Sodium in the structure of Exploring Thrombin S1 Pocket (pdb 2zdv)

The binding sites of Sodium atom in the structure of Exploring Thrombin S1 Pocket (pdb code 2zdv). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2zdv structure was solved by B.BAUM, A.HEINE, G.KLEBE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.7 Space group C121 a (A) 70.500 b (A) 71.400 c (A) 72.800 alpha (°) 90.00 beta (°) 100.60 gamma (°) 90.00 Rfactor (%) 18.9 Rfree (%) 24.3 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2zdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2zdv. 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: Hoh1021, H: Hoh1027, H: Hoh1059, H: Hoh1063, H: Hoh1093, H: Hoh1095, H: Hoh1127, conact list: Atom Atom Distance (A) Na O H:Tyr184A 4.09 Na O H:Asp221 4.78 Na C H:Asp221 4.21 Na OD1 H:Asp221 4.76 Na CA H:Asp221 4.42 Na O H:Arg221A 2.39 Na N H:Arg221A 3.97 Na C H:Arg221A 3.44 Na CA H:Arg221A 4.32 Na N H:Asp222 4.28 Na C H:Asp222 4.53 Na CA H:Asp222 4.34 Na N H:Gly223 4.27 Na C H:Gly223 4.85 Na O H:Lys224 2.28 Na N H:Lys224 3.85 Na CB H:Lys224 4.59 Na C H:Lys224 3.37 Na CA H:Lys224 4.13 Na N H:Tyr225 4.36 Na CD2 H:Tyr225 4.89 Na CA H:Tyr225 4.67 Na O H:Hoh1021 3.87 Na O H:Hoh1027 4.12 Na O H:Hoh1059 2.37 Na O H:Hoh1063 4.06 Na O H:Hoh1093 2.77 Na O H:Hoh1095 2.40 Na O H:Hoh1127 2.21 interactive model: Sodium binding site 2 out of 2 in 2zdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2zdv. 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: Hoh1045, H: Hoh1051, H: Hoh1066, H: Hoh1164, conact list: Atom Atom Distance (A) Na O H:Lys169 2.34 Na CB H:Lys169 4.92 Na C H:Lys169 3.43 Na CA H:Lys169 4.49 Na O H:Asp170 4.84 Na N H:Asp170 4.14 Na C H:Asp170 4.40 Na OD1 H:Asp170 4.72 Na CA H:Asp170 4.01 Na N H:Ser171 4.82 Na O H:Thr172 2.25 Na N H:Thr172 4.27 Na CG2 H:Thr172 4.67 Na C H:Thr172 3.48 Na CA H:Thr172 4.49 Na N H:Arg173 4.37 Na C H:Arg173 4.98 Na CA H:Arg173 4.44 Na O H:Hoh1045 2.39 Na O H:Hoh1051 2.59 Na O H:Hoh1066 4.97 Na O H:Hoh1164 2.54 interactive model: