Sodium in the structure of Crystal Structure of Human Alpha-Thrombin Inhibited With SEL2711. (pdb 7kme)

The binding sites of Sodium atom in the structure of Crystal Structure of Human Alpha-Thrombin Inhibited With SEL2711. (pdb code 7kme). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 7kme structure was solved by I.MOCHALKIN, A.TULINSKY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 9.0-2.1 Space group C121 a (A) 71.050 b (A) 71.820 c (A) 73.450 alpha (°) 90.00 beta (°) 101.20 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 7kme Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 7kme. 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: H: Lys169, H: Asp170, H: Thr172, H: Arg173, H: Ile174, H: Hoh493, H: Hoh495, conact list: Atom Atom Distance (A) Na O H:Lys169 2.71 Na CB H:Lys169 4.90 Na C H:Lys169 3.77 Na CA H:Lys169 4.69 Na N H:Asp170 4.49 Na OD1 H:Asp170 4.78 Na CA H:Asp170 4.47 Na O H:Thr172 2.59 Na N H:Thr172 4.84 Na C H:Thr172 3.78 Na CA H:Thr172 4.92 Na O H:Arg173 4.79 Na N H:Arg173 4.48 Na C H:Arg173 4.60 Na CA H:Arg173 4.27 Na O H:Ile174 4.55 Na O H:Hoh493 2.66 Na O H:Hoh495 2.68 interactive model: Sodium binding site 2 out of 2 in 7kme Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 7kme. 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: H: Tyr184A, H: Asp221, H: Arg221A, H: Asp222, H: Gly223, H: Lys224, H: Tyr225, H: Hoh405, H: Hoh458, H: Hoh463, H: Hoh492, H: Hoh494, H: Hoh522, H: Hoh531, H: Hoh548, conact list: Atom Atom Distance (A) Na O H:Tyr184A 4.03 Na O H:Asp221 4.49 Na C H:Asp221 4.09 Na OD1 H:Asp221 4.21 Na CA H:Asp221 4.37 Na O H:Arg221A 2.62 Na N H:Arg221A 4.00 Na C H:Arg221A 3.48 Na CA H:Arg221A 4.40 Na N H:Asp222 4.16 Na C H:Asp222 4.48 Na CA H:Asp222 4.11 Na N H:Gly223 4.34 Na C H:Gly223 4.94 Na O H:Lys224 2.54 Na N H:Lys224 3.84 Na CB H:Lys224 4.99 Na C H:Lys224 3.69 Na CA H:Lys224 4.34 Na N H:Tyr225 4.80 Na O H:Hoh405 4.68 Na O H:Hoh458 3.92 Na O H:Hoh463 3.84 Na O H:Hoh492 2.44 Na O H:Hoh494 3.83 Na O H:Hoh522 2.62 Na O H:Hoh531 2.70 Na O H:Hoh548 2.52 interactive model: