Sodium in the structure of Crystal Structures Of Thrombin With Thiazole-Containing Inhibitors: Probes of the S1' Binding Site (pdb 1a4w)

The binding sites of Sodium atom in the structure of Crystal Structures Of Thrombin With Thiazole-Containing Inhibitors: Probes of the S1' Binding Site (pdb code 1a4w). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1a4w structure was solved by J.H.MATTHEWS, R.KRISHNAN, M.J.COSTANZO, B.E.MARYANOFF, A.TULINSKY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 7.0-1.8 Space group C121 a (A) 71.470 b (A) 72.000 c (A) 73.390 alpha (°) 90.00 beta (°) 101.13 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 1a4w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1a4w. 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: Hoh403, H: Hoh410, H: Hoh436, H: Hoh438, H: Hoh460, H: Hoh464, H: Hoh490, H: Hoh497, conact list: Atom Atom Distance (A) Na O H:Tyr184A 4.19 Na O H:Asp221 4.63 Na C H:Asp221 4.10 Na OD1 H:Asp221 4.77 Na CA H:Asp221 4.41 Na O H:Arg221A 2.44 Na N H:Arg221A 3.89 Na CB H:Arg221A 4.94 Na C H:Arg221A 3.56 Na CA H:Arg221A 4.33 Na N H:Asp222 4.40 Na C H:Asp222 4.59 Na CA H:Asp222 4.43 Na N H:Gly223 4.47 Na C H:Gly223 4.83 Na O H:Lys224 2.32 Na N H:Lys224 3.82 Na CB H:Lys224 4.56 Na C H:Lys224 3.44 Na CA H:Lys224 4.16 Na N H:Tyr225 4.38 Na CA H:Tyr225 4.64 Na O H:Hoh403 2.91 Na O H:Hoh410 4.67 Na O H:Hoh436 4.31 Na O H:Hoh438 3.80 Na O H:Hoh460 2.41 Na O H:Hoh464 2.37 Na O H:Hoh490 4.29 Na O H:Hoh497 2.20 interactive model: Sodium binding site 2 out of 2 in 1a4w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1a4w. 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: Hoh467, H: Hoh515, H: Hoh518, conact list: Atom Atom Distance (A) Na O H:Lys169 2.36 Na CB H:Lys169 4.87 Na C H:Lys169 3.46 Na CA H:Lys169 4.51 Na O H:Asp170 4.89 Na N H:Asp170 4.17 Na C H:Asp170 4.47 Na OD1 H:Asp170 4.49 Na CA H:Asp170 4.03 Na N H:Ser171 4.83 Na O H:Thr172 2.33 Na N H:Thr172 4.18 Na CG2 H:Thr172 4.87 Na C H:Thr172 3.56 Na CA H:Thr172 4.51 Na N H:Arg173 4.44 Na C H:Arg173 4.92 Na CA H:Arg173 4.42 Na O H:Hoh467 2.39 Na O H:Hoh515 2.84 Na O H:Hoh518 2.53 interactive model: