Sodium in the structure of Exploring Thrombin S3 Pocket (pdb 2zhw)

The binding sites of Sodium atom in the structure of Exploring Thrombin S3 Pocket (pdb code 2zhw). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2zhw structure was solved by T.BRANDT, B.BAUM, A.HEINE, G.KLEBE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.0 Space group C121 a (A) 68.900 b (A) 71.500 c (A) 71.300 alpha (°) 90.00 beta (°) 99.10 gamma (°) 90.00 Rfactor (%) 20.2 Rfree (%) 29.2 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2zhw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2zhw. 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, conact list: Atom Atom Distance (A) Na O H:Lys169 2.35 Na CB H:Lys169 4.96 Na C H:Lys169 3.49 Na CA H:Lys169 4.45 Na O H:Asp170 4.91 Na N H:Asp170 4.28 Na C H:Asp170 4.51 Na OD1 H:Asp170 4.93 Na CA H:Asp170 4.21 Na N H:Ser171 4.87 Na O H:Thr172 2.14 Na N H:Thr172 4.21 Na CG2 H:Thr172 4.70 Na C H:Thr172 3.36 Na CA H:Thr172 4.36 Na N H:Arg173 4.22 Na C H:Arg173 4.81 Na CA H:Arg173 4.30 Na O H:Ile174 4.88 interactive model: Sodium binding site 2 out of 2 in 2zhw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2zhw. 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: Gly188, H: Asp189, H: Asp221, H: Arg221A, H: Asp222, H: Lys224, H: Tyr225, H: Hoh1037, H: Hoh1045, H: Hoh1085, H: Hoh1101, conact list: Atom Atom Distance (A) Na O H:Gly188 4.93 Na CB H:Asp189 4.84 Na OD2 H:Asp189 4.37 Na CG H:Asp189 4.78 Na O H:Asp221 4.49 Na N H:Asp221 4.31 Na CB H:Asp221 4.83 Na C H:Asp221 3.60 Na OD1 H:Asp221 4.20 Na CG H:Asp221 4.90 Na CA H:Asp221 3.63 Na O H:Arg221A 2.66 Na N H:Arg221A 3.21 Na CB H:Arg221A 4.89 Na C H:Arg221A 3.44 Na CA H:Arg221A 3.93 Na N H:Asp222 4.45 Na CA H:Asp222 4.80 Na O H:Lys224 2.52 Na N H:Lys224 4.32 Na CB H:Lys224 4.42 Na C H:Lys224 3.48 Na CA H:Lys224 4.26 Na N H:Tyr225 4.33 Na CA H:Tyr225 4.56 Na O H:Hoh1037 4.59 Na O H:Hoh1045 2.97 Na O H:Hoh1085 2.84 Na O H:Hoh1101 4.49 interactive model: