Sodium in the structure of Thrombin Complexed With Hirugen and A Beta-Strand Mimetic Inhibitor (pdb 1a46)

The binding sites of Sodium atom in the structure of Thrombin Complexed With Hirugen and A Beta-Strand Mimetic Inhibitor (pdb code 1a46). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1a46 structure was solved by R.ST CHARLES, J.H.MATTHEWS, E.ZHANG, A.TULINSKY, M.KAHN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 7.0-2.1 Space group C121 a (A) 71.300 b (A) 73.090 c (A) 73.820 alpha (°) 90.00 beta (°) 101.12 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 1a46 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1a46. 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: Hoh391, H: Hoh398, H: Hoh416, H: Hoh443, H: Hoh453, H: Hoh460, H: Hoh530, H: Hoh531, conact list: Atom Atom Distance (A) Na O H:Tyr184A 4.38 Na O H:Asp221 4.43 Na N H:Asp221 4.96 Na C H:Asp221 4.02 Na OD1 H:Asp221 4.31 Na CA H:Asp221 4.25 Na O H:Arg221A 2.35 Na N H:Arg221A 3.84 Na C H:Arg221A 3.39 Na CA H:Arg221A 4.26 Na N H:Asp222 4.21 Na C H:Asp222 4.56 Na CA H:Asp222 4.28 Na N H:Gly223 4.39 Na O H:Lys224 2.46 Na N H:Lys224 3.99 Na CB H:Lys224 4.67 Na C H:Lys224 3.52 Na CA H:Lys224 4.27 Na N H:Tyr225 4.51 Na CA H:Tyr225 4.87 Na O H:Hoh391 4.91 Na O H:Hoh398 3.74 Na O H:Hoh416 2.70 Na O H:Hoh443 2.90 Na O H:Hoh453 4.23 Na O H:Hoh460 3.98 Na O H:Hoh530 2.11 Na O H:Hoh531 2.51 interactive model: Sodium binding site 2 out of 2 in 1a46 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1a46. 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: Hoh468, H: Hoh526, H: Hoh529, conact list: Atom Atom Distance (A) Na O H:Lys169 2.38 Na CB H:Lys169 4.78 Na CE H:Lys169 4.90 Na C H:Lys169 3.52 Na CA H:Lys169 4.54 Na O H:Asp170 4.97 Na N H:Asp170 4.20 Na C H:Asp170 4.39 Na OD1 H:Asp170 4.79 Na CA H:Asp170 4.08 Na N H:Ser171 4.67 Na O H:Thr172 2.24 Na N H:Thr172 4.19 Na CG2 H:Thr172 4.86 Na C H:Thr172 3.51 Na CA H:Thr172 4.48 Na N H:Arg173 4.40 Na C H:Arg173 4.98 Na CA H:Arg173 4.46 Na O H:Hoh468 2.39 Na O H:Hoh526 4.70 Na O H:Hoh529 2.30 interactive model: