Sodium in the structure of Unliganded Wild-Type Human Thrombin (pdb 3u69)

The binding sites of Sodium atom in the structure of Unliganded Wild-Type Human Thrombin (pdb code 3u69). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3u69 structure was solved by A.C.FIGUEIREDO, C.C.CLEMENT, M.PHILIPP, P.J.BARBOSA PEREIRA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.3-1.6 Space group P212121 a (A) 57.555 b (A) 72.995 c (A) 83.042 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 13.3 Rfree (%) 16.7 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3u69 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3u69. 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: Tyr510, H: Asp552, H: Arg553, H: Asp554, H: Gly555, H: Lys556, H: Tyr557, H: Hoh6, H: Hoh11, H: Hoh18, H: Hoh19, H: Hoh27, H: Hoh29, H: Hoh52, H: Hoh65, H: Hoh66, conact list: Atom Atom Distance (A) Na O H:Tyr510 4.09 Na O H:Asp552 4.57 Na HA H:Asp552 3.66 Na H H:Asp552 5.00 Na OD1 H:Asp552 4.60 Na C H:Asp552 4.08 Na CA H:Asp552 4.36 Na HB2 H:Arg553 4.85 Na N H:Arg553 3.88 Na C H:Arg553 3.38 Na CA H:Arg553 4.24 Na O H:Arg553 2.30 Na HA H:Arg553 4.94 Na H H:Arg553 3.94 Na N H:Asp554 4.28 Na HA H:Asp554 3.81 Na C H:Asp554 4.61 Na CA H:Asp554 4.39 Na N H:Gly555 4.29 Na H H:Gly555 3.89 Na C H:Gly555 4.91 Na HB2 H:Lys556 3.85 Na N H:Lys556 3.90 Na CB H:Lys556 4.50 Na HB3 H:Lys556 4.96 Na C H:Lys556 3.44 Na CA H:Lys556 4.15 Na O H:Lys556 2.35 Na H H:Lys556 3.30 Na N H:Tyr557 4.46 Na CA H:Tyr557 4.75 Na HA H:Tyr557 4.04 Na O H:Hoh6 2.38 Na O H:Hoh11 2.42 Na O H:Hoh18 3.90 Na O H:Hoh19 2.44 Na O H:Hoh27 4.20 Na O H:Hoh29 2.61 Na O H:Hoh52 4.99 Na O H:Hoh65 4.92 Na O H:Hoh66 4.01 interactive model: