Sodium in the structure of Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA (pdb 2ofi)

The binding sites of Sodium atom in the structure of Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA (pdb code 2ofi). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2ofi structure was solved by A.H.METZ, T.HOLLIS, B.F.EICHMAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.9 Space group P63 a (A) 101.963 b (A) 101.963 c (A) 55.461 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 17.6 Rfree (%) 19.8 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2ofi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2ofi. 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: Trp117, A: Ser118, A: Phe119, A: Val120, A: Asp121, A: Gly122, A: Hoh416, A: Hoh417, A: Hoh418, A: Hoh419, conact list: Atom Atom Distance (A) Na CB A:Trp117 4.46 Na C A:Trp117 3.39 Na CE3 A:Trp117 4.78 Na CA A:Trp117 4.41 Na O A:Trp117 2.25 Na O A:Ser118 4.69 Na N A:Ser118 4.19 Na C A:Ser118 4.44 Na CA A:Ser118 4.15 Na N A:Phe119 4.97 Na O A:Val120 2.25 Na N A:Val120 4.13 Na CB A:Val120 4.53 Na CG2 A:Val120 4.15 Na C A:Val120 3.35 Na CG1 A:Val120 4.82 Na CA A:Val120 4.14 Na N A:Asp121 4.33 Na C A:Asp121 4.86 Na CA A:Asp121 4.54 Na O A:Gly122 4.70 Na N A:Gly122 4.28 Na O A:Hoh416 4.72 Na O A:Hoh417 2.83 Na O A:Hoh418 2.14 Na O A:Hoh419 2.57 interactive model: