Sodium in the structure of Structure of Thrombin Complexed With Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties At P1 (pdb 1d6w)

The binding sites of Sodium atom in the structure of Structure of Thrombin Complexed With Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties At P1 (pdb code 1d6w). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1d6w structure was solved by I.MOCHALKIN, A.TULINSKY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 9.0-2.0 Space group C121 a (A) 71.430 b (A) 71.670 c (A) 72.450 alpha (°) 90.00 beta (°) 101.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 1d6w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1d6w. 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: A: Lys169, A: Asp170, A: Ser171, A: Thr172, A: Arg173, A: Hoh493, A: Hoh494, A: Hoh497, conact list: Atom Atom Distance (A) Na O A:Lys169 2.52 Na C A:Lys169 3.62 Na CA A:Lys169 4.65 Na O A:Asp170 4.97 Na N A:Asp170 4.21 Na OD2 A:Asp170 4.51 Na C A:Asp170 4.47 Na CA A:Asp170 4.11 Na N A:Ser171 4.95 Na O A:Thr172 2.39 Na N A:Thr172 4.36 Na CG2 A:Thr172 4.94 Na C A:Thr172 3.58 Na CA A:Thr172 4.62 Na N A:Arg173 4.39 Na CA A:Arg173 4.47 Na O A:Hoh493 4.74 Na O A:Hoh494 2.24 Na O A:Hoh497 2.88 interactive model: Sodium binding site 2 out of 2 in 1d6w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1d6w. 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: A: Tyr184A, A: Asp189, A: Asp221, A: Arg221A, A: Asp222, A: Gly223, A: Lys224, A: Tyr225, A: Hoh405, A: Hoh407, A: Hoh415, A: Hoh430, A: Hoh459, A: Hoh460, A: Hoh496, A: Hoh530, conact list: Atom Atom Distance (A) Na O A:Tyr184A 4.26 Na OD1 A:Asp189 4.53 Na O A:Asp221 4.47 Na N A:Asp221 4.73 Na C A:Asp221 3.92 Na OD1 A:Asp221 4.14 Na CA A:Asp221 4.04 Na O A:Arg221A 2.39 Na N A:Arg221A 3.68 Na C A:Arg221A 3.37 Na CA A:Arg221A 4.15 Na N A:Asp222 4.32 Na C A:Asp222 4.81 Na CA A:Asp222 4.54 Na N A:Gly223 4.72 Na O A:Lys224 2.38 Na N A:Lys224 4.01 Na CB A:Lys224 4.74 Na C A:Lys224 3.44 Na CA A:Lys224 4.22 Na N A:Tyr225 4.42 Na CA A:Tyr225 4.66 Na O A:Hoh405 3.52 Na O A:Hoh407 4.02 Na O A:Hoh415 4.31 Na O A:Hoh430 3.32 Na O A:Hoh459 2.16 Na O A:Hoh460 2.66 Na O A:Hoh496 4.01 Na O A:Hoh530 2.72 interactive model: