Sodium in the structure of Bovine Heart Cytochrome C Oxidase At the Fully Oxidized State (pdb 2occ)

The binding sites of Sodium atom in the structure of Bovine Heart Cytochrome C Oxidase At the Fully Oxidized State (pdb code 2occ). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2occ structure was solved by T.TSUKIHARA, M.YAO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-2.3 Space group P212121 a (A) 189.100 b (A) 210.500 c (A) 178.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.9 Rfree (%) 24.4 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2occ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2occ. 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: Glu40, A: Leu41, A: Gln43, A: Pro44, A: Gly45, A: Thr46, A: Leu47, A: Ser441, A: Asp442, conact list: Atom Atom Distance (A) Na O A:Glu40 2.45 Na OE1 A:Glu40 4.54 Na CB A:Glu40 4.58 Na OE2 A:Glu40 2.42 Na CD A:Glu40 3.40 Na C A:Glu40 3.43 Na CG A:Glu40 3.68 Na CA A:Glu40 4.34 Na N A:Leu41 4.25 Na CD2 A:Leu41 4.56 Na CA A:Leu41 4.30 Na O A:Gln43 3.93 Na C A:Pro44 5.00 Na O A:Gly45 2.40 Na N A:Gly45 4.40 Na C A:Gly45 3.55 Na CA A:Gly45 4.61 Na N A:Thr46 4.26 Na CB A:Thr46 4.92 Na C A:Thr46 4.83 Na CA A:Thr46 4.02 Na N A:Leu47 4.65 Na O A:Ser441 2.34 Na C A:Ser441 3.51 Na CA A:Ser441 4.69 Na N A:Asp442 4.14 Na CB A:Asp442 4.07 Na OD2 A:Asp442 4.83 Na OD1 A:Asp442 4.14 Na CG A:Asp442 4.17 Na CA A:Asp442 3.85 interactive model: Sodium binding site 2 out of 2 in 2occ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2occ. 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: N: Glu40, N: Leu41, N: Gln43, N: Pro44, N: Gly45, N: Thr46, N: Leu47, N: Ser441, N: Asp442, N: Tyr443, conact list: Atom Atom Distance (A) Na O N:Glu40 2.39 Na OE1 N:Glu40 4.60 Na CB N:Glu40 4.62 Na OE2 N:Glu40 2.46 Na CD N:Glu40 3.46 Na C N:Glu40 3.41 Na CG N:Glu40 3.73 Na CA N:Glu40 4.35 Na N N:Leu41 4.22 Na CD2 N:Leu41 4.57 Na CA N:Leu41 4.27 Na O N:Gln43 3.86 Na C N:Gln43 5.00 Na C N:Pro44 4.86 Na O N:Gly45 2.39 Na N N:Gly45 4.35 Na C N:Gly45 3.54 Na CA N:Gly45 4.60 Na N N:Thr46 4.27 Na CB N:Thr46 4.99 Na C N:Thr46 4.91 Na CA N:Thr46 4.08 Na N N:Leu47 4.75 Na O N:Ser441 2.39 Na C N:Ser441 3.56 Na CA N:Ser441 4.76 Na N N:Asp442 4.16 Na CB N:Asp442 4.05 Na OD2 N:Asp442 4.81 Na OD1 N:Asp442 4.08 Na CG N:Asp442 4.14 Na CA N:Asp442 3.83 Na CE2 N:Tyr443 4.92 interactive model: