Sodium in the structure of Human Thrombin in Complex With MI354 (pdb 3rm0)

The binding sites of Sodium atom in the structure of Human Thrombin in Complex With MI354 (pdb code 3rm0). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3rm0 structure was solved by A.BIELA, A.HEINE, G.KLEBE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 21.5-1.3 Space group C121 a (A) 70.500 b (A) 71.300 c (A) 72.500 alpha (°) 90.00 beta (°) 100.50 gamma (°) 90.00 Rfactor (%) 14 Rfree (%) 16.6 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3rm0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3rm0. 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: Ser171, H: Thr172, H: Arg173, H: Ile174, H: Hoh1094, H: Hoh1145, H: Hoh1193, H: Hoh1196, H: Hoh1294, conact list: Atom Atom Distance (A) Na O H:Lys169 2.38 Na CB H:Lys169 4.85 Na C H:Lys169 3.45 Na CA H:Lys169 4.50 Na O H:Asp170 4.77 Na N H:Asp170 4.15 Na C H:Asp170 4.41 Na OD1 H:Asp170 4.67 Na CA H:Asp170 4.02 Na N H:Ser171 4.88 Na O H:Thr172 2.34 Na N H:Thr172 4.29 Na CG2 H:Thr172 4.80 Na C H:Thr172 3.56 Na CA H:Thr172 4.53 Na N H:Arg173 4.42 Na C H:Arg173 4.89 Na CA H:Arg173 4.39 Na O H:Ile174 4.97 Na O H:Hoh1094 2.36 Na O H:Hoh1145 4.92 Na O H:Hoh1193 2.42 Na O H:Hoh1196 2.56 Na O H:Hoh1294 4.29 interactive model: Sodium binding site 2 out of 2 in 3rm0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3rm0. 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: Hoh1058, H: Hoh1059, H: Hoh1096, H: Hoh1110, H: Hoh1155, H: Hoh1182, H: Hoh1183, H: Hoh1190, conact list: Atom Atom Distance (A) Na O H:Tyr184A 4.06 Na O H:Asp221 4.52 Na C H:Asp221 4.08 Na OD1 H:Asp221 4.63 Na CA H:Asp221 4.39 Na O H:Arg221A 2.34 Na N H:Arg221A 3.96 Na C H:Arg221A 3.39 Na CA H:Arg221A 4.31 Na N H:Asp222 4.21 Na C H:Asp222 4.48 Na CA H:Asp222 4.28 Na N H:Gly223 4.17 Na C H:Gly223 4.82 Na O H:Lys224 2.42 Na N H:Lys224 3.86 Na CB H:Lys224 4.57 Na C H:Lys224 3.50 Na CA H:Lys224 4.19 Na N H:Tyr225 4.50 Na CA H:Tyr225 4.76 Na O H:Hoh1058 2.48 Na O H:Hoh1059 4.25 Na O H:Hoh1096 2.35 Na O H:Hoh1110 2.39 Na O H:Hoh1155 3.92 Na O H:Hoh1182 2.59 Na O H:Hoh1183 4.75 Na O H:Hoh1190 3.94 interactive model: