Sodium in the structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State (pdb 1oco)

The binding sites of Sodium atom in the structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State (pdb code 1oco). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1oco structure was solved by T.TSUKIHARA, M.YAO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 7.0-2.8 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 (%) 21.3 Rfree (%) 25.6 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1oco Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1oco. 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: Ser441, A: Asp442, A: Tyr443, conact list: Atom Atom Distance (A) Na O A:Glu40 2.41 Na OE1 A:Glu40 4.78 Na CB A:Glu40 4.97 Na OE2 A:Glu40 2.53 Na CD A:Glu40 3.67 Na C A:Glu40 3.49 Na CG A:Glu40 4.12 Na CA A:Glu40 4.62 Na N A:Leu41 4.13 Na CB A:Leu41 4.83 Na CD2 A:Leu41 4.01 Na C A:Leu41 4.75 Na CG A:Leu41 4.72 Na CA A:Leu41 3.92 Na O A:Gln43 3.64 Na C A:Gln43 4.78 Na C A:Pro44 4.86 Na O A:Gly45 2.44 Na N A:Gly45 4.10 Na C A:Gly45 3.61 Na CA A:Gly45 4.46 Na N A:Thr46 4.54 Na CA A:Thr46 4.59 Na O A:Ser441 2.42 Na C A:Ser441 3.52 Na CA A:Ser441 4.73 Na N A:Asp442 4.12 Na CB A:Asp442 4.12 Na OD2 A:Asp442 4.62 Na OD1 A:Asp442 3.85 Na CG A:Asp442 3.99 Na CA A:Asp442 3.79 Na CE2 A:Tyr443 4.46 Na CD2 A:Tyr443 4.91 interactive model: Sodium binding site 2 out of 2 in 1oco Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1oco. 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: Ser441, N: Asp442, N: Tyr443, conact list: Atom Atom Distance (A) Na O N:Glu40 2.46 Na OE1 N:Glu40 4.81 Na OE2 N:Glu40 2.56 Na CD N:Glu40 3.72 Na C N:Glu40 3.58 Na CG N:Glu40 4.22 Na CA N:Glu40 4.72 Na N N:Leu41 4.24 Na CB N:Leu41 4.93 Na CD2 N:Leu41 4.06 Na C N:Leu41 4.81 Na CG N:Leu41 4.80 Na CA N:Leu41 4.00 Na O N:Gln43 3.59 Na C N:Gln43 4.72 Na C N:Pro44 4.72 Na CA N:Pro44 4.98 Na O N:Gly45 2.37 Na N N:Gly45 4.00 Na C N:Gly45 3.53 Na CA N:Gly45 4.37 Na N N:Thr46 4.45 Na CA N:Thr46 4.54 Na O N:Ser441 2.43 Na C N:Ser441 3.55 Na CA N:Ser441 4.79 Na N N:Asp442 4.12 Na CB N:Asp442 4.01 Na OD2 N:Asp442 4.49 Na OD1 N:Asp442 3.73 Na CG N:Asp442 3.87 Na CA N:Asp442 3.74 Na CD1 N:Tyr443 4.89 Na CE1 N:Tyr443 4.44 interactive model: