Sodium in the structure of Crystal Structure of Human HDAC8 Complexed With Trichostatin A (pdb 1t64)

The binding sites of Sodium atom in the structure of Crystal Structure of Human HDAC8 Complexed With Trichostatin A (pdb code 1t64). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1t64 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) 81.7-1.9 Space group P43 a (A) 81.014 b (A) 81.014 c (A) 114.178 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.2 Rfree (%) 22.1 Sodium Binding Sites: Sodium binding site 1 out of 4 in 1t64 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1t64. 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: Phe189, A: Ser190, A: Phe191, A: Thr192, A: Ser193, A: Val195, A: Met196, A: Thr197, A: Gly222, A: Tyr225, A: Ser226, A: Hoh426, A: Hoh560, conact list: Atom Atom Distance (A) Na O A:Phe189 2.31 Na CB A:Phe189 4.05 Na C A:Phe189 3.38 Na CA A:Phe189 4.30 Na O A:Ser190 4.54 Na N A:Ser190 4.22 Na C A:Ser190 4.39 Na CA A:Ser190 4.25 Na N A:Phe191 4.90 Na O A:Thr192 2.41 Na N A:Thr192 4.16 Na CB A:Thr192 4.98 Na CG2 A:Thr192 4.27 Na C A:Thr192 3.62 Na CA A:Thr192 4.38 Na N A:Ser193 4.65 Na CA A:Ser193 4.85 Na O A:Val195 2.30 Na N A:Val195 4.59 Na CB A:Val195 4.79 Na C A:Val195 3.54 Na CA A:Val195 4.51 Na N A:Met196 4.41 Na CA A:Met196 4.39 Na N A:Thr197 4.88 Na O A:Gly222 4.57 Na CA A:Gly222 4.68 Na O A:Tyr225 3.50 Na CB A:Tyr225 3.70 Na C A:Tyr225 4.02 Na CG A:Tyr225 4.88 Na CA A:Tyr225 4.49 Na N A:Ser226 4.74 Na OG A:Ser226 4.29 Na O A:Hoh426 2.32 Na O A:Hoh560 2.87 interactive model: Sodium binding site 2 out of 4 in 1t64 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1t64. 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: His142, A: Asp176, A: Leu177, A: Asp178, A: Leu179, A: His180, A: His181, A: Gly182, A: Ser199, A: Leu200, A: His201, A: Hoh396, conact list: Atom Atom Distance (A) Na CE1 A:His142 4.79 Na O A:Asp176 2.74 Na CB A:Asp176 3.89 Na OD2 A:Asp176 4.40 Na C A:Asp176 3.41 Na OD1 A:Asp176 2.52 Na CG A:Asp176 3.45 Na CA A:Asp176 4.27 Na O A:Leu177 4.55 Na N A:Leu177 4.03 Na C A:Leu177 3.84 Na CA A:Leu177 4.12 Na O A:Asp178 2.34 Na N A:Asp178 3.40 Na CB A:Asp178 3.88 Na C A:Asp178 3.32 Na CA A:Asp178 3.75 Na O A:Leu179 4.78 Na N A:Leu179 4.47 Na C A:Leu179 4.43 Na CA A:Leu179 4.90 Na O A:His180 2.60 Na N A:His180 4.24 Na C A:His180 3.63 Na CA A:His180 4.56 Na N A:His181 4.41 Na C A:His181 4.83 Na CA A:His181 4.49 Na N A:Gly182 4.52 Na CB A:Ser199 4.22 Na OG A:Ser199 2.96 Na C A:Ser199 4.53 Na CA A:Ser199 4.48 Na O A:Leu200 2.37 Na N A:Leu200 3.97 Na C A:Leu200 3.44 Na CA A:Leu200 4.38 Na N A:His201 4.23 Na CB A:His201 3.77 Na ND1 A:His201 4.39 Na CG A:His201 4.57 Na CA A:His201 4.17 Na O A:Hoh396 4.27 interactive model: Sodium binding site 3 out of 4 in 1t64 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1t64. 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: Hoh420, conact list: Atom Atom Distance (A) Na CE1 B:His142 4.94 Na O B:Asp176 2.74 Na CB B:Asp176 3.84 Na OD2 B:Asp176 4.42 Na C B:Asp176 3.38 Na OD1 B:Asp176 2.56 Na CG B:Asp176 3.45 Na CA B:Asp176 4.22 Na O B:Leu177 4.67 Na N B:Leu177 3.98 Na C B:Leu177 3.93 Na CA B:Leu177 4.15 Na O B:Asp178 2.43 Na N B:Asp178 3.47 Na CB B:Asp178 3.89 Na C B:Asp178 3.40 Na CA B:Asp178 3.83 Na O B:Leu179 4.84 Na N B:Leu179 4.55 Na C B:Leu179 4.51 Na CA B:Leu179 4.99 Na O B:His180 2.64 Na N B:His180 4.32 Na C B:His180 3.67 Na CA B:His180 4.61 Na N B:His181 4.43 Na C B:His181 4.79 Na CA B:His181 4.47 Na N B:Gly182 4.43 Na CB B:Ser199 4.10 Na OG B:Ser199 2.86 Na C B:Ser199 4.41 Na CA B:Ser199 4.34 Na O B:Leu200 2.43 Na N B:Leu200 3.80 Na C B:Leu200 3.46 Na CA B:Leu200 4.32 Na N B:His201 4.28 Na CB B:His201 3.77 Na ND1 B:His201 4.29 Na CG B:His201 4.52 Na CA B:His201 4.25 Na O B:Hoh420 4.29 interactive model: Sodium binding site 4 out of 4 in 1t64 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1t64. 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: Phe189, B: Ser190, B: Phe191, B: Thr192, B: Ser193, B: Val195, B: Met196, B: Thr197, B: Gly222, B: Tyr225, B: Ser226, B: Hoh439, B: Hoh548, conact list: Atom Atom Distance (A) Na O B:Phe189 2.24 Na CB B:Phe189 4.06 Na C B:Phe189 3.35 Na CA B:Phe189 4.30 Na O B:Ser190 4.51 Na N B:Ser190 4.18 Na C B:Ser190 4.29 Na CA B:Ser190 4.16 Na N B:Phe191 4.75 Na O B:Thr192 2.38 Na N B:Thr192 4.08 Na CB B:Thr192 4.93 Na CG2 B:Thr192 4.22 Na C B:Thr192 3.57 Na CA B:Thr192 4.31 Na N B:Ser193 4.61 Na CA B:Ser193 4.82 Na O B:Val195 2.32 Na N B:Val195 4.60 Na CB B:Val195 4.76 Na C B:Val195 3.56 Na CA B:Val195 4.53 Na N B:Met196 4.42 Na CA B:Met196 4.41 Na N B:Thr197 4.96 Na O B:Gly222 4.49 Na CA B:Gly222 4.68 Na O B:Tyr225 3.56 Na CB B:Tyr225 3.65 Na C B:Tyr225 3.99 Na CG B:Tyr225 4.86 Na CA B:Tyr225 4.43 Na N B:Ser226 4.68 Na OG B:Ser226 4.22 Na O B:Hoh439 2.15 Na O B:Hoh548 3.50 interactive model: