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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7y44:

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

Zinc Binding Sites:

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 7y44

Go back to Zinc Binding Sites List in 7y44
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 7y44

Go back to Zinc Binding Sites List in 7y44
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

Reference:

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
Page generated: Sat Apr 8 06:12:00 2023

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