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Chlorine in PDB 6csp: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate, PDB code: 6csp was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.28 / 1.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.700, 91.830, 96.549, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 15.3

Other elements in 6csp:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate also contains other interesting chemical elements:

Potassium (K) 4 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate (pdb code 6csp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate, PDB code: 6csp:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6csp

Go back to Chlorine Binding Sites List in 6csp
Chlorine binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:13.2
occ:1.00
HE2 A:HIS614 2.3 7.8 1.0
O A:HOH1124 3.1 10.8 1.0
H11 A:FBM807 3.2 12.7 1.0
NE2 A:HIS614 3.2 6.5 1.0
O A:HOH1026 3.2 10.8 1.0
HB3 A:PHE643 3.5 8.4 1.0
HB3 A:LEU712 3.5 8.9 1.0
HB2 A:PHE643 3.7 8.4 1.0
HZ A:PHE642 3.7 10.7 1.0
H9 A:FBM807 3.8 12.2 1.0
H1 A:FBM807 3.8 12.1 1.0
CZ A:PHE642 3.8 8.9 1.0
H21 A:EDO811 3.8 38.2 0.9
HD22 A:LEU712 3.9 13.8 1.0
C09 A:FBM807 4.0 10.6 1.0
HD13 A:LEU712 4.0 13.2 1.0
CB A:PHE643 4.0 7.0 1.0
CD2 A:HIS614 4.1 5.7 1.0
CE2 A:PHE642 4.1 8.5 1.0
HD2 A:HIS614 4.1 6.8 1.0
CE1 A:HIS614 4.1 5.1 1.0
HE2 A:PHE642 4.1 10.2 1.0
H A:PHE643 4.2 9.1 1.0
HE1 A:HIS614 4.2 6.1 1.0
C08 A:FBM807 4.3 10.2 1.0
CE1 A:PHE642 4.4 9.4 1.0
C10 A:FBM807 4.4 10.1 1.0
CB A:LEU712 4.4 7.4 1.0
HE1 A:PHE642 4.6 11.3 1.0
H8 A:FBM807 4.6 12.2 1.0
H10 A:FBM807 4.7 12.7 1.0
O A:LEU712 4.7 8.0 1.0
CD2 A:LEU712 4.8 11.5 1.0
CD2 A:PHE642 4.8 7.5 1.0
C2 A:EDO811 4.8 31.8 0.9
CD1 A:LEU712 4.9 11.0 1.0
HB2 A:LEU712 4.9 8.9 1.0
H22 A:EDO811 4.9 38.2 0.9
N A:PHE643 4.9 7.6 1.0
CG A:LEU712 4.9 9.0 1.0
CG A:PHE643 4.9 7.6 1.0

Chlorine binding site 2 out of 4 in 6csp

Go back to Chlorine Binding Sites List in 6csp
Chlorine binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl805

b:13.2
occ:1.00
HE2 B:HIS614 2.3 7.9 1.0
HZ2 A:LYS658 2.4 23.3 1.0
HD3 A:LYS658 2.9 19.9 1.0
H10 B:FBM805 3.1 11.5 1.0
O B:HOH1126 3.1 11.2 1.0
NE2 B:HIS614 3.1 6.6 1.0
O B:HOH1010 3.2 12.3 1.0
NZ A:LYS658 3.3 19.4 1.0
HB3 B:PHE643 3.5 8.5 1.0
HB3 B:LEU712 3.5 9.3 1.0
HB2 B:PHE643 3.7 8.5 1.0
HZ B:PHE642 3.7 11.2 1.0
HZ1 A:LYS658 3.7 23.3 1.0
CD A:LYS658 3.7 16.6 1.0
H9 B:FBM805 3.8 11.7 1.0
HE2 A:LYS658 3.8 22.1 1.0
CZ B:PHE642 3.8 9.3 1.0
HZ3 A:LYS658 3.8 23.3 1.0
H1 B:FBM805 3.8 11.6 1.0
CE A:LYS658 3.8 18.4 1.0
C09 B:FBM805 3.9 9.6 1.0
HD22 B:LEU712 4.0 14.3 1.0
CD2 B:HIS614 4.0 5.7 1.0
CE2 B:PHE642 4.0 8.5 1.0
HD2 B:HIS614 4.0 6.8 1.0
CB B:PHE643 4.0 7.1 1.0
HE2 B:PHE642 4.1 10.2 1.0
HD13 B:LEU712 4.1 12.4 1.0
HD2 A:LYS658 4.1 19.9 1.0
CE1 B:HIS614 4.1 6.3 1.0
H B:PHE643 4.2 8.7 1.0
HE1 B:HIS614 4.2 7.5 1.0
C08 B:FBM805 4.3 9.7 1.0
CE1 B:PHE642 4.4 9.6 1.0
C10 B:FBM805 4.4 9.7 1.0
CB B:LEU712 4.5 7.7 1.0
H8 B:FBM805 4.6 11.7 1.0
H11 B:FBM805 4.6 11.5 1.0
HE1 B:PHE642 4.6 11.5 1.0
O B:LEU712 4.7 8.6 1.0
CD2 B:PHE642 4.8 8.6 1.0
HE3 A:LYS658 4.8 22.1 1.0
CD2 B:LEU712 4.8 11.9 1.0
HB2 A:LYS658 4.8 13.7 1.0
N B:PHE643 4.9 7.3 1.0
CD1 B:LEU712 4.9 10.3 1.0
HG2 A:LYS658 4.9 18.0 1.0
CG A:LYS658 5.0 15.0 1.0
HB2 B:LEU712 5.0 9.3 1.0
CG B:PHE643 5.0 6.6 1.0
CG B:LEU712 5.0 9.6 1.0
H2 B:FBM805 5.0 11.6 1.0

Chlorine binding site 3 out of 4 in 6csp

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Chlorine binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl806

b:22.9
occ:1.00
O A:HOH1252 2.8 18.4 1.0
O A:HOH1179 4.7 18.2 1.0

Chlorine binding site 4 out of 4 in 6csp

Go back to Chlorine Binding Sites List in 6csp
Chlorine binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl804

b:24.3
occ:0.80
H B:ARG488 2.0 7.9 1.0
N B:ARG488 2.8 6.6 1.0
HB3 B:ARG488 2.9 9.4 1.0
HA B:HIS487 3.1 8.4 1.0
HB2 B:ARG488 3.2 9.4 1.0
CB B:ARG488 3.4 7.9 1.0
ND1 B:HIS487 3.6 12.3 1.0
CA B:ARG488 3.6 6.9 1.0
C B:HIS487 3.8 6.5 1.0
CA B:HIS487 3.8 7.0 1.0
CE1 B:HIS487 4.0 14.2 1.0
HE1 B:HIS487 4.1 17.1 1.0
O B:ARG488 4.2 10.7 1.0
O B:HOH1024 4.2 39.9 1.0
O B:CYS486 4.2 11.1 1.0
CG B:HIS487 4.2 10.2 1.0
C B:ARG488 4.4 7.9 1.0
HA B:ARG488 4.4 8.3 1.0
CB B:HIS487 4.6 8.3 1.0
NE2 B:HIS487 4.8 14.9 1.0
CG B:ARG488 4.8 8.8 1.0
CD2 B:HIS487 4.9 12.9 1.0
N B:HIS487 4.9 7.3 1.0
HB2 B:HIS487 4.9 10.0 1.0
HG2 B:ARG488 5.0 10.6 1.0
O B:HIS487 5.0 8.4 1.0
O B:HOH1190 5.0 14.6 1.0

Reference:

N.J.Porter, F.F.Wagner, D.W.Christianson. Entropy As A Driver of Selectivity For Inhibitor Binding to Histone Deacetylase 6. Biochemistry V. 57 3916 2018.
ISSN: ISSN 1520-4995
PubMed: 29775292
DOI: 10.1021/ACS.BIOCHEM.8B00367
Page generated: Sat Dec 12 12:51:17 2020

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