Zinc in PDB 1t64: Crystal Structure of Human HDAC8 Complexed with Trichostatin A

The structure of Crystal Structure of Human HDAC8 Complexed with Trichostatin A, PDB code: 1t64 was solved by J.R.Somoza, R.J.Skene, B.A.Katz, C.Mol, J.D.Ho, A.J.Jennings, C.Luong, A.Arvai, J.J.Buggy, E.Chi, J.Tang, B.-C.Sang, E.Verner, R.Wynands, E.M.Leahy, D.R.Dougan, G.Snell, M.Navre, M.W.Knuth, R.V.Swanson, D.E.Mcree, L.W.Tari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.65 / 1.90
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	81.014, 81.014, 114.178, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.1

The structure of Crystal Structure of Human HDAC8 Complexed with Trichostatin A also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Sodium	(Na)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A (pdb code 1t64). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A, PDB code: 1t64:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A


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 Human HDAC8 Complexed with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn388 b:26.1 occ:1.00 OD2 A:ASP267 1.9 14.5 1.0 OD2 A:ASP178 2.0 12.1 1.0 O1 A:TSN386 2.0 28.1 1.0 ND1 A:HIS180 2.2 12.7 1.0 O2 A:TSN386 2.2 28.5 1.0 N1 A:TSN386 2.7 30.5 1.0 C13 A:TSN386 2.7 30.4 1.0 CG A:ASP178 2.8 13.2 1.0 OD1 A:ASP178 3.0 12.8 1.0 CG A:ASP267 3.0 16.4 1.0 CE1 A:HIS180 3.0 12.4 1.0 CG A:HIS180 3.2 12.7 1.0 OD1 A:ASP267 3.4 14.4 1.0 CB A:HIS180 3.6 12.5 1.0 N A:HIS180 3.8 12.9 1.0 C12 A:TSN386 4.1 29.4 1.0 CA A:GLY304 4.1 15.5 1.0 NE2 A:HIS180 4.2 13.6 1.0 CB A:ASP178 4.3 13.3 1.0 N A:LEU179 4.3 12.9 1.0 CD2 A:HIS180 4.3 12.9 1.0 CA A:HIS180 4.3 12.6 1.0 OH A:TYR306 4.3 16.9 1.0 CB A:ASP267 4.3 13.9 1.0 N A:GLY304 4.4 15.9 1.0 NE2 A:HIS142 4.4 16.2 1.0 CB A:LEU179 4.4 12.2 1.0 C A:LEU179 4.7 12.9 1.0 CE1 A:TYR306 4.7 15.5 1.0 C11 A:TSN386 4.7 28.3 1.0 CA A:LEU179 4.7 12.6 1.0 NE2 A:HIS143 4.8 14.8 1.0 CE1 A:HIS142 4.8 17.7 1.0 C A:ASP178 4.9 13.6 1.0 CA A:ASP178 5.0 13.4 1.0 CZ A:TYR306 5.0 16.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A


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 Human HDAC8 Complexed with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1388 b:26.3 occ:1.00 OD2 B:ASP267 2.0 14.2 1.0 OD2 B:ASP178 2.0 13.5 1.0 O1 B:TSN1386 2.0 29.7 1.0 ND1 B:HIS180 2.1 11.3 1.0 O2 B:TSN1386 2.3 28.2 1.0 N1 B:TSN1386 2.8 28.9 1.0 C13 B:TSN1386 2.8 29.3 1.0 CG B:ASP178 2.9 14.3 1.0 CE1 B:HIS180 3.0 13.6 1.0 OD1 B:ASP178 3.0 13.8 1.0 CG B:ASP267 3.0 14.5 1.0 CG B:HIS180 3.2 12.2 1.0 OD1 B:ASP267 3.4 13.6 1.0 CB B:HIS180 3.6 12.7 1.0 N B:HIS180 3.8 12.6 1.0 CA B:GLY304 4.1 15.2 1.0 NE2 B:HIS180 4.1 13.4 1.0 C12 B:TSN1386 4.2 27.5 1.0 CD2 B:HIS180 4.2 10.9 1.0 CB B:ASP178 4.3 13.1 1.0 NE2 B:HIS142 4.3 16.7 1.0 CA B:HIS180 4.3 12.6 1.0 N B:LEU179 4.4 13.1 1.0 OH B:TYR306 4.4 15.1 1.0 CB B:ASP267 4.4 13.2 1.0 N B:GLY304 4.4 15.4 1.0 CB B:LEU179 4.6 12.6 1.0 CE1 B:HIS142 4.7 16.3 1.0 CE1 B:TYR306 4.7 13.1 1.0 C B:LEU179 4.7 12.9 1.0 C11 B:TSN1386 4.8 26.9 1.0 CA B:LEU179 4.8 12.9 1.0 NE2 B:HIS143 4.9 15.0 1.0 C B:ASP178 4.9 13.2 1.0 CA B:ASP178 5.0 13.0 1.0 CZ B:TYR306 5.0 13.9 1.0

J.R.Somoza, R.J.Skene, B.A.Katz, C.Mol, J.D.Ho, A.J.Jennings, C.Luong, A.Arvai, J.J.Buggy, E.Chi, J.Tang, B.-C.Sang, E.Verner, R.Wynands, E.M.Leahy, D.R.Dougan, G.Snell, M.Navre, M.W.Knuth, R.V.Swanson, D.E.Mcree, L.W.Tari. Structural Snapshots of Human HDAC8 Provide Insights Into the Class I Histone Deacetylases Structure V. 12 1325 2004.
ISSN: ISSN 0969-2126
PubMed: 15242608
DOI: 10.1016/J.STR.2004.04.012