Sodium in the structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb 1ocr)

The binding sites of Sodium atom in the structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 1ocr). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1ocr structure was solved by T.TSUKIHARA, M.YAO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-2.4 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 (%) 20.3 Rfree (%) 24.7 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1ocr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1ocr. 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: 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 4.51 Na CB A:Glu40 4.42 Na OE2 A:Glu40 2.44 Na CD A:Glu40 3.33 Na C A:Glu40 3.39 Na CG A:Glu40 3.45 Na CA A:Glu40 4.24 Na N A:Leu41 4.19 Na CD2 A:Leu41 4.53 Na CA A:Leu41 4.25 Na O A:Gln43 3.95 Na O A:Gly45 2.40 Na N A:Gly45 4.50 Na C A:Gly45 3.55 Na CA A:Gly45 4.69 Na N A:Thr46 4.20 Na CB A:Thr46 4.90 Na C A:Thr46 4.68 Na CA A:Thr46 3.90 Na N A:Leu47 4.57 Na O A:Ser441 2.36 Na C A:Ser441 3.55 Na CA A:Ser441 4.68 Na N A:Asp442 4.23 Na CB A:Asp442 4.20 Na OD2 A:Asp442 4.73 Na OD1 A:Asp442 4.44 Na CG A:Asp442 4.27 Na CA A:Asp442 3.97 interactive model: Sodium binding site 2 out of 2 in 1ocr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1ocr. 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: Gly45, N: Thr46, N: Leu47, N: Ser441, N: Asp442, conact list: Atom Atom Distance (A) Na O N:Glu40 2.40 Na OE1 N:Glu40 4.55 Na CB N:Glu40 4.44 Na OE2 N:Glu40 2.47 Na CD N:Glu40 3.36 Na C N:Glu40 3.35 Na CG N:Glu40 3.49 Na CA N:Glu40 4.24 Na N N:Leu41 4.15 Na CD2 N:Leu41 4.59 Na CA N:Leu41 4.21 Na O N:Gln43 3.87 Na O N:Gly45 2.41 Na N N:Gly45 4.51 Na C N:Gly45 3.57 Na CA N:Gly45 4.71 Na N N:Thr46 4.21 Na CB N:Thr46 4.94 Na C N:Thr46 4.69 Na CA N:Thr46 3.93 Na N N:Leu47 4.60 Na O N:Ser441 2.41 Na C N:Ser441 3.60 Na CA N:Ser441 4.74 Na N N:Asp442 4.29 Na CB N:Asp442 4.26 Na OD2 N:Asp442 4.70 Na OD1 N:Asp442 4.46 Na CG N:Asp442 4.29 Na CA N:Asp442 4.02 interactive model: