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Zinc in PDB 5b8d: Crystal Structure of A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

Enzymatic activity of Crystal Structure of A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

All present enzymatic activity of Crystal Structure of A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 5b8d was solved by R.J.Harding, W.Tempel, P.Collins, N.Pearce, J.Brandao-Neto, A.Douangamath, M.Ravichandran, M.Schapira, C.Bountra, A.M.Edwards, F.Von Delft, V.Santhakumar, C.M.Arrowsmith, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.80 / 1.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.434, 44.157, 56.549, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 14.6

Other elements in 5b8d:

The structure of Crystal Structure of A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain (pdb code 5b8d). 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 A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 5b8d:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5b8d

Go back to Zinc Binding Sites List in 5b8d
Zinc binding site 1 out of 3 in the Crystal Structure of A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to 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 A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1301

b:9.1
occ:1.00
 UNK A:UNX1313 2.0 8.5 1.0
ND1 A:HIS1170 2.1 8.9 1.0
NE2 A:HIS1164 2.1 8.9 1.0
SG A:CYS1145 2.3 8.9 1.0
CE1 A:HIS1164 3.1 9.4 1.0
CE1 A:HIS1170 3.1 9.7 1.0
CG A:HIS1170 3.1 9.1 1.0
CD2 A:HIS1164 3.1 8.7 1.0
CB A:CYS1145 3.2 8.5 1.0
SG A:CYS1148 3.2 10.1 1.0
UNK A:UNX1314 3.3 10.0 1.0
CB A:HIS1170 3.4 8.7 1.0
N A:CYS1148 3.9 9.1 1.0
CB A:CYS1148 4.1 10.1 1.0
OG A:SER1168 4.2 10.0 1.0
ND1 A:HIS1164 4.2 9.8 1.0
NE2 A:HIS1170 4.2 10.3 1.0
CD2 A:HIS1170 4.2 9.8 1.0
CG A:HIS1164 4.2 8.9 1.0
CB A:SER1147 4.5 9.2 1.0
CA A:CYS1148 4.5 9.2 1.0
CA A:CYS1145 4.6 7.9 1.0
O A:HOH1455 4.6 20.6 1.0
CB A:SER1168 4.8 10.5 1.0
C A:SER1147 4.9 9.4 1.0
CA A:HIS1170 4.9 8.8 1.0
CA A:SER1147 5.0 8.8 1.0
N A:SER1147 5.0 8.2 1.0

Zinc binding site 2 out of 3 in 5b8d

Go back to Zinc Binding Sites List in 5b8d
Zinc binding site 2 out of 3 in the Crystal Structure of A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to 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 A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1302

b:9.6
occ:1.00
 ND1 A:HIS1160 2.1 10.2 1.0
SG A:CYS1136 2.3 10.9 1.0
SG A:CYS1153 2.4 9.1 1.0
SG A:CYS1133 2.4 9.0 1.0
CE1 A:HIS1160 3.1 11.1 1.0
CG A:HIS1160 3.1 10.3 1.0
CB A:CYS1133 3.3 9.5 1.0
CB A:CYS1153 3.4 8.8 1.0
CB A:HIS1160 3.5 9.4 1.0
CB A:CYS1136 3.5 11.8 1.0
N A:CYS1136 3.8 12.0 1.0
N A:CYS1153 4.0 7.8 1.0
OG1 A:THR1138 4.1 11.8 0.1
CB A:ASN1158 4.2 12.2 1.0
CA A:CYS1136 4.2 12.0 1.0
CG2 A:THR1138 4.2 11.6 0.8
NE2 A:HIS1160 4.2 12.3 1.0
CD2 A:HIS1160 4.3 11.9 1.0
CA A:CYS1153 4.3 8.0 1.0
ND2 A:ASN1158 4.5 14.6 1.0
CB A:ASP1135 4.6 12.4 0.6
N A:HIS1160 4.6 9.4 1.0
CB A:ASP1135 4.6 14.0 0.4
CA A:HIS1160 4.7 8.9 1.0
CA A:CYS1133 4.8 9.1 1.0
C A:ASP1135 4.8 13.3 0.4
C A:ASP1135 4.9 12.7 0.6
CG A:ASN1158 4.9 13.7 1.0
C A:CYS1136 4.9 11.4 1.0

Zinc binding site 3 out of 3 in 5b8d

Go back to Zinc Binding Sites List in 5b8d
Zinc binding site 3 out of 3 in the Crystal Structure of A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to 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 A Low Occupancy Fragment Candidate (N-(4-Methyl- 1,3-Thiazol-2-Yl)Propanamide) Bound Adjacent to the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:11.4
occ:1.00
 ND1 A:HIS1115 2.2 11.6 1.0
SG A:CYS1183 2.4 9.7 1.0
SG A:CYS1113 2.4 10.7 1.0
SG A:CYS1186 2.5 14.3 1.0
CE1 A:HIS1115 3.1 12.1 1.0
CG A:HIS1115 3.2 11.5 1.0
CB A:CYS1113 3.3 11.8 1.0
CB A:CYS1183 3.3 9.2 1.0
CB A:CYS1186 3.5 11.6 1.0
CB A:HIS1115 3.5 11.2 1.0
N A:CYS1186 4.0 11.2 1.0
N A:HIS1115 4.0 11.4 1.0
CD A:PRO1114 4.2 13.8 1.0
NE2 A:HIS1115 4.2 13.7 1.0
CD2 A:HIS1115 4.3 12.9 1.0
CA A:CYS1186 4.4 11.4 1.0
N A:PRO1114 4.4 12.8 1.0
CA A:HIS1115 4.4 11.4 1.0
CA A:CYS1113 4.5 11.7 1.0
CB A:TYR1185 4.6 11.2 1.0
C A:CYS1113 4.6 11.9 1.0
CA A:CYS1183 4.8 8.7 1.0
CG A:PRO1114 4.8 16.3 1.0
C A:TYR1185 5.0 11.2 1.0
C A:PRO1114 5.0 12.7 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: Thu Aug 21 00:58:01 2025

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