Sodium in the structure of Thrombin Inhibition By Pyridin Derivatives (pdb 3qto)

The binding sites of Sodium atom in the structure of Thrombin Inhibition By Pyridin Derivatives (pdb code 3qto). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3qto 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) 35.7-1.5 Space group C121 a (A) 69.800 b (A) 71.400 c (A) 72.500 alpha (°) 90.00 beta (°) 100.30 gamma (°) 90.00 Rfactor (%) 15.5 Rfree (%) 16.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3qto Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3qto. 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: Hoh3123, H: Hoh3191, H: Hoh3268, H: Hoh3345, conact list: Atom Atom Distance (A) Na O H:Lys169 2.35 Na CB H:Lys169 4.92 Na C H:Lys169 3.45 Na CG H:Lys169 4.18 Na CA H:Lys169 4.52 Na O H:Asp170 4.77 Na N H:Asp170 4.17 Na C H:Asp170 4.39 Na OD1 H:Asp170 4.73 Na CA H:Asp170 4.03 Na N H:Ser171 4.82 Na O H:Thr172 2.33 Na N H:Thr172 4.25 Na CG2 H:Thr172 4.86 Na C H:Thr172 3.56 Na CA H:Thr172 4.53 Na N H:Arg173 4.43 Na C H:Arg173 4.96 Na CA H:Arg173 4.41 Na O H:Hoh3123 2.71 Na O H:Hoh3191 2.62 Na O H:Hoh3268 2.42 Na O H:Hoh3345 4.32 interactive model: Sodium binding site 2 out of 2 in 3qto Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3qto. 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: Hoh3058, H: Hoh3101, H: Hoh3129, H: Hoh3184, H: Hoh3189, H: Hoh3193, H: Hoh3202, H: Hoh3312, conact list: Atom Atom Distance (A) Na O H:Tyr184A 4.19 Na O H:Asp221 4.50 Na C H:Asp221 4.01 Na OD1 H:Asp221 4.63 Na CA H:Asp221 4.34 Na O H:Arg221A 2.24 Na N H:Arg221A 3.83 Na C H:Arg221A 3.29 Na CA H:Arg221A 4.18 Na N H:Asp222 4.13 Na C H:Asp222 4.44 Na CA H:Asp222 4.24 Na N H:Gly223 4.17 Na C H:Gly223 4.82 Na O H:Lys224 2.37 Na N H:Lys224 3.80 Na CB H:Lys224 4.44 Na C H:Lys224 3.41 Na CA H:Lys224 4.09 Na N H:Tyr225 4.41 Na CA H:Tyr225 4.69 Na O H:Hoh3058 4.31 Na O H:Hoh3101 3.88 Na O H:Hoh3129 2.56 Na O H:Hoh3184 2.45 Na O H:Hoh3189 4.98 Na O H:Hoh3193 3.96 Na O H:Hoh3202 2.74 Na O H:Hoh3312 2.39 interactive model: