186 SITE 1 BC3 6 PRO A 99 ALA A 296 VAL A 299 ASP A 300 SITE 2 BC3 6 LYS A 301 CYS A 302 SITE 1 BC4 6 HOH A 14 SER A 216 TRP A 217 VAL A 218 SITE 2 BC4 6 PHE A 336 LEU A 337 SITE 1 BC5 12 NI A 2 EDO A 9 THR A 246 HIS A 249 SITE 2 BC5 12 ASP A 251 TYR A 259 LYS A 266 TYR A 321 SITE 3 BC5 12 THR A 323 HIS A 335 HOH A 462 HOH A 482 CRYST1 109.575 65.767 66.612 90.00 102.09 90.00 C 1 2 1 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 0.009126 0.000000 0.001954 0.00000 SCALE2 0.000000 0.015205 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015353 0.00000