Sodium in the structure of Crystal Structure of TTHB049 From Thermus Thermophilus HB8 (pdb 2p6m)

The binding sites of Sodium atom in the structure of Crystal Structure of TTHB049 From Thermus Thermophilus HB8 (pdb code 2p6m). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2p6m structure was solved by M.SUGAHARA, Y.MATSUURA, Y.MORIKAWA, H.SHIMADA, N.KUNISHIMA, RIKENSTRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-1.9 Space group I222 a (A) 85.145 b (A) 92.101 c (A) 109.793 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.9 Rfree (%) 21.1 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2p6m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2p6m. 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: Gly78, B: Ala79, B: Leu80, B: Glu81, B: Gly82, B: Ala83, conact list: Atom Atom Distance (A) Na O B:Gly78 4.18 Na O B:Ala79 2.26 Na N B:Ala79 4.97 Na C B:Ala79 3.13 Na CB B:Ala79 4.90 Na CA B:Ala79 3.93 Na O B:Leu80 4.41 Na N B:Leu80 3.96 Na C B:Leu80 3.77 Na CA B:Leu80 4.12 Na O B:Glu81 2.30 Na N B:Glu81 3.40 Na CB B:Glu81 4.08 Na C B:Glu81 3.36 Na CA B:Glu81 3.83 Na N B:Gly82 4.54 Na CA B:Gly82 4.93 Na N B:Ala83 4.87 interactive model: