Sodium in the structure of Crystal Structure of Thrombin in Complex With Fibrinogen Gamma' Peptide (pdb 2hwl)

The binding sites of Sodium atom in the structure of Crystal Structure of Thrombin in Complex With Fibrinogen Gamma' Peptide (pdb code 2hwl). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2hwl structure was solved by A.O.PINEDA, Z.W.CHEN, F.MARINO, F.S.MATHEWS, M.W.MOSESSON, E.DI CERA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-2.4 Space group P1211 a (A) 66.397 b (A) 81.523 c (A) 70.256 alpha (°) 90.00 beta (°) 109.35 gamma (°) 90.00 Rfactor (%) 21.4 Rfree (%) 24.9 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2hwl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2hwl. 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: B: Tyr184A, B: Asp221, B: Arg221A, B: Asp222, B: Gly223, B: Lys224, B: Tyr225, B: Hoh1050, B: Hoh1051, B: Hoh1085, B: Hoh1110, B: Hoh1124, B: Hoh1134, conact list: Atom Atom Distance (A) Na O B:Tyr184A 4.09 Na O B:Asp221 4.68 Na C B:Asp221 4.04 Na OD1 B:Asp221 4.40 Na CA B:Asp221 4.33 Na O B:Arg221A 2.18 Na N B:Arg221A 3.66 Na C B:Arg221A 3.21 Na CA B:Arg221A 4.09 Na N B:Asp222 4.06 Na C B:Asp222 4.53 Na CA B:Asp222 4.15 Na N B:Gly223 4.40 Na O B:Lys224 2.61 Na N B:Lys224 4.12 Na CB B:Lys224 4.77 Na C B:Lys224 3.72 Na CA B:Lys224 4.42 Na N B:Tyr225 4.74 Na CA B:Tyr225 4.94 Na O B:Hoh1050 4.02 Na O B:Hoh1051 4.04 Na O B:Hoh1085 2.68 Na O B:Hoh1110 2.48 Na O B:Hoh1124 2.21 Na O B:Hoh1134 2.44 interactive model: Sodium binding site 2 out of 2 in 2hwl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2hwl. 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: D: Tyr184A, D: Asp221, D: Arg221A, D: Asp222, D: Gly223, D: Lys224, D: Tyr225, D: Hoh1034, D: Hoh1038, D: Hoh1061, D: Hoh1076, D: Hoh1086, D: Hoh1109, D: Hoh1135, conact list: Atom Atom Distance (A) Na O D:Tyr184A 3.96 Na O D:Asp221 4.65 Na C D:Asp221 4.18 Na OD1 D:Asp221 4.41 Na CA D:Asp221 4.40 Na O D:Arg221A 2.69 Na N D:Arg221A 4.06 Na C D:Arg221A 3.66 Na CA D:Arg221A 4.53 Na N D:Asp222 4.45 Na C D:Asp222 4.79 Na CA D:Asp222 4.46 Na N D:Gly223 4.56 Na O D:Lys224 2.50 Na N D:Lys224 4.20 Na CB D:Lys224 4.91 Na C D:Lys224 3.67 Na CA D:Lys224 4.48 Na N D:Tyr225 4.64 Na CD1 D:Tyr225 4.92 Na CA D:Tyr225 4.75 Na O D:Hoh1034 2.64 Na O D:Hoh1038 2.36 Na O D:Hoh1061 3.82 Na O D:Hoh1076 3.73 Na O D:Hoh1086 3.70 Na O D:Hoh1109 2.49 Na O D:Hoh1135 2.68 interactive model: