Sodium in the structure of Crystal Structure of Human HDAC8 Complexed With Cra-19156 (pdb 1vkg)

The binding sites of Sodium atom in the structure of Crystal Structure of Human HDAC8 Complexed With Cra-19156 (pdb code 1vkg). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1vkg structure 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, brief refinement statistics is given in the table below: Resolution (A) 7.0-2.2 Space group P212121 a (A) 82.630 b (A) 92.710 c (A) 98.760 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.7 Rfree (%) 30.4 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1vkg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1vkg. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp176, A: Leu177, A: Asp178, A: Leu179, A: Leu200, A: His201, A: Ile231, A: Tyr240, A: Thr268, A: Phe277, A: Hoh465, conact list: Atom Atom Distance (A) Na O A:Asp176 4.32 Na C A:Asp176 4.93 Na HB2 A:Leu177 4.99 Na HD21 A:Leu177 4.67 Na N A:Leu177 4.70 Na CB A:Leu177 4.29 Na HD22 A:Leu177 4.56 Na HB3 A:Leu177 3.88 Na C A:Leu177 2.98 Na CA A:Leu177 3.47 Na O A:Leu177 2.50 Na HA A:Leu177 2.92 Na O A:Asp178 2.88 Na N A:Asp178 3.78 Na HA A:Asp178 4.53 Na H A:Asp178 4.42 Na C A:Asp178 3.47 Na CA A:Asp178 4.25 Na N A:Leu179 4.05 Na C A:Leu179 4.92 Na CA A:Leu179 4.21 Na HA A:Leu179 3.44 Na H A:Leu179 4.76 Na HB2 A:Leu200 3.03 Na N A:Leu200 4.84 Na CB A:Leu200 3.86 Na HB3 A:Leu200 3.86 Na C A:Leu200 3.67 Na CA A:Leu200 4.38 Na O A:Leu200 2.95 Na H A:Leu200 4.40 Na N A:His201 4.36 Na CA A:His201 4.46 Na HA A:His201 3.62 Na HD12 A:Ile231 4.58 Na CD1 A:Tyr240 4.99 Na OH A:Tyr240 2.46 Na HE1 A:Tyr240 3.22 Na CE2 A:Tyr240 4.61 Na HH A:Tyr240 3.21 Na CZ A:Tyr240 3.43 Na CE1 A:Tyr240 3.69 Na HE2 A:Tyr240 4.92 Na HB A:Thr268 4.96 Na CB A:Thr268 4.90 Na CG2 A:Thr268 3.68 Na HG21 A:Thr268 4.07 Na HG22 A:Thr268 3.74 Na HG23 A:Thr268 2.81 Na CD1 A:Phe277 4.56 Na HD1 A:Phe277 4.35 Na HE1 A:Phe277 2.96 Na CZ A:Phe277 4.76 Na HZ A:Phe277 4.73 Na CE1 A:Phe277 3.88 Na O A:Hoh465 4.69 Na H2 A:Hoh465 3.94 interactive model: Sodium binding site 2 out of 2 in 1vkg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1vkg. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His142, B: Asp176, B: Leu177, B: Asp178, B: Leu179, B: His180, B: His181, B: Gly182, B: Ser199, B: Leu200, B: His201, B: Gln263, B: Hoh492, conact list: Atom Atom Distance (A) Na HD1 B:His142 4.82 Na HE1 B:His142 4.67 Na O B:Asp176 2.68 Na CB B:Asp176 3.99 Na HB3 B:Asp176 3.63 Na OD2 B:Asp176 4.50 Na OD1 B:Asp176 2.64 Na C B:Asp176 3.53 Na CG B:Asp176 3.52 Na CA B:Asp176 4.39 Na HD21 B:Leu177 4.99 Na N B:Leu177 4.21 Na C B:Leu177 4.20 Na CA B:Leu177 4.26 Na HA B:Leu177 3.79 Na O B:Asp178 2.45 Na N B:Asp178 3.44 Na CB B:Asp178 4.57 Na HB3 B:Asp178 3.99 Na H B:Asp178 2.81 Na C B:Asp178 3.55 Na CA B:Asp178 4.09 Na N B:Leu179 4.65 Na C B:Leu179 4.56 Na O B:Leu179 4.86 Na N B:His180 4.36 Na C B:His180 3.60 Na CA B:His180 4.53 Na O B:His180 2.60 Na H B:His180 4.51 Na N B:His181 4.40 Na CA B:His181 4.48 Na HA B:His181 3.69 Na N B:Gly182 4.78 Na H B:Gly182 4.20 Na HB2 B:Ser199 4.73 Na HG B:Ser199 3.52 Na CB B:Ser199 4.19 Na HB3 B:Ser199 4.94 Na HA B:Ser199 3.96 Na OG B:Ser199 3.01 Na C B:Ser199 4.32 Na CA B:Ser199 4.33 Na HB2 B:Leu200 4.52 Na N B:Leu200 3.68 Na C B:Leu200 3.41 Na CA B:Leu200 4.34 Na O B:Leu200 2.33 Na H B:Leu200 3.13 Na HB2 B:His201 4.06 Na N B:His201 4.12 Na CB B:His201 3.44 Na HB3 B:His201 2.44 Na CD2 B:His201 4.52 Na CG B:His201 4.35 Na CA B:His201 3.94 Na HD2 B:His201 3.95 Na HA B:His201 3.69 Na HE21 B:Gln263 4.73 Na O B:Hoh492 3.76 Na H1 B:Hoh492 3.42 Na H2 B:Hoh492 4.55 interactive model: