Zinc in PDB 7y44: Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution

All present enzymatic activity of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution:
7.1.1.9;

The structure of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution, PDB code: 7y44 was solved by T.Tsukihara, K.Hirata, H.Ago, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.31 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.6, 204.51, 178.29, 90, 90, 90
R / Rfree (%)	18.5 / 22.7

The structure of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution (pdb code 7y44). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution, PDB code: 7y44:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:22.3 occ:1.00 SG F:CYS62 2.3 22.3 1.0 SG F:CYS60 2.3 23.9 1.0 SG F:CYS85 2.4 24.2 1.0 SG F:CYS82 2.4 21.9 1.0 CB F:CYS82 3.2 23.1 1.0 CB F:CYS62 3.3 21.2 1.0 CB F:CYS60 3.3 29.7 1.0 CB F:CYS85 3.4 20.5 1.0 CA F:CYS62 3.6 28.9 1.0 N F:CYS85 3.8 20.4 1.0 N F:CYS62 4.1 24.7 1.0 CA F:CYS85 4.2 22.2 1.0 O F:CYS60 4.4 16.7 1.0 C F:CYS60 4.4 23.4 1.0 CA F:CYS60 4.5 22.7 1.0 CB F:SER84 4.5 21.9 1.0 O F:HOH213 4.5 43.8 1.0 OG1 F:THR87 4.5 51.5 0.7 CG2 F:THR87 4.6 35.0 0.3 CA F:CYS82 4.7 25.6 1.0 OG F:SER84 4.8 30.0 1.0 C F:SER84 4.8 24.8 1.0 C F:ILE61 4.9 31.6 1.0 C F:CYS85 4.9 27.4 1.0 C F:CYS62 4.9 43.0 1.0 CB F:ILE70 4.9 24.8 1.0

Zinc binding site 2 out of 2 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn101 b:22.8 occ:1.00 SG S:CYS82 2.3 23.6 1.0 SG S:CYS85 2.3 22.8 1.0 SG S:CYS62 2.3 25.5 1.0 SG S:CYS60 2.4 21.9 1.0 CB S:CYS82 3.1 19.8 1.0 CB S:CYS60 3.3 26.2 1.0 CB S:CYS62 3.3 17.8 1.0 CB S:CYS85 3.4 22.9 1.0 N S:CYS85 3.7 23.3 1.0 CA S:CYS62 3.7 23.5 1.0 CA S:CYS85 4.1 29.5 1.0 N S:CYS62 4.2 21.3 1.0 OG1 S:THR87 4.2 54.7 1.0 CB S:SER84 4.4 27.0 1.0 C S:CYS60 4.5 24.8 1.0 O S:CYS60 4.5 19.8 1.0 CA S:CYS60 4.5 21.2 1.0 O S:HOH221 4.5 35.9 1.0 CA S:CYS82 4.6 22.4 1.0 C S:SER84 4.7 30.2 1.0 OG S:SER84 4.7 32.4 1.0 C S:CYS85 4.8 36.6 1.0 CA S:SER84 4.9 33.9 1.0 N S:GLY86 4.9 22.1 1.0 C S:ILE61 4.9 23.2 1.0 N S:SER84 5.0 25.7 1.0 CB S:ILE70 5.0 24.0 1.0 C S:CYS62 5.0 32.2 1.0

K.Hirata, T.Tsukihara, H.Ago. Determination of Damage-Free Crystal Structure of An X-Ray-Sensitive Protein Using An Xfel Nature Methods V. 11 734 2014.
DOI: 10.1038/NMETH.2962