Sodium in the structure of Human Thrombin in Complex With UBTHR97 (pdb 3sha)

The binding sites of Sodium atom in the structure of Human Thrombin in Complex With UBTHR97 (pdb code 3sha). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3sha 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) 31.9-1.5 Space group C121 a (A) 69.800 b (A) 71.400 c (A) 72.200 alpha (°) 90.00 beta (°) 100.00 gamma (°) 90.00 Rfactor (%) 16.1 Rfree (%) 19 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3sha Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3sha. 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: Hoh1139, H: Hoh1171, H: Hoh1214, conact list: Atom Atom Distance (A) Na O H:Lys169 2.35 Na CB H:Lys169 4.90 Na C H:Lys169 3.43 Na CG H:Lys169 4.21 Na CA H:Lys169 4.50 Na NZ H:Lys169 4.87 Na O H:Asp170 4.75 Na N H:Asp170 4.15 Na C H:Asp170 4.37 Na OD1 H:Asp170 4.72 Na CA H:Asp170 4.01 Na N H:Ser171 4.83 Na O H:Thr172 2.36 Na N H:Thr172 4.27 Na CG2 H:Thr172 4.84 Na C H:Thr172 3.58 Na CA H:Thr172 4.54 Na N H:Arg173 4.46 Na C H:Arg173 4.97 Na CA H:Arg173 4.45 Na O H:Hoh1139 2.58 Na O H:Hoh1171 2.39 Na O H:Hoh1214 4.39 interactive model: Sodium binding site 2 out of 2 in 3sha Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3sha. 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: Hoh1137, H: Hoh1149, H: Hoh1150, H: Hoh1152, H: Hoh1155, H: Hoh1168, H: Hoh1222, H: Hoh1275, conact list: Atom Atom Distance (A) Na O H:Tyr184A 4.11 Na O H:Asp221 4.64 Na C H:Asp221 4.09 Na OD1 H:Asp221 4.66 Na CA H:Asp221 4.36 Na O H:Arg221A 2.28 Na N H:Arg221A 3.85 Na C H:Arg221A 3.35 Na CA H:Arg221A 4.23 Na N H:Asp222 4.22 Na C H:Asp222 4.51 Na CA H:Asp222 4.32 Na N H:Gly223 4.25 Na C H:Gly223 4.86 Na O H:Lys224 2.37 Na N H:Lys224 3.82 Na CB H:Lys224 4.46 Na C H:Lys224 3.42 Na CA H:Lys224 4.11 Na N H:Tyr225 4.43 Na CA H:Tyr225 4.73 Na O H:Hoh1137 2.42 Na O H:Hoh1149 3.97 Na O H:Hoh1150 4.86 Na O H:Hoh1152 3.88 Na O H:Hoh1155 4.23 Na O H:Hoh1168 2.64 Na O H:Hoh1222 2.37 Na O H:Hoh1275 2.37 interactive model: