Sodium in PDB 8gbt: Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase

All present enzymatic activity of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase:
1.9.3.1;

The structure of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase, PDB code: 8gbt was solved by I.Ishigami, S.-R.Yeh, D.L.Rousseau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	178.3, 189, 209, 90, 90, 90
R / Rfree (%)	22.3 / 26.9

The structure of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase also contains other interesting chemical elements:

Copper	(Cu)	6 atoms
Iron	(Fe)	4 atoms
Zinc	(Zn)	2 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Sodium atom in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase (pdb code 8gbt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase, PDB code: 8gbt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:38.4 occ:1.00 O A:SER441 2.3 33.6 1.0 O A:GLU40 2.5 45.8 1.0 O A:GLY45 2.5 55.0 1.0 OE1 A:GLU40 2.5 44.0 1.0 C A:SER441 3.4 35.1 1.0 C A:GLU40 3.5 43.2 1.0 OD1 A:ASP442 3.5 35.0 1.0 CD A:GLU40 3.6 49.7 1.0 CA A:ASP442 3.7 35.0 1.0 O A:GLN43 3.7 43.7 1.0 C A:GLY45 3.7 50.8 1.0 CB A:ASP442 3.8 36.4 1.0 CG A:ASP442 3.9 36.2 1.0 N A:ASP442 4.0 33.2 1.0 CG A:GLU40 4.0 47.8 1.0 CA A:LEU41 4.1 42.4 1.0 N A:LEU41 4.2 43.0 1.0 N A:GLY45 4.4 46.3 1.0 CD2 A:LEU41 4.4 44.2 1.0 CA A:THR46 4.4 58.6 1.0 N A:THR46 4.5 54.7 1.0 CE2 A:TYR443 4.5 57.9 1.0 CA A:GLU40 4.6 45.0 1.0 CA A:SER441 4.6 36.0 1.0 CA A:GLY45 4.7 49.6 1.0 OE2 A:GLU40 4.7 49.1 1.0 OD2 A:ASP442 4.9 39.0 1.0 C A:GLN43 4.9 48.9 1.0 CB A:GLU40 4.9 45.4 1.0 C A:PRO44 4.9 44.7 1.0 C A:LEU41 4.9 43.1 1.0 CD2 A:TYR443 4.9 53.7 1.0

Sodium binding site 2 out of 2 in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ N:Na605 b:63.8 occ:1.00 O N:GLU40 2.4 50.3 1.0 O N:GLY45 2.5 63.8 1.0 O N:SER441 2.9 50.1 1.0 O N:GLN43 3.2 72.3 1.0 OE1 N:GLU40 3.3 54.9 1.0 OD1 N:ASP442 3.3 51.7 1.0 C N:GLU40 3.6 55.4 1.0 C N:GLY45 3.7 65.3 1.0 CE1 N:TYR443 3.9 60.2 1.0 CA N:LEU41 3.9 61.9 1.0 CA N:ASP442 3.9 58.1 1.0 CG N:ASP442 3.9 56.5 1.0 C N:SER441 3.9 57.7 1.0 N N:GLY45 4.1 66.5 1.0 N N:LEU41 4.1 58.4 1.0 CB N:ASP442 4.2 58.6 1.0 C N:GLN43 4.2 74.4 1.0 C N:PRO44 4.3 69.2 1.0 CD N:GLU40 4.3 59.5 1.0 OH N:TYR443 4.3 62.0 1.0 CZ N:TYR443 4.3 59.5 1.0 N N:ASP442 4.4 54.2 1.0 CD2 N:LEU41 4.4 67.7 1.0 CA N:PRO44 4.4 69.2 1.0 CA N:GLY45 4.5 65.8 1.0 C N:LEU41 4.5 60.2 1.0 CD1 N:TYR443 4.5 62.9 1.0 N N:THR46 4.7 69.2 1.0 CG N:GLU40 4.7 57.0 1.0 N N:PRO44 4.7 69.8 1.0 CA N:GLU40 4.8 56.4 1.0 OD2 N:ASP442 4.8 56.9 1.0 CA N:THR46 4.9 73.3 1.0 O N:PRO44 4.9 67.8 1.0 O N:LEU41 4.9 49.8 1.0 CB N:LEU41 5.0 64.3 1.0

I.Ishigami, S.-R.Yeh, D.L.Rousseau. Detection of A Geminate Photoproduct of Bovine Cytochrome C Oxidase By Time-Resolved Serial Femtosecond Crystallography To Be Published.