Sodium in the structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State At 100 K (pdb 3ag4)
The binding sites of Sodium atom in the structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State At 100 K (pdb code 3ag4). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3ag4 structure was solved by K.MURAMOTO, K.OHTA, K.SHINZAWA-ITOH, K.KANDA, M.TANIGUCHI, H.NABEKURA, E.YAMASHITA, T.TSUKIHARA, S.YOSHIKAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 40.0-2.0 | | Space group | P212121 | | a (A) | 183.364 | | b (A) | 206.648 | | c (A) | 178.137 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 90.00 | | Rfactor (%) | 18.6 | | Rfree (%) | 21.9 |
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Sodium Binding Sites:Sodium binding site 1 out of 2 in 3ag4
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ag4. 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: Hoh2258, A: Hoh2563, A: Hoh2691, A: Hoh2693, | conact list:
| Atom | Atom | Distance (A) | | Na | O A:Glu40 | 2.29 | | Na | OE1 A:Glu40 | 2.29 | | Na | CB A:Glu40 | 4.47 | | Na | OE2 A:Glu40 | 4.27 | | Na | CD A:Glu40 | 3.20 | | Na | C A:Glu40 | 3.36 | | Na | CG A:Glu40 | 3.49 | | Na | CA A:Glu40 | 4.22 | | Na | N A:Leu41 | 4.24 | | Na | CD2 A:Leu41 | 4.75 | | Na | CA A:Leu41 | 4.36 | | Na | O A:Gln43 | 3.90 | | Na | O A:Gly45 | 2.29 | | Na | N A:Gly45 | 4.39 | | Na | C A:Gly45 | 3.47 | | Na | CA A:Gly45 | 4.58 | | Na | N A:Thr46 | 4.18 | | Na | C A:Thr46 | 4.62 | | Na | CA A:Thr46 | 3.98 | | Na | N A:Leu47 | 4.41 | | Na | O A:Ser441 | 2.28 | | Na | C A:Ser441 | 3.58 | | Na | CA A:Ser441 | 4.72 | | Na | N A:Asp442 | 4.30 | | Na | CB A:Asp442 | 4.02 | | Na | OD2 A:Asp442 | 4.12 | | Na | OD1 A:Asp442 | 4.73 | | Na | CG A:Asp442 | 4.09 | | Na | CA A:Asp442 | 3.99 | | Na | O A:Hoh2258 | 2.23 | | Na | O A:Hoh2563 | 3.46 | | Na | O A:Hoh2691 | 3.85 | | Na | O A:Hoh2693 | 4.97 |
| interactive model:
| Sodium binding site 2 out of 2 in 3ag4
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3ag4. 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: Hoh3258, N: Hoh3563, N: Hoh3691, | conact list:
| Atom | Atom | Distance (A) | | Na | O N:Glu40 | 2.27 | | Na | OE1 N:Glu40 | 2.25 | | Na | CB N:Glu40 | 4.49 | | Na | OE2 N:Glu40 | 4.35 | | Na | CD N:Glu40 | 3.23 | | Na | C N:Glu40 | 3.38 | | Na | CG N:Glu40 | 3.59 | | Na | CA N:Glu40 | 4.24 | | Na | N N:Leu41 | 4.27 | | Na | CD2 N:Leu41 | 4.87 | | Na | CA N:Leu41 | 4.44 | | Na | O N:Gln43 | 3.91 | | Na | C N:Pro44 | 4.92 | | Na | O N:Gly45 | 2.24 | | Na | N N:Gly45 | 4.32 | | Na | C N:Gly45 | 3.37 | | Na | CA N:Gly45 | 4.48 | | Na | N N:Thr46 | 4.08 | | Na | C N:Thr46 | 4.57 | | Na | CA N:Thr46 | 3.93 | | Na | N N:Leu47 | 4.40 | | Na | O N:Ser441 | 2.30 | | Na | C N:Ser441 | 3.57 | | Na | CA N:Ser441 | 4.77 | | Na | N N:Asp442 | 4.26 | | Na | CB N:Asp442 | 4.10 | | Na | OD2 N:Asp442 | 4.08 | | Na | OD1 N:Asp442 | 4.70 | | Na | CG N:Asp442 | 4.09 | | Na | CA N:Asp442 | 4.01 | | Na | O N:Hoh3258 | 2.21 | | Na | O N:Hoh3563 | 3.35 | | Na | O N:Hoh3691 | 3.99 |
| interactive model:
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