Zinc in PDB 6nmf: Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

The structure of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature, PDB code: 6nmf was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	178.700, 189.800, 211.300, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.2

The structure of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	4 atoms
Copper	(Cu)	6 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature (pdb code 6nmf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature, PDB code: 6nmf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:65.7 occ:1.00 SG F:CYS82 2.3 55.9 1.0 SG F:CYS60 2.3 61.0 1.0 SG F:CYS62 2.3 60.4 1.0 SG F:CYS85 2.4 63.9 1.0 CB F:CYS60 3.3 56.9 1.0 CB F:CYS82 3.3 55.5 1.0 CB F:CYS85 3.4 64.2 1.0 CB F:CYS62 3.4 58.0 1.0 CA F:CYS62 3.6 58.7 1.0 N F:CYS85 3.8 64.8 1.0 N F:CYS62 4.0 56.0 1.0 CA F:CYS85 4.2 65.6 1.0 O F:CYS60 4.3 54.9 1.0 CB F:SER84 4.4 67.3 1.0 OG1 F:THR87 4.4 62.8 1.0 C F:CYS60 4.5 56.1 1.0 CA F:CYS60 4.5 54.0 1.0 O F:HOH223 4.6 63.1 1.0 CA F:CYS82 4.8 53.4 1.0 C F:SER84 4.8 64.0 1.0 C F:CYS62 4.9 59.2 1.0 C F:ILE61 4.9 56.5 1.0 C F:CYS85 4.9 66.0 1.0 OG F:SER84 5.0 70.5 1.0 CA F:SER84 5.0 66.5 1.0

Zinc binding site 2 out of 2 in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn101 b:72.4 occ:1.00 SG S:CYS60 2.3 60.1 1.0 SG S:CYS62 2.3 69.1 1.0 SG S:CYS85 2.4 66.7 1.0 SG S:CYS82 2.4 63.7 1.0 CB S:CYS82 3.2 65.4 1.0 CB S:CYS60 3.3 62.2 1.0 CB S:CYS85 3.4 69.8 1.0 CB S:CYS62 3.4 67.7 1.0 OG1 S:THR87 3.6 74.5 0.5 CA S:CYS62 3.7 64.6 1.0 N S:CYS85 3.8 68.0 1.0 CG2 S:THR87 3.9 72.1 0.5 CA S:CYS85 4.1 67.8 1.0 N S:CYS62 4.2 68.4 1.0 CB S:SER84 4.4 72.4 1.0 CA S:CYS60 4.6 62.8 1.0 CA S:CYS82 4.7 69.2 1.0 C S:CYS60 4.7 63.0 1.0 C S:SER84 4.8 72.1 1.0 C S:CYS85 4.8 67.2 1.0 N S:GLY86 4.9 69.4 1.0 O S:CYS60 4.9 62.9 1.0 CA S:SER84 5.0 73.3 1.0 N S:SER84 5.0 73.4 1.0

I.Ishigami, A.Lewis-Ballester, A.Echelmeier, G.Brehm, N.A.Zatsepin, T.D.Grant, J.D.Coe, S.Lisova, G.Nelson, S.Zhang, Z.F.Dobson, S.Boutet, R.G.Sierra, A.Batyuk, P.Fromme, R.Fromme, J.C.H.Spence, A.Ros, S.R.Yeh, D.L.Rousseau. Snapshot of An Oxygen Intermediate in the Catalytic Reaction of Cytochromecoxidase. Proc. Natl. Acad. Sci. V. 116 3572 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30808749
DOI: 10.1073/PNAS.1814526116