Sodium in the structure of X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008 (pdb 1ypl)

The binding sites of Sodium atom in the structure of X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008 (pdb code 1ypl). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1ypl structure was solved by J.FOKKENS, G.RADAU, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.9 Space group C121 a (A) 70.131 b (A) 71.630 c (A) 72.198 alpha (°) 90.00 beta (°) 100.45 gamma (°) 90.00 Rfactor (%) 19.5 Rfree (%) 26.3 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1ypl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1ypl. 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: Hoh9011, H: Hoh9018, H: Hoh9027, H: Hoh9048, H: Hoh9053, H: Hoh9087, H: Hoh9096, H: Hoh9100, conact list: Atom Atom Distance (A) Na O H:Tyr184A 4.06 Na O H:Asp221 4.53 Na C H:Asp221 4.06 Na OD1 H:Asp221 4.45 Na CA H:Asp221 4.36 Na O H:Arg221A 2.15 Na N H:Arg221A 3.91 Na C H:Arg221A 3.26 Na CA H:Arg221A 4.21 Na N H:Asp222 4.07 Na C H:Asp222 4.46 Na CA H:Asp222 4.19 Na N H:Gly223 4.26 Na C H:Gly223 4.80 Na O H:Lys224 2.41 Na N H:Lys224 3.86 Na CB H:Lys224 4.59 Na C H:Lys224 3.45 Na CA H:Lys224 4.14 Na N H:Tyr225 4.46 Na CA H:Tyr225 4.86 Na O H:Hoh9011 3.98 Na O H:Hoh9018 4.25 Na O H:Hoh9027 3.75 Na O H:Hoh9048 2.78 Na O H:Hoh9053 2.29 Na O H:Hoh9087 4.72 Na O H:Hoh9096 2.65 Na O H:Hoh9100 2.21 interactive model: Sodium binding site 2 out of 2 in 1ypl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1ypl. 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: Hoh9067, H: Hoh9095, H: Hoh9140, conact list: Atom Atom Distance (A) Na O H:Lys169 2.33 Na CB H:Lys169 4.99 Na C H:Lys169 3.39 Na CG H:Lys169 4.60 Na CA H:Lys169 4.52 Na O H:Asp170 4.69 Na N H:Asp170 4.02 Na C H:Asp170 4.37 Na OD1 H:Asp170 4.64 Na CA H:Asp170 3.96 Na N H:Ser171 4.91 Na O H:Thr172 2.28 Na N H:Thr172 4.25 Na CG2 H:Thr172 4.87 Na C H:Thr172 3.50 Na CA H:Thr172 4.47 Na N H:Arg173 4.35 Na C H:Arg173 4.94 Na CA H:Arg173 4.33 Na O H:Hoh9067 2.88 Na O H:Hoh9095 2.57 Na O H:Hoh9140 4.60 interactive model: