Sodium in PDB 1t67: Crystal Structure of Human HDAC8 Complexed with Ms-344

The structure of Crystal Structure of Human HDAC8 Complexed with Ms-344, PDB code: 1t67 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)	69.01 / 2.31
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.644, 80.644, 105.523, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 27.4

The structure of Crystal Structure of Human HDAC8 Complexed with Ms-344 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human HDAC8 Complexed with Ms-344 (pdb code 1t67). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human HDAC8 Complexed with Ms-344, PDB code: 1t67:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human HDAC8 Complexed with Ms-344


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human HDAC8 Complexed with Ms-344 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na379 b:61.6 occ:1.00 OD1 A:ASP176 2.3 38.0 1.0 O A:LEU200 2.7 33.6 1.0 O A:HIS180 2.8 33.5 1.0 O A:ASP178 2.8 34.6 1.0 OG A:SER199 3.0 33.9 1.0 O A:ASP176 3.1 33.4 1.0 CG A:ASP176 3.2 35.4 1.0 N A:ASP178 3.6 33.6 1.0 C A:ASP178 3.6 34.3 1.0 C A:ASP176 3.6 33.2 1.0 C A:LEU200 3.7 33.9 1.0 C A:HIS180 3.7 33.3 1.0 CB A:HIS201 3.7 33.8 1.0 CB A:ASP176 3.9 33.9 1.0 CB A:ASP178 3.9 34.0 1.0 CA A:ASP178 3.9 34.1 1.0 N A:LEU200 4.0 33.7 1.0 OD2 A:ASP176 4.1 37.8 1.0 N A:LEU177 4.1 33.2 1.0 C A:LEU177 4.1 33.8 1.0 N A:GLY182 4.2 33.5 1.0 CD2 A:HIS201 4.2 35.7 1.0 CB A:SER199 4.2 33.2 1.0 CA A:HIS181 4.2 33.1 1.0 N A:HIS181 4.3 33.3 1.0 CG A:HIS201 4.3 35.4 1.0 CA A:ASP176 4.3 33.3 1.0 CA A:HIS201 4.3 34.1 1.0 CA A:LEU177 4.4 33.2 1.0 N A:HIS201 4.4 33.8 1.0 N A:HIS180 4.4 34.0 1.0 CA A:SER199 4.5 33.1 1.0 CA A:LEU200 4.5 33.8 1.0 C A:HIS181 4.5 33.2 1.0 C A:SER199 4.6 33.4 1.0 O A:HOH388 4.6 37.6 1.0 C A:LEU179 4.6 33.9 1.0 CE1 A:HIS142 4.7 30.7 1.0 N A:LEU179 4.7 34.5 1.0 CA A:HIS180 4.7 33.4 1.0 O A:LEU177 4.9 34.0 1.0 O A:LEU179 5.0 33.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human HDAC8 Complexed with Ms-344


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human HDAC8 Complexed with Ms-344 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na380 b:57.7 occ:1.00 O A:PHE189 2.4 29.1 1.0 O A:VAL195 2.4 35.5 1.0 O A:HOH480 2.5 49.8 1.0 O A:THR192 2.5 32.8 1.0 O A:HOH418 3.1 60.3 1.0 C A:PHE189 3.5 29.6 1.0 O A:TYR225 3.5 32.5 1.0 CB A:TYR225 3.6 30.8 1.0 C A:VAL195 3.6 35.1 1.0 C A:THR192 3.7 32.2 1.0 C A:TYR225 4.0 32.1 1.0 CA A:SER190 4.1 31.2 1.0 N A:THR192 4.2 30.9 1.0 CB A:PHE189 4.2 29.6 1.0 C A:SER190 4.2 31.1 1.0 N A:SER190 4.3 30.4 1.0 O A:GLY222 4.3 33.9 1.0 CG2 A:THR192 4.3 28.8 1.0 CA A:MET196 4.3 35.8 1.0 O A:SER190 4.4 31.3 1.0 CA A:TYR225 4.4 31.5 1.0 N A:MET196 4.4 35.5 1.0 CA A:THR192 4.4 31.4 1.0 OG A:SER226 4.4 34.0 1.0 CA A:PHE189 4.5 29.5 1.0 CA A:VAL195 4.7 34.8 1.0 CA A:GLY222 4.7 33.8 1.0 N A:SER226 4.7 32.1 1.0 N A:SER193 4.7 32.9 1.0 N A:VAL195 4.7 35.5 1.0 N A:PHE191 4.7 31.1 1.0 CG A:TYR225 4.8 29.9 1.0 N A:THR197 4.9 34.8 1.0 CA A:SER193 4.9 33.8 1.0 CB A:VAL195 4.9 34.5 1.0 C A:GLY222 5.0 33.8 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