HEADER OXIDOREDUCTASE 27-SEP-12 4BBQ TITLE CRYSTAL STRUCTURE OF THE CXXC AND PHD DOMAIN OF HUMAN LYSINE-SPECIFIC TITLE 2 DEMETHYLASE 2A (KDM2A)(FBXL11) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 2A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CXXC AND PHD DOMAIN, RESIDUES 567-681; COMPND 5 SYNONYM: CXXC-TYPE ZINC FINGER PROTEIN 8, F-BOX AND LEUCINE-RICH COMPND 6 REPEAT PROTEIN 11, F-BOX PROTEIN FBL7, F-BOX PROTEIN LILINA, F- COMPND 7 BOX/LRR-REPEAT PROTEIN 11, JMJC DOMAIN-CONTAINING HISTONE COMPND 8 DEMETHYLATION PROTEIN 1A, [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A; COMPND 9 EC: 1.14.11.27; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: R3-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS OXIDOREDUCTASE, UBIQUITIN, LIGASE, UBIQUITINATION, DEMETHYLATION, ZF- KEYWDS 2 CXXC DNA BINDING DOMAIN, CPG ISLAND, CHROMATIN, KDM2A, FBXL11 EXPDTA X-RAY DIFFRACTION AUTHOR C.K.ALLERSTON,A.A.WATSON,C.EDLICH,B.LI,Y.CHEN,L.BALL,T.KROJER, AUTHOR 2 C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,F.VON DELFT,E.D.LAUE,O.GILEADI REVDAT 3 08-MAY-24 4BBQ 1 REMARK LINK REVDAT 2 24-JAN-18 4BBQ 1 AUTHOR JRNL REVDAT 1 10-OCT-12 4BBQ 0 JRNL AUTH C.K.ALLERSTON,A.A.WATSON,C.EDLICH,B.LI,Y.CHEN,L.BALL, JRNL AUTH 2 T.KROJER,C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,F.VON DELFT, JRNL AUTH 3 E.D.LAUE,O.GILEADI JRNL TITL CRYSTAL STRUCTURE OF THE CXXC AND PHD DOMAIN OF HUMAN JRNL TITL 2 LYSINE-SPECIFIC DEMETHYLASE 2A (KDM2A)(FBXL11) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 13045 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 + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 643 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.24 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.42 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.98 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2666 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2015 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2530 REMARK 3 BIN R VALUE (WORKING SET) : 0.1996 REMARK 3 BIN FREE R VALUE : 0.2343 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 136 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1564 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.99380 REMARK 3 B22 (A**2) : 8.55890 REMARK 3 B33 (A**2) : 3.43490 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 6.32550 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.311 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.246 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.182 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.225 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.176 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1592 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2139 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 750 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 32 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 238 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1592 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 2 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 204 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1756 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.09 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.41 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.95 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 4.1910 17.1060 65.8942 REMARK 3 T TENSOR REMARK 3 T11: 0.0153 T22: -0.0778 REMARK 3 T33: -0.0405 T12: 0.0121 REMARK 3 T13: -0.0536 T23: -0.0313 REMARK 3 L TENSOR REMARK 3 L11: 0.3334 L22: 2.0309 REMARK 3 L33: 3.6596 L12: -0.6868 REMARK 3 L13: 1.1002 L23: -2.9205 REMARK 3 S TENSOR REMARK 3 S11: 0.0444 S12: -0.0131 S13: 0.0308 REMARK 3 S21: 0.2050 S22: -0.0626 S23: -0.0736 REMARK 3 S31: -0.3318 S32: 0.2827 S33: 0.0181 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -21.5774 -15.4700 71.4614 REMARK 3 T TENSOR REMARK 3 T11: -0.0532 T22: -0.0139 REMARK 3 T33: -0.0864 T12: 0.0064 REMARK 3 T13: 0.0381 T23: 0.0218 REMARK 3 L TENSOR REMARK 3 L11: 1.4599 L22: 2.5425 REMARK 3 L33: 4.3012 L12: 1.5757 REMARK 3 L13: -2.1276 L23: -2.8803 REMARK 3 S TENSOR REMARK 3 S11: 0.0013 S12: 0.3406 S13: 0.0871 REMARK 3 S21: -0.1763 S22: 0.1028 S23: -0.1209 REMARK 3 S31: 0.1941 S32: -0.0664 S33: -0.1041 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IDEAL-DIST CONTACT TERM CONTACT SETUP. REMARK 3 RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER WITH REMARK 3 APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON- REMARK 3 BONDED CONTACTS=8. REMARK 4 REMARK 4 4BBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1290054219. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AP_SCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13091 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240 REMARK 200 RESOLUTION RANGE LOW (A) : 90.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: ANOMALOUS SCATTERING FROM ENDOGENOUS ZINC USED FOR PHASING REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, PH 6.5, 20%(W/V) PEG REMARK 280 METHYL ETHER 5000, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 15.02650 REMARK 290 SMTRY3 2 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 SER A -1 REMARK 465 GLN A 677 REMARK 465 GLU A 678 REMARK 465 ASP A 679 REMARK 465 SER A 680 REMARK 465 SER A 681 REMARK 465 SER B -1 REMARK 465 GLU B 630 REMARK 465 GLU B 631 REMARK 465 THR B 632 REMARK 465 GLN B 633 REMARK 465 ASP B 634 REMARK 465 GLN B 677 REMARK 465 GLU B 678 REMARK 465 ASP B 679 REMARK 465 SER B 680 REMARK 465 SER B 681 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 567 CD NE CZ NH1 NH2 REMARK 470 LYS A 573 NZ REMARK 470 LYS A 575 CD CE NZ REMARK 470 LYS A 592 CE NZ REMARK 470 ARG A 613 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 616 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 625 CD OE1 OE2 REMARK 470 GLU A 630 CG CD OE1 OE2 REMARK 470 GLU A 631 CG CD OE1 OE2 REMARK 470 THR A 632 OG1 CG2 REMARK 470 GLN A 633 CG CD OE1 NE2 REMARK 470 LYS A 637 CG CD CE NZ REMARK 470 LEU A 662 CD1 CD2 REMARK 470 GLU A 664 CG CD OE1 OE2 REMARK 470 GLU A 665 OE1 OE2 REMARK 470 ARG B 567 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 572 NE CZ NH1 NH2 REMARK 470 LYS B 573 CG CD CE NZ REMARK 470 LYS B 575 CG CD CE NZ REMARK 470 ARG B 589 NE CZ NH1 NH2 REMARK 470 ARG B 599 NE CZ NH1 NH2 REMARK 470 GLU B 625 CG CD OE1 OE2 REMARK 470 GLN B 628 CG CD OE1 NE2 REMARK 470 ASN B 629 CG OD1 ND2 REMARK 470 GLU B 636 CG CD OE1 OE2 REMARK 470 LYS B 637 CG CD CE NZ REMARK 470 ILE B 644 CG1 CG2 CD1 REMARK 470 GLN B 655 CG CD OE1 NE2 REMARK 470 GLU B 659 CG CD OE1 OE2 REMARK 470 LEU B 662 CD1 CD2 REMARK 470 GLU B 664 CG CD OE1 OE2 REMARK 470 GLU B 665 CG CD OE1 OE2 REMARK 470 LYS B 674 CE NZ REMARK 470 TYR B 676 CG CD1 CD2 CE1 CE2 CZ OH 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 ILE A 644 -60.16 -102.50 REMARK 500 ILE B 644 -60.39 -101.96 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 A1679 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 571 SG REMARK 620 2 CYS A 574 SG 107.8 REMARK 620 3 CYS A 577 SG 114.0 102.9 REMARK 620 4 CYS A 609 SG 101.5 121.9 109.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1678 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 582 SG REMARK 620 2 CYS A 585 SG 104.5 REMARK 620 3 CYS A 588 SG 117.7 107.2 REMARK 620 4 CYS A 604 SG 105.2 115.6 107.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1681 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 620 SG REMARK 620 2 CYS A 623 SG 106.8 REMARK 620 3 HIS A 650 ND1 107.1 96.1 REMARK 620 4 CYS A 653 SG 121.7 110.9 111.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1680 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 642 SG REMARK 620 2 CYS A 645 SG 101.7 REMARK 620 3 CYS A 672 SG 112.5 116.0 REMARK 620 4 CYS A 675 SG 109.2 103.9 112.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1678 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 571 SG REMARK 620 2 CYS B 574 SG 104.9 REMARK 620 3 CYS B 577 SG 116.5 102.7 REMARK 620 4 CYS B 609 SG 103.4 117.3 112.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1677 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 582 SG REMARK 620 2 CYS B 585 SG 107.7 REMARK 620 3 CYS B 588 SG 117.9 106.5 REMARK 620 4 CYS B 604 SG 105.3 115.2 104.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1680 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 620 SG REMARK 620 2 CYS B 623 SG 111.5 REMARK 620 3 HIS B 650 ND1 107.2 94.3 REMARK 620 4 CYS B 653 SG 126.3 109.6 102.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1679 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 642 SG REMARK 620 2 CYS B 645 SG 105.4 REMARK 620 3 CYS B 672 SG 111.8 112.5 REMARK 620 4 CYS B 675 SG 114.0 104.5 108.6 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 EDO A 1677 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1677 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1678 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1679 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1678 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1680 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1681 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1679 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1680 DBREF 4BBQ A 567 681 UNP Q9Y2K7 KDM2A_HUMAN 567 681 DBREF 4BBQ B 567 681 UNP Q9Y2K7 KDM2A_HUMAN 567 681 SEQADV 4BBQ SER A -1 UNP Q9Y2K7 EXPRESSION TAG SEQADV 4BBQ MET A 0 UNP Q9Y2K7 EXPRESSION TAG SEQADV 4BBQ SER B -1 UNP Q9Y2K7 EXPRESSION TAG SEQADV 4BBQ MET B 0 UNP Q9Y2K7 EXPRESSION TAG SEQRES 1 A 117 SER MET ARG ARG VAL ARG CYS ARG LYS CYS LYS ALA CYS SEQRES 2 A 117 VAL GLN GLY GLU CYS GLY VAL CYS HIS TYR CYS ARG ASP SEQRES 3 A 117 MET LYS LYS PHE GLY GLY PRO GLY ARG MET LYS GLN SER SEQRES 4 A 117 CYS VAL LEU ARG GLN CYS LEU ALA PRO ARG LEU PRO HIS SEQRES 5 A 117 SER VAL THR CYS SER LEU CYS GLY GLU VAL ASP GLN ASN SEQRES 6 A 117 GLU GLU THR GLN ASP PHE GLU LYS LYS LEU MET GLU CYS SEQRES 7 A 117 CYS ILE CYS ASN GLU ILE VAL HIS PRO GLY CYS LEU GLN SEQRES 8 A 117 MET ASP GLY GLU GLY LEU LEU ASN GLU GLU LEU PRO ASN SEQRES 9 A 117 CYS TRP GLU CYS PRO LYS CYS TYR GLN GLU ASP SER SER SEQRES 1 B 117 SER MET ARG ARG VAL ARG CYS ARG LYS CYS LYS ALA CYS SEQRES 2 B 117 VAL GLN GLY GLU CYS GLY VAL CYS HIS TYR CYS ARG ASP SEQRES 3 B 117 MET LYS LYS PHE GLY GLY PRO GLY ARG MET LYS GLN SER SEQRES 4 B 117 CYS VAL LEU ARG GLN CYS LEU ALA PRO ARG LEU PRO HIS SEQRES 5 B 117 SER VAL THR CYS SER LEU CYS GLY GLU VAL ASP GLN ASN SEQRES 6 B 117 GLU GLU THR GLN ASP PHE GLU LYS LYS LEU MET GLU CYS SEQRES 7 B 117 CYS ILE CYS ASN GLU ILE VAL HIS PRO GLY CYS LEU GLN SEQRES 8 B 117 MET ASP GLY GLU GLY LEU LEU ASN GLU GLU LEU PRO ASN SEQRES 9 B 117 CYS TRP GLU CYS PRO LYS CYS TYR GLN GLU ASP SER SER HET EDO A1677 4 HET ZN A1678 1 HET ZN A1679 1 HET ZN A1680 1 HET ZN A1681 1 HET ZN B1677 1 HET ZN B1678 1 HET ZN B1679 1 HET ZN B1680 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO C2 H6 O2 FORMUL 4 ZN 8(ZN 2+) FORMUL 12 HOH *106(H2 O) HELIX 1 1 CYS A 574 GLN A 579 1 6 HELIX 2 2 CYS A 585 MET A 591 1 7 HELIX 3 3 LYS A 592 GLY A 595 5 4 HELIX 4 4 CYS A 604 GLN A 608 5 5 HELIX 5 5 GLN A 628 GLN A 633 1 6 HELIX 6 6 ASP A 634 LYS A 638 5 5 HELIX 7 7 HIS A 650 LEU A 654 5 5 HELIX 8 8 CYS B 574 GLN B 579 1 6 HELIX 9 9 CYS B 585 MET B 591 1 7 HELIX 10 10 LYS B 592 GLY B 595 5 4 HELIX 11 11 CYS B 604 GLN B 608 5 5 HELIX 12 12 HIS B 650 LEU B 654 5 5 SHEET 1 AA 4 ILE A 648 VAL A 649 0 SHEET 2 AA 4 MET A 640 CYS A 642 -1 O MET A 640 N VAL A 649 SHEET 3 AA 4 CYS A 669 GLU A 671 1 N TRP A 670 O GLU A 641 SHEET 4 AA 4 LEU A 661 LEU A 662 -1 O LEU A 661 N GLU A 671 SHEET 1 BA 4 ILE B 648 VAL B 649 0 SHEET 2 BA 4 MET B 640 CYS B 642 -1 O MET B 640 N VAL B 649 SHEET 3 BA 4 CYS B 669 GLU B 671 1 N TRP B 670 O GLU B 641 SHEET 4 BA 4 LEU B 661 LEU B 662 -1 O LEU B 661 N GLU B 671 LINK SG CYS A 571 ZN ZN A1679 1555 1555 2.52 LINK SG CYS A 574 ZN ZN A1679 1555 1555 2.23 LINK SG CYS A 577 ZN ZN A1679 1555 1555 2.35 LINK SG CYS A 582 ZN ZN A1678 1555 1555 2.39 LINK SG CYS A 585 ZN ZN A1678 1555 1555 2.51 LINK SG CYS A 588 ZN ZN A1678 1555 1555 2.29 LINK SG CYS A 604 ZN ZN A1678 1555 1555 2.28 LINK SG CYS A 609 ZN ZN A1679 1555 1555 2.22 LINK SG CYS A 620 ZN ZN A1681 1555 1555 2.31 LINK SG CYS A 623 ZN ZN A1681 1555 1555 2.43 LINK SG CYS A 642 ZN ZN A1680 1555 1555 2.26 LINK SG CYS A 645 ZN ZN A1680 1555 1555 2.42 LINK ND1 HIS A 650 ZN ZN A1681 1555 1555 2.17 LINK SG CYS A 653 ZN ZN A1681 1555 1555 2.30 LINK SG CYS A 672 ZN ZN A1680 1555 1555 2.37 LINK SG CYS A 675 ZN ZN A1680 1555 1555 2.30 LINK SG CYS B 571 ZN ZN B1678 1555 1555 2.47 LINK SG CYS B 574 ZN ZN B1678 1555 1555 2.33 LINK SG CYS B 577 ZN ZN B1678 1555 1555 2.30 LINK SG CYS B 582 ZN ZN B1677 1555 1555 2.31 LINK SG CYS B 585 ZN ZN B1677 1555 1555 2.46 LINK SG CYS B 588 ZN ZN B1677 1555 1555 2.33 LINK SG CYS B 604 ZN ZN B1677 1555 1555 2.30 LINK SG CYS B 609 ZN ZN B1678 1555 1555 2.16 LINK SG CYS B 620 ZN ZN B1680 1555 1555 2.24 LINK SG CYS B 623 ZN ZN B1680 1555 1555 2.42 LINK SG CYS B 642 ZN ZN B1679 1555 1555 2.17 LINK SG CYS B 645 ZN ZN B1679 1555 1555 2.41 LINK ND1 HIS B 650 ZN ZN B1680 1555 1555 2.27 LINK SG CYS B 653 ZN ZN B1680 1555 1555 2.26 LINK SG CYS B 672 ZN ZN B1679 1555 1555 2.53 LINK SG CYS B 675 ZN ZN B1679 1555 1555 2.23 SITE 1 AC1 7 ASP A 657 GLY A 658 HOH A2049 LYS B 601 SITE 2 AC1 7 GLN B 602 HOH B2006 HOH B2029 SITE 1 AC2 4 CYS B 582 CYS B 585 CYS B 588 CYS B 604 SITE 1 AC3 4 CYS A 582 CYS A 585 CYS A 588 CYS A 604 SITE 1 AC4 4 CYS A 571 CYS A 574 CYS A 577 CYS A 609 SITE 1 AC5 4 CYS B 571 CYS B 574 CYS B 577 CYS B 609 SITE 1 AC6 4 CYS A 642 CYS A 645 CYS A 672 CYS A 675 SITE 1 AC7 4 CYS A 620 CYS A 623 HIS A 650 CYS A 653 SITE 1 AC8 4 CYS B 642 CYS B 645 CYS B 672 CYS B 675 SITE 1 AC9 4 CYS B 620 CYS B 623 HIS B 650 CYS B 653 CRYST1 49.024 30.053 90.824 90.00 91.66 90.00 P 1 21 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 0.020398 0.000000 0.000591 0.00000 SCALE2 0.000000 0.033275 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011015 0.00000