Sodium in the structure of Divalent Cation Tolerance Protein (Cut A1) From Thermus Thermophilus HB8 (pdb 1nza)

The binding sites of Sodium atom in the structure of Divalent Cation Tolerance Protein (Cut A1) From Thermus Thermophilus HB8 (pdb code 1nza). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1nza structure was solved by B.BAGAUTDINOV, M.MIYANO, T.H.TAHIROV, RIKEN STRUCTURALGENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-1.7 Space group I23 a (A) 83.003 b (A) 83.003 c (A) 83.003 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.9 Rfree (%) 24.6 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1nza Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1nza. 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: Thr8, A: Ser39, A: Glu52, A: Glu81, A: Cl109, A: Hoh510, A: Hoh512, A: Hoh518, A: Hoh520, conact list: Atom Atom Distance (A) Na O A:Thr8 4.72 Na CB A:Thr8 3.24 Na CG2 A:Thr8 4.00 Na OG1 A:Thr8 2.29 Na C A:Thr8 4.66 Na CA A:Thr8 4.48 Na CB A:Ser39 4.70 Na OG A:Ser39 4.42 Na OE1 A:Glu52 2.42 Na OE2 A:Glu52 2.42 Na CD A:Glu52 2.75 Na CG A:Glu52 4.26 Na CB A:Glu81 4.69 Na OE2 A:Glu81 3.89 Na CD A:Glu81 4.99 Na CL A:Cl109 3.29 Na O A:Hoh510 2.40 Na O A:Hoh512 4.11 Na O A:Hoh518 4.41 Na O A:Hoh520 2.53 interactive model: Sodium binding site 2 out of 2 in 1nza Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1nza. 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: Pro10, A: Asp50, A: Gln51, A: Tyr77, A: Hoh501, A: Hoh502, conact list: Atom Atom Distance (A) Na O A:Pro10 4.72 Na CB A:Pro10 4.51 Na CB A:Asp50 4.52 Na OD2 A:Asp50 3.45 Na OD1 A:Asp50 2.22 Na CG A:Asp50 3.18 Na CA A:Asp50 4.84 Na O A:Gln51 3.97 Na N A:Gln51 4.23 Na C A:Gln51 4.90 Na OH A:Tyr77 4.45 Na O A:Hoh501 2.36 Na O A:Hoh502 2.40 interactive model: