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Zinc in PDB 5kh3: Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

Enzymatic activity of Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

All present enzymatic activity of Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 5kh3 was solved by R.J.Harding, A.Dong, M.Ravichandran, R.Ferreira De Freitas, M.Schapira, C.Bountra, A.M.Edwards, V.Santhakumar, C.M.Arrowsmith, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.61 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.700, 44.027, 55.895, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 19.1

Other elements in 5kh3:

The structure of Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain (pdb code 5kh3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 5kh3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5kh3

Go back to Zinc Binding Sites List in 5kh3
Zinc binding site 1 out of 3 in the Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1301

b:11.4
occ:1.00
 NE2 A:HIS1164 2.1 11.6 1.0
ND1 A:HIS1170 2.1 10.8 1.0
SG A:CYS1145 2.3 10.3 1.0
SG A:CYS1148 2.4 15.2 1.0
CE1 A:HIS1164 3.0 10.9 1.0
CE1 A:HIS1170 3.1 11.9 1.0
CG A:HIS1170 3.1 11.0 1.0
CB A:CYS1145 3.2 9.6 1.0
CD2 A:HIS1164 3.2 10.4 1.0
CB A:HIS1170 3.5 10.5 1.0
CB A:CYS1148 3.6 12.8 1.0
N A:CYS1148 3.8 11.3 1.0
ND1 A:HIS1164 4.2 11.4 1.0
NE2 A:HIS1170 4.2 11.4 1.0
CA A:CYS1148 4.2 11.9 1.0
OG A:SER1168 4.2 11.7 1.0
CD2 A:HIS1170 4.2 11.2 1.0
CG A:HIS1164 4.3 10.4 1.0
CB A:SER1147 4.5 9.9 1.0
CA A:CYS1145 4.6 9.4 1.0
C A:SER1147 4.7 12.2 1.0
CB A:SER1168 4.8 11.8 1.0
C A:CYS1148 4.9 11.4 1.0
N A:SER1147 4.9 9.8 1.0
CA A:SER1147 4.9 10.7 1.0
N A:TYR1149 4.9 10.0 1.0
CA A:HIS1170 5.0 10.4 1.0

Zinc binding site 2 out of 3 in 5kh3

Go back to Zinc Binding Sites List in 5kh3
Zinc binding site 2 out of 3 in the Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1302

b:11.5
occ:1.00
 ND1 A:HIS1160 2.1 13.0 1.0
SG A:CYS1136 2.3 11.9 1.0
SG A:CYS1153 2.3 11.0 1.0
SG A:CYS1133 2.4 10.7 1.0
CE1 A:HIS1160 3.1 13.4 1.0
CG A:HIS1160 3.1 11.8 1.0
CB A:CYS1133 3.3 10.9 1.0
CB A:CYS1153 3.4 10.9 1.0
CB A:CYS1136 3.5 13.2 1.0
CB A:HIS1160 3.5 11.2 1.0
N A:CYS1136 3.7 14.0 1.0
N A:CYS1153 4.0 8.5 1.0
CB A:ASN1158 4.0 15.0 1.0
CA A:CYS1136 4.1 13.1 1.0
CG2 A:THR1138 4.2 12.1 1.0
NE2 A:HIS1160 4.2 12.9 1.0
CD2 A:HIS1160 4.2 13.0 1.0
CA A:CYS1153 4.3 9.7 1.0
ND2 A:ASN1158 4.4 15.1 1.0
CB A:ASP1135 4.5 16.3 0.7
CB A:ASP1135 4.5 15.1 0.3
N A:HIS1160 4.6 10.8 1.0
CA A:HIS1160 4.6 10.7 1.0
C A:ASP1135 4.7 14.4 0.3
CA A:CYS1133 4.7 10.6 1.0
CG A:ASN1158 4.8 16.9 1.0
C A:ASP1135 4.8 14.6 0.7
C A:CYS1136 4.8 13.1 1.0
CA A:ASN1158 4.9 13.8 1.0
N A:GLY1137 5.0 13.0 1.0
N A:ASP1135 5.0 14.3 0.3
CA A:ASP1135 5.0 14.8 0.3
N A:ASN1158 5.0 12.7 1.0

Zinc binding site 3 out of 3 in 5kh3

Go back to Zinc Binding Sites List in 5kh3
Zinc binding site 3 out of 3 in the Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Fragment (3-(5-Chloro-1,3-Benzothiazol-2-Yl) Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:10.9
occ:1.00
 ND1 A:HIS1115 2.1 11.2 1.0
SG A:CYS1183 2.3 10.0 1.0
SG A:CYS1113 2.3 11.4 1.0
SG A:CYS1186 2.3 12.1 1.0
CE1 A:HIS1115 3.1 11.9 1.0
CG A:HIS1115 3.1 10.5 1.0
CB A:CYS1113 3.3 11.9 1.0
CB A:CYS1183 3.3 9.5 1.0
CB A:CYS1186 3.4 12.7 1.0
CB A:HIS1115 3.5 11.0 1.0
N A:CYS1186 3.9 12.0 1.0
N A:HIS1115 3.9 11.8 1.0
CD A:PRO1114 4.1 12.6 1.0
NE2 A:HIS1115 4.2 11.3 1.0
CA A:CYS1186 4.2 12.1 1.0
CD2 A:HIS1115 4.2 11.0 1.0
N A:PRO1114 4.3 11.8 1.0
CA A:HIS1115 4.4 12.1 1.0
CA A:CYS1113 4.5 11.4 1.0
CB A:TYR1185 4.5 12.2 1.0
C A:CYS1113 4.6 11.1 1.0
CG A:PRO1114 4.7 13.3 1.0
CA A:CYS1183 4.7 9.4 1.0
C A:TYR1185 4.9 12.2 1.0
O A:HOH1478 4.9 17.7 1.0
C A:PRO1114 4.9 13.1 1.0

Reference:

R.J.Harding, R.Ferreira De Freitas, P.Collins, I.Franzoni, M.Ravichandran, H.Ouyang, K.A.Juarez-Ornelas, M.Lautens, M.Schapira, F.Von Delft, V.Santhakumar, C.H.Arrowsmith. Small Molecule Antagonists of the Interaction Between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin. J. Med. Chem. V. 60 9090 2017.
ISSN: ISSN 1520-4804
PubMed: 29019676
DOI: 10.1021/ACS.JMEDCHEM.7B00933
Page generated: Sun Oct 27 20:23:54 2024

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