Sodium in the structure of Crystal Structure of Human HDAC2 Complexed With An N-(2-Aminophenyl) Benzamide (pdb 3max)

The binding sites of Sodium atom in the structure of Crystal Structure of Human HDAC2 Complexed With An N-(2-Aminophenyl) Benzamide (pdb code 3max). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3max structure was solved by R.J.SKENE, A.J.JENNINGS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.0 Space group P212121 a (A) 92.311 b (A) 97.227 c (A) 138.849 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.4 Rfree (%) 20.4 Sodium Binding Sites: Sodium binding site 1 out of 3 in 3max Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3max. 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: Phe192, A: Tyr193, A: Thr194, A: Thr195, A: Asp196, A: Val198, A: Met199, A: Thr200, A: Gly224, A: Tyr227, A: Hoh396, A: Hoh425, conact list: Atom Atom Distance (A) Na O A:Phe192 2.18 Na CB A:Phe192 3.87 Na C A:Phe192 3.31 Na CA A:Phe192 4.20 Na O A:Tyr193 4.38 Na N A:Tyr193 4.20 Na C A:Tyr193 4.27 Na CA A:Tyr193 4.28 Na N A:Thr194 4.75 Na O A:Thr195 2.50 Na N A:Thr195 4.11 Na CB A:Thr195 4.93 Na CG2 A:Thr195 4.10 Na C A:Thr195 3.70 Na CA A:Thr195 4.41 Na N A:Asp196 4.75 Na CA A:Asp196 4.96 Na O A:Val198 2.33 Na N A:Val198 4.58 Na CB A:Val198 4.57 Na C A:Val198 3.55 Na CA A:Val198 4.47 Na N A:Met199 4.46 Na CA A:Met199 4.47 Na N A:Thr200 4.88 Na O A:Gly224 4.66 Na CA A:Gly224 4.59 Na O A:Tyr227 3.66 Na CB A:Tyr227 3.88 Na C A:Tyr227 4.24 Na CA A:Tyr227 4.69 Na O A:Hoh396 2.41 Na O A:Hoh425 2.58 interactive model: Sodium binding site 2 out of 3 in 3max Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3max. 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: Phe192, B: Tyr193, B: Thr194, B: Thr195, B: Asp196, B: Val198, B: Met199, B: Thr200, B: Gly224, B: Tyr227, B: Ala228, B: Hoh385, B: Hoh441, conact list: Atom Atom Distance (A) Na O B:Phe192 2.34 Na CB B:Phe192 4.08 Na C B:Phe192 3.46 Na CA B:Phe192 4.37 Na O B:Tyr193 4.31 Na N B:Tyr193 4.33 Na C B:Tyr193 4.31 Na CA B:Tyr193 4.34 Na N B:Thr194 4.87 Na O B:Thr195 2.50 Na N B:Thr195 4.14 Na CB B:Thr195 4.98 Na CG2 B:Thr195 4.26 Na C B:Thr195 3.69 Na CA B:Thr195 4.42 Na N B:Asp196 4.72 Na CA B:Asp196 4.88 Na O B:Val198 2.34 Na N B:Val198 4.61 Na CB B:Val198 4.64 Na C B:Val198 3.57 Na CA B:Val198 4.52 Na N B:Met199 4.46 Na CA B:Met199 4.47 Na N B:Thr200 4.85 Na O B:Gly224 4.63 Na CA B:Gly224 4.65 Na O B:Tyr227 3.61 Na CB B:Tyr227 3.69 Na C B:Tyr227 4.09 Na CG B:Tyr227 4.92 Na CA B:Tyr227 4.50 Na N B:Ala228 4.82 Na O B:Hoh385 2.33 Na O B:Hoh441 2.52 interactive model: Sodium binding site 3 out of 3 in 3max Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3max. 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: C: Phe192, C: Tyr193, C: Thr194, C: Thr195, C: Asp196, C: Val198, C: Met199, C: Thr200, C: Gly224, C: Tyr227, C: Ala228, C: Hoh389, C: Hoh464, conact list: Atom Atom Distance (A) Na O C:Phe192 2.30 Na CB C:Phe192 4.04 Na C C:Phe192 3.48 Na CA C:Phe192 4.36 Na O C:Tyr193 4.25 Na N C:Tyr193 4.38 Na C C:Tyr193 4.24 Na CA C:Tyr193 4.39 Na N C:Thr194 4.75 Na O C:Thr195 2.38 Na N C:Thr195 4.05 Na CB C:Thr195 4.83 Na CG2 C:Thr195 4.07 Na C C:Thr195 3.58 Na CA C:Thr195 4.30 Na N C:Asp196 4.64 Na CA C:Asp196 4.82 Na O C:Val198 2.33 Na N C:Val198 4.61 Na CB C:Val198 4.72 Na C C:Val198 3.57 Na CA C:Val198 4.53 Na N C:Met199 4.46 Na CA C:Met199 4.47 Na N C:Thr200 4.96 Na O C:Gly224 4.53 Na CA C:Gly224 4.44 Na O C:Tyr227 3.61 Na CB C:Tyr227 3.83 Na C C:Tyr227 4.17 Na CA C:Tyr227 4.61 Na N C:Ala228 4.94 Na O C:Hoh389 2.26 Na O C:Hoh464 2.67 interactive model: