Sodium in the structure of Crystal Structure Of the N-Terminal Domain of Dnad From Bacillus Subtilis (pdb 2v79)

The binding sites of Sodium atom in the structure of Crystal Structure Of the N-Terminal Domain of Dnad From Bacillus Subtilis (pdb code 2v79). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2v79 structure was solved by S.SCHNEIDER, W.ZHANG, P.SOULTANAS, M.PAOLI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.0 Space group P3121 a (A) 78.666 b (A) 78.666 c (A) 124.558 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.1 Rfree (%) 21 Sodium Binding Sites: Sodium binding site 1 out of 3 in 2v79 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2v79. 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: Gln58, A: Glu59, A: Gly60, A: Met61, A: Ser62, A: Ile63, A: Ser64, B: Lys26, A: Hoh2075, A: Hoh2077, A: Hoh2080, conact list: Atom Atom Distance (A) Na O A:Gln58 2.51 Na NE2 A:Gln58 4.31 Na OE1 A:Gln58 2.35 Na CB A:Gln58 3.88 Na CD A:Gln58 3.41 Na C A:Gln58 3.46 Na CG A:Gln58 4.24 Na CA A:Gln58 4.15 Na N A:Glu59 4.38 Na C A:Glu59 4.87 Na CA A:Glu59 4.60 Na N A:Gly60 4.64 Na O A:Met61 2.41 Na N A:Met61 3.95 Na CB A:Met61 4.33 Na C A:Met61 3.42 Na CA A:Met61 4.10 Na O A:Ser62 4.42 Na N A:Ser62 4.42 Na C A:Ser62 4.20 Na CA A:Ser62 4.68 Na O A:Ile63 2.33 Na N A:Ile63 4.15 Na C A:Ile63 3.48 Na CA A:Ile63 4.45 Na N A:Ser64 4.32 Na C A:Ser64 4.96 Na CA A:Ser64 4.37 Na NZ B:Lys26 4.32 Na O A:Hoh2075 4.82 Na O A:Hoh2077 2.79 Na O A:Hoh2080 2.41 interactive model: Sodium binding site 2 out of 3 in 2v79 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2v79. 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: Thr14, A: Ser15, A: Thr16, A: Lys42, A: Glu46, A: Hoh2025, A: Hoh2026, A: Hoh2063, B: Hoh2029, conact list: Atom Atom Distance (A) Na O A:Thr14 3.45 Na C A:Thr14 4.53 Na N A:Ser15 4.98 Na C A:Ser15 4.37 Na CA A:Ser15 4.42 Na N A:Thr16 3.78 Na CB A:Thr16 3.84 Na CG2 A:Thr16 3.77 Na OG1 A:Thr16 2.92 Na CA A:Thr16 4.41 Na NZ A:Lys42 4.01 Na OE1 A:Glu46 2.71 Na OE2 A:Glu46 3.53 Na CD A:Glu46 3.36 Na CG A:Glu46 4.60 Na O A:Hoh2025 4.64 Na O A:Hoh2026 2.31 Na O A:Hoh2063 3.32 Na O B:Hoh2029 4.24 interactive model: Sodium binding site 3 out of 3 in 2v79 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2v79. 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: Lys26, B: Gln58, B: Glu59, B: Gly60, B: Met61, B: Ser62, B: Ile63, B: Ser64, A: Hoh2039, B: Hoh2079, B: Hoh2081, B: Hoh2085, conact list: Atom Atom Distance (A) Na NZ A:Lys26 4.18 Na O B:Gln58 2.35 Na NE2 B:Gln58 4.19 Na OE1 B:Gln58 2.31 Na CB B:Gln58 3.77 Na CD B:Gln58 3.31 Na C B:Gln58 3.31 Na CG B:Gln58 4.12 Na CA B:Gln58 4.03 Na N B:Glu59 4.25 Na C B:Glu59 4.83 Na CA B:Glu59 4.50 Na N B:Gly60 4.49 Na O B:Met61 2.57 Na N B:Met61 3.96 Na CB B:Met61 4.36 Na C B:Met61 3.57 Na CA B:Met61 4.19 Na O B:Ser62 4.82 Na N B:Ser62 4.54 Na C B:Ser62 4.38 Na CA B:Ser62 4.80 Na O B:Ile63 2.28 Na N B:Ile63 4.10 Na C B:Ile63 3.46 Na CA B:Ile63 4.40 Na N B:Ser64 4.33 Na C B:Ser64 4.97 Na CA B:Ser64 4.39 Na O A:Hoh2039 2.79 Na O B:Hoh2079 3.92 Na O B:Hoh2081 4.74 Na O B:Hoh2085 2.44 interactive model: