Sodium in the structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb 2eik)

The binding sites of Sodium atom in the structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 2eik). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2eik structure was solved by K.MURAMOTO, K.HIRATA, K.SHINZAWA-ITOH, S.YOKO-O, E.YAMASHITA, H.AOYAMA, T.TSUKIHARA, S.YOSHIKAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-2.1 Space group P212121 a (A) 183.321 b (A) 206.525 c (A) 178.159 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.9 Rfree (%) 22.8 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2eik Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2eik. 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, A: Hoh2026, A: Hoh2060, A: Hoh2069, conact list: Atom Atom Distance (A) Na O A:Glu40 2.30 Na OE1 A:Glu40 2.22 Na CB A:Glu40 4.38 Na OE2 A:Glu40 4.25 Na CD A:Glu40 3.12 Na C A:Glu40 3.32 Na CG A:Glu40 3.42 Na CA A:Glu40 4.18 Na N A:Leu41 4.19 Na CD2 A:Leu41 4.57 Na CA A:Leu41 4.29 Na O A:Gln43 4.05 Na O A:Gly45 2.41 Na N A:Gly45 4.60 Na C A:Gly45 3.59 Na CA A:Gly45 4.73 Na N A:Thr46 4.26 Na C A:Thr46 4.72 Na CA A:Thr46 4.06 Na N A:Leu47 4.54 Na O A:Ser441 2.31 Na C A:Ser441 3.53 Na CA A:Ser441 4.66 Na N A:Asp442 4.25 Na CB A:Asp442 4.20 Na OD2 A:Asp442 4.27 Na OD1 A:Asp442 4.82 Na CG A:Asp442 4.24 Na CA A:Asp442 4.04 Na O A:Hoh2026 2.51 Na O A:Hoh2060 3.42 Na O A:Hoh2069 4.08 interactive model: Sodium binding site 2 out of 2 in 2eik Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2eik. 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, N: Hoh3026, N: Hoh3060, N: Hoh3069, conact list: Atom Atom Distance (A) Na O N:Glu40 2.30 Na OE1 N:Glu40 2.21 Na CB N:Glu40 4.31 Na OE2 N:Glu40 4.27 Na CD N:Glu40 3.10 Na C N:Glu40 3.34 Na CG N:Glu40 3.31 Na CA N:Glu40 4.16 Na N N:Leu41 4.25 Na CD2 N:Leu41 4.77 Na CA N:Leu41 4.42 Na O N:Gln43 4.19 Na O N:Gly45 2.38 Na N N:Gly45 4.67 Na C N:Gly45 3.55 Na CA N:Gly45 4.74 Na N N:Thr46 4.17 Na CB N:Thr46 4.94 Na C N:Thr46 4.54 Na CA N:Thr46 3.87 Na N N:Leu47 4.36 Na O N:Ser441 2.32 Na CB N:Ser441 4.98 Na C N:Ser441 3.54 Na CA N:Ser441 4.63 Na N N:Asp442 4.28 Na CB N:Asp442 4.20 Na OD2 N:Asp442 4.20 Na CG N:Asp442 4.31 Na CA N:Asp442 4.12 Na O N:Hoh3026 2.57 Na O N:Hoh3060 3.37 Na O N:Hoh3069 4.08 interactive model: