PDB Short entry for 3MZ7 HEADER HYDROLASE 11-MAY-10 3MZ7 TITLE CRYSTAL STRUCTURE OF D101L CO2+ HDAC8 COMPLEXED WITH M344 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HD8; COMPND 5 EC: 3.5.1.98; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HDAC8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHD2-XA-HIS KEYWDS HYDROLASE, METALLOHYDROLASE, ARGINASE-LIKE EXPDTA X-RAY DIFFRACTION AUTHOR D.P.DOWLING,S.G.GATTIS,C.A.FIERKE,D.W.CHRISTIANSON REVDAT 3 06-SEP-23 3MZ7 1 REMARK SEQADV LINK REVDAT 2 02-MAR-11 3MZ7 1 HETNAM HETSYN REVDAT 1 23-JUN-10 3MZ7 0 JRNL AUTH D.P.DOWLING,S.G.GATTIS,C.A.FIERKE,D.W.CHRISTIANSON JRNL TITL STRUCTURES OF METAL-SUBSTITUTED HUMAN HISTONE DEACETYLASE 8 JRNL TITL 2 PROVIDE MECHANISTIC INFERENCES ON BIOLOGICAL FUNCTION. JRNL REF BIOCHEMISTRY V. 49 5048 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20545365 JRNL DOI 10.1021/BI1005046 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 30366 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1576 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1625 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2780 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 146 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.06000 REMARK 3 B22 (A**2) : 0.18000 REMARK 3 B33 (A**2) : -3.24000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.135 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.000 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.006 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2889 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3911 ; 1.327 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 355 ; 6.974 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;37.176 ;24.146 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 479 ;17.077 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;20.694 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 428 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2178 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1768 ; 1.280 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2848 ; 2.120 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1121 ; 3.439 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1063 ; 5.017 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3MZ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000059178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0720 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 : 33586 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.49200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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: 3EW8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROP COMPOSITION: 25 MM TRIS, 2.5% REMARK 280 GLYCEROL, 75 MM KCL, 1-5% PEG MME 550, 50 MM MES, 1 MM TRI(2- REMARK 280 CARBOXYETHYL)PHOSPHINE (TCEP), 0.03 MM GLY-GLY-GLY, PH 5.8, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 45.89950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.21550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.89950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.21550 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 4 REMARK 465 GLU A 5 REMARK 465 GLU A 6 REMARK 465 PRO A 7 REMARK 465 ALA A 8 REMARK 465 ASP A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 GLN A 12 REMARK 465 SER A 13 REMARK 465 GLY A 86 REMARK 465 ASP A 87 REMARK 465 ASP A 88 REMARK 465 ASP A 89 REMARK 465 HIS A 90 REMARK 465 PRO A 91 REMARK 465 ASP A 92 REMARK 465 SER A 93 REMARK 465 ILE A 94 REMARK 465 GLU A 379 REMARK 465 GLY A 380 REMARK 465 ARG A 381 REMARK 465 GLY A 382 REMARK 465 SER A 383 REMARK 465 HIS A 384 REMARK 465 HIS A 385 REMARK 465 HIS A 386 REMARK 465 HIS A 387 REMARK 465 HIS A 388 REMARK 465 HIS A 389 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 GLU A 85 OE1 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 TYR A 20 141.61 -175.51 REMARK 500 TYR A 96 60.07 -119.54 REMARK 500 LEU A 98 49.87 -77.91 REMARK 500 ASP A 128 22.04 -70.47 REMARK 500 TYR A 224 -4.55 83.54 REMARK 500 SER A 276 -74.12 -117.30 REMARK 500 ALA A 297 107.69 -41.63 REMARK 500 GLU A 335 -37.16 -38.98 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 K A 391 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 OD1 REMARK 620 2 ASP A 176 O 72.5 REMARK 620 3 ASP A 178 O 104.2 108.9 REMARK 620 4 HIS A 180 O 87.9 158.2 84.7 REMARK 620 5 SER A 199 OG 104.0 84.8 151.3 90.9 REMARK 620 6 LEU A 200 O 146.1 78.5 68.9 123.0 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 390 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD2 REMARK 620 2 HIS A 180 ND1 104.8 REMARK 620 3 ASP A 267 OD2 106.0 95.4 REMARK 620 4 HOH A 537 O 141.7 105.2 94.3 REMARK 620 5 HOH A 538 O 120.6 81.8 132.6 43.0 REMARK 620 6 B3N A 701 O4 87.1 100.6 156.0 64.4 35.1 REMARK 620 7 B3N A 701 O2 162.5 82.3 88.9 24.2 43.8 75.9 REMARK 620 8 B3N A 701 N3 110.9 81.3 142.6 51.9 10.0 27.5 53.7 REMARK 620 9 B3N A 701 C1 139.5 75.7 114.4 34.4 19.1 53.9 26.1 28.6 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 392 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 189 O REMARK 620 2 THR A 192 O 79.1 REMARK 620 3 VAL A 195 O 111.0 83.0 REMARK 620 4 TYR A 225 O 161.8 116.1 82.0 REMARK 620 5 HOH A 393 O 74.4 153.4 108.2 89.7 REMARK 620 6 HOH A 394 O 91.1 91.4 155.5 79.2 87.2 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 CO A 390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B3N A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 706 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T67 RELATED DB: PDB REMARK 900 ZN2+ HDAC8 COMPLEXED WITH M344 REMARK 900 RELATED ID: 3EW8 RELATED DB: PDB REMARK 900 D101L ZN2+ HDAC8 COMPLEXED WITH M344 REMARK 900 RELATED ID: 3MZ3 RELATED DB: PDB REMARK 900 CO2+ HDAC8 COMPLEXED WITH M344 REMARK 900 RELATED ID: 3MZ4 RELATED DB: PDB REMARK 900 D101L MN2+ HDAC8 COMPLEXED WITH M344 REMARK 900 RELATED ID: 3MZ6 RELATED DB: PDB REMARK 900 D101L FE2+ HDAC8 COMPLEXED WITH M344 DBREF 3MZ7 A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 3MZ7 LEU A 101 UNP Q9BY41 ASP 101 ENGINEERED MUTATION SEQADV 3MZ7 ILE A 378 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 GLU A 379 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 GLY A 380 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 ARG A 381 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 GLY A 382 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 SER A 383 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 HIS A 384 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 HIS A 385 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 HIS A 386 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 HIS A 387 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 HIS A 388 UNP Q9BY41 EXPRESSION TAG SEQADV 3MZ7 HIS A 389 UNP Q9BY41 EXPRESSION TAG SEQRES 1 A 389 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 A 389 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 A 389 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 A 389 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 A 389 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 A 389 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 A 389 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 A 389 ASP SER ILE GLU TYR GLY LEU GLY TYR LEU CYS PRO ALA SEQRES 9 A 389 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 A 389 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 A 389 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 A 389 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 A 389 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 A 389 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 A 389 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 A 389 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 A 389 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 A 389 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 A 389 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 A 389 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 A 389 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 A 389 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 A 389 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 A 389 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 A 389 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 A 389 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 A 389 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 A 389 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 A 389 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 30 A 389 ILE GLU GLY ARG GLY SER HIS HIS HIS HIS HIS HIS HET CO A 390 1 HET K A 391 1 HET K A 392 1 HET B3N A 701 22 HET GOL A 706 8 HETNAM CO COBALT (II) ION HETNAM K POTASSIUM ION HETNAM B3N 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7- HETNAM 2 B3N OXOHEPTYL]BENZAMIDE HETNAM GOL GLYCEROL HETSYN B3N M344 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CO CO 2+ FORMUL 3 K 2(K 1+) FORMUL 5 B3N C16 H25 N3 O3 FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *146(H2 O) HELIX 1 1 SER A 21 SER A 30 1 10 HELIX 2 2 LYS A 36 TYR A 48 1 13 HELIX 3 3 SER A 63 ALA A 68 1 6 HELIX 4 4 THR A 72 SER A 83 1 12 HELIX 5 5 GLY A 107 ASP A 128 1 22 HELIX 6 6 ASN A 156 ARG A 166 1 11 HELIX 7 7 GLY A 182 PHE A 189 1 8 HELIX 8 8 LEU A 219 ARG A 223 5 5 HELIX 9 9 GLN A 236 ASN A 256 1 21 HELIX 10 10 GLY A 265 ILE A 269 5 5 HELIX 11 11 THR A 280 GLN A 293 1 14 HELIX 12 12 ASN A 307 LEU A 323 1 17 HELIX 13 13 PHE A 336 GLY A 341 5 6 HELIX 14 14 GLU A 358 HIS A 375 1 18 SHEET 1 A 8 ARG A 55 VAL A 57 0 SHEET 2 A 8 VAL A 17 ILE A 19 1 N TYR A 18 O ARG A 55 SHEET 3 A 8 VAL A 133 ASN A 136 1 O VAL A 133 N VAL A 17 SHEET 4 A 8 ALA A 297 LEU A 301 1 O ILE A 300 N ALA A 134 SHEET 5 A 8 ALA A 259 GLN A 263 1 N LEU A 262 O LEU A 299 SHEET 6 A 8 ILE A 172 ASP A 176 1 N VAL A 175 O GLN A 263 SHEET 7 A 8 VAL A 195 LYS A 202 1 O MET A 196 N TYR A 174 SHEET 8 A 8 SER A 226 ILE A 231 1 O VAL A 227 N THR A 197 LINK OD1 ASP A 176 K K A 391 1555 1555 2.71 LINK O ASP A 176 K K A 391 1555 1555 2.92 LINK OD2 ASP A 178 CO CO A 390 1555 1555 2.03 LINK O ASP A 178 K K A 391 1555 1555 2.75 LINK ND1 HIS A 180 CO CO A 390 1555 1555 2.12 LINK O HIS A 180 K K A 391 1555 1555 2.78 LINK O PHE A 189 K K A 392 1555 1555 2.69 LINK O THR A 192 K K A 392 1555 1555 2.93 LINK O VAL A 195 K K A 392 1555 1555 2.70 LINK OG SER A 199 K K A 391 1555 1555 2.90 LINK O LEU A 200 K K A 391 1555 1555 2.65 LINK O TYR A 225 K K A 392 1555 1555 2.90 LINK OD2 ASP A 267 CO CO A 390 1555 1555 1.99 LINK CO CO A 390 O BHOH A 537 1555 1555 2.06 LINK CO CO A 390 O BHOH A 538 1555 1555 2.74 LINK CO CO A 390 O4 AB3N A 701 1555 1555 1.82 LINK CO CO A 390 O2 AB3N A 701 1555 1555 2.43 LINK CO CO A 390 N3 AB3N A 701 1555 1555 2.53 LINK CO CO A 390 C1 AB3N A 701 1555 1555 2.79 LINK K K A 392 O HOH A 393 1555 1555 2.73 LINK K K A 392 O HOH A 394 1555 1555 2.59 CISPEP 1 PHE A 208 PRO A 209 0 -5.31 CISPEP 2 GLY A 341 PRO A 342 0 0.27 SITE 1 AC1 6 ASP A 178 HIS A 180 ASP A 267 HOH A 537 SITE 2 AC1 6 HOH A 538 B3N A 701 SITE 1 AC2 5 ASP A 176 ASP A 178 HIS A 180 SER A 199 SITE 2 AC2 5 LEU A 200 SITE 1 AC3 6 PHE A 189 THR A 192 VAL A 195 TYR A 225 SITE 2 AC3 6 HOH A 393 HOH A 394 SITE 1 AC4 14 LEU A 101 HIS A 142 HIS A 143 GLY A 151 SITE 2 AC4 14 PHE A 152 ASP A 178 HIS A 180 PHE A 208 SITE 3 AC4 14 ASP A 267 TYR A 306 CO A 390 HOH A 537 SITE 4 AC4 14 HOH A 538 GOL A 706 SITE 1 AC5 9 TRP A 141 GLY A 151 PHE A 152 GLY A 303 SITE 2 AC5 9 GLY A 304 TYR A 306 HOH A 537 HOH A 538 SITE 3 AC5 9 B3N A 701 CRYST1 91.799 88.431 52.503 90.00 90.00 90.00 P 21 21 2 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 0.010893 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019047 0.00000