Zinc in PDB 1vkg: Crystal Structure of Human HDAC8 Complexed with Cra-19156

The structure of Crystal Structure of Human HDAC8 Complexed with Cra-19156, PDB code: 1vkg 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)	7.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.630, 92.710, 98.760, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 30.4

The structure of Crystal Structure of Human HDAC8 Complexed with Cra-19156 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human HDAC8 Complexed with Cra-19156 (pdb code 1vkg). 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 Cra-19156, PDB code: 1vkg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human HDAC8 Complexed with Cra-19156


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 Cra-19156 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:36.7 occ:1.00 O A:CRI402 1.8 54.4 1.0 ND1 A:HIS180 2.0 18.9 1.0 OD2 A:ASP178 2.0 25.7 1.0 OD2 A:ASP267 2.1 42.7 1.0 CG A:ASP178 2.7 31.2 1.0 OD1 A:ASP178 2.7 34.5 1.0 CE1 A:HIS180 2.8 20.0 1.0 C A:CRI402 2.8 60.2 1.0 HE1 A:HIS180 2.9 22.4 1.0 OH A:CRI402 2.9 68.7 1.0 CG A:ASP267 3.1 38.4 1.0 CG A:HIS180 3.1 30.4 1.0 HB2 A:HIS180 3.2 29.9 1.0 H A:HIS180 3.2 26.0 1.0 N A:CRI402 3.3 62.6 1.0 HA3 A:GLY304 3.5 37.2 1.0 OD1 A:ASP267 3.5 40.2 1.0 CB A:HIS180 3.7 29.7 1.0 HB3 A:LEU179 3.7 19.9 1.0 H A:GLY304 3.9 39.4 1.0 N A:HIS180 3.9 30.4 1.0 NE2 A:HIS180 3.9 25.8 1.0 H8 A:CRI402 3.9 46.1 1.0 H A:LEU179 4.0 26.0 1.0 C2 A:CRI402 4.0 50.1 1.0 HH A:TYR306 4.1 48.8 1.0 CD2 A:HIS180 4.1 25.2 1.0 OH A:TYR306 4.1 47.7 1.0 HE2 A:HIS142 4.1 25.2 1.0 CB A:ASP178 4.2 26.3 1.0 HE1 A:TYR306 4.2 46.6 1.0 CB A:ASP267 4.2 33.2 1.0 HE1 A:HIS142 4.2 20.7 1.0 HN A:CRI402 4.3 63.3 1.0 HB2 A:ASP267 4.3 33.3 1.0 HB3 A:ASP267 4.4 30.2 1.0 N A:LEU179 4.4 28.8 1.0 C3 A:CRI402 4.4 43.8 1.0 CA A:HIS180 4.4 32.8 1.0 CA A:GLY304 4.4 36.1 1.0 HB3 A:HIS180 4.5 31.3 1.0 N A:GLY304 4.5 40.9 1.0 HB3 A:ASP178 4.6 30.3 1.0 CB A:LEU179 4.7 17.7 1.0 HB2 A:ASP178 4.7 26.8 1.0 HE2 A:HIS180 4.7 21.8 1.0 NE2 A:HIS142 4.7 26.6 1.0 C A:LEU179 4.8 28.8 1.0 HD21 A:LEU179 4.8 21.5 1.0 CE1 A:HIS142 4.8 19.1 1.0 CA A:LEU179 4.9 20.0 1.0 CE1 A:TYR306 4.9 45.5 1.0 HA3 A:GLY265 4.9 35.1 1.0 NE2 A:HIS143 4.9 37.2 1.0 CZ A:TYR306 4.9 46.0 1.0 HA2 A:GLY304 4.9 38.1 1.0 C A:ASP178 4.9 33.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human HDAC8 Complexed with Cra-19156


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 Cra-19156 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:44.5 occ:1.00 O B:CRI402 1.9 60.3 1.0 OH B:CRI402 2.0 78.1 1.0 OD2 B:ASP178 2.1 29.2 1.0 OD2 B:ASP267 2.1 29.9 1.0 ND1 B:HIS180 2.3 35.0 1.0 C B:CRI402 2.5 65.7 1.0 N B:CRI402 2.6 73.5 1.0 CG B:ASP178 2.8 27.9 1.0 OD1 B:ASP178 2.9 32.0 1.0 CE1 B:HIS180 3.0 33.5 1.0 CG B:ASP267 3.1 26.6 1.0 HE1 B:HIS180 3.1 34.6 1.0 H B:HIS180 3.1 29.2 1.0 CG B:HIS180 3.3 31.3 1.0 HA3 B:GLY304 3.3 17.2 1.0 HB2 B:HIS180 3.3 22.6 1.0 HB3 B:LEU179 3.3 18.8 1.0 OD1 B:ASP267 3.5 19.5 1.0 HN B:CRI402 3.6 72.5 1.0 CB B:HIS180 3.8 22.3 1.0 C2 B:CRI402 3.9 63.6 1.0 N B:HIS180 3.9 28.9 1.0 HE2 B:HIS142 3.9 22.2 1.0 OH B:TYR306 4.0 35.9 1.0 HE1 B:TYR306 4.0 41.4 1.0 HE1 B:HIS142 4.0 21.8 1.0 H B:GLY304 4.1 17.0 1.0 NE2 B:HIS180 4.1 32.0 1.0 H7 B:CRI402 4.1 60.8 1.0 HH B:TYR306 4.2 40.9 1.0 CA B:GLY304 4.3 18.2 1.0 CB B:LEU179 4.3 22.8 1.0 CB B:ASP178 4.3 27.8 1.0 CD2 B:HIS180 4.3 33.6 1.0 CB B:ASP267 4.3 28.7 1.0 HB3 B:ASP267 4.4 25.8 1.0 H B:LEU179 4.4 27.5 1.0 N B:LEU179 4.4 28.6 1.0 C1 B:CRI402 4.5 58.2 1.0 CA B:HIS180 4.5 22.5 1.0 NE2 B:HIS142 4.5 18.9 1.0 HB2 B:LEU179 4.5 21.8 1.0 HB2 B:ASP267 4.6 25.0 1.0 N B:GLY304 4.6 12.9 1.0 CE1 B:HIS142 4.6 21.6 1.0 HB3 B:HIS180 4.7 26.6 1.0 HD21 B:LEU179 4.7 22.8 1.0 C B:ASP178 4.7 39.0 1.0 CA B:LEU179 4.7 23.4 1.0 HB3 B:ASP178 4.7 25.6 1.0 CE1 B:TYR306 4.7 42.8 1.0 C B:LEU179 4.8 24.8 1.0 HA2 B:GLY304 4.8 15.3 1.0 CZ B:TYR306 4.8 39.0 1.0 HA3 B:GLY265 4.9 26.4 1.0 O B:HOH403 4.9 36.8 1.0 HB2 B:ASP178 4.9 29.2 1.0 HE2 B:HIS180 4.9 28.4 1.0 C3 B:CRI402 5.0 63.1 1.0 NE2 B:HIS143 5.0 37.8 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