Sodium in the structure of Thrombin Inhibitors With Rigid Tripeptidyl Aldehydes (pdb 1bb0)

The binding sites of Sodium atom in the structure of Thrombin Inhibitors With Rigid Tripeptidyl Aldehydes (pdb code 1bb0). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1bb0 structure was solved by R.KRISHNAN, E.ZHANG, K.HAKANSSON, R.K.ARNI, A.TULINSKY, M.S.L.LIM-WILBY, O.E.LEVY, J.E.SEMPLE, T.K.BRUNCK, 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) 71.140 b (A) 72.260 c (A) 72.730 alpha (°) 90.00 beta (°) 100.70 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 1bb0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1bb0. 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: Hoh428, B: Hoh462, B: Hoh473, B: Hoh485, B: Hoh496, B: Hoh501, B: Hoh518, B: Hoh536, conact list: Atom Atom Distance (A) Na O B:Tyr184A 4.08 Na O B:Asp221 4.75 Na C B:Asp221 4.32 Na OD1 B:Asp221 4.70 Na CA B:Asp221 4.57 Na O B:Arg221A 2.49 Na N B:Arg221A 4.04 Na C B:Arg221A 3.61 Na CA B:Arg221A 4.45 Na N B:Asp222 4.45 Na C B:Asp222 4.58 Na CA B:Asp222 4.40 Na N B:Gly223 4.36 Na C B:Gly223 4.76 Na O B:Lys224 2.35 Na N B:Lys224 3.70 Na CB B:Lys224 4.74 Na C B:Lys224 3.36 Na CA B:Lys224 4.08 Na N B:Tyr225 4.34 Na CD1 B:Tyr225 4.94 Na CA B:Tyr225 4.69 Na O B:Hoh428 2.53 Na O B:Hoh462 4.15 Na O B:Hoh473 2.64 Na O B:Hoh485 3.99 Na O B:Hoh496 3.93 Na O B:Hoh501 2.35 Na O B:Hoh518 2.27 Na O B:Hoh536 4.74 interactive model: Sodium binding site 2 out of 2 in 1bb0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1bb0. 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: Lys169, B: Asp170, B: Ser171, B: Thr172, B: Arg173, B: Ile174, B: Hoh446, B: Hoh595, B: Hoh596, conact list: Atom Atom Distance (A) Na O B:Lys169 2.46 Na CB B:Lys169 4.94 Na C B:Lys169 3.57 Na CA B:Lys169 4.66 Na O B:Asp170 4.94 Na N B:Asp170 4.25 Na C B:Asp170 4.43 Na OD1 B:Asp170 4.59 Na CA B:Asp170 4.08 Na N B:Ser171 4.83 Na O B:Thr172 2.21 Na N B:Thr172 4.22 Na CG2 B:Thr172 4.91 Na C B:Thr172 3.45 Na CA B:Thr172 4.45 Na N B:Arg173 4.32 Na C B:Arg173 4.85 Na CA B:Arg173 4.38 Na O B:Ile174 4.90 Na O B:Hoh446 2.75 Na O B:Hoh595 2.39 Na O B:Hoh596 2.43 interactive model: