Zinc in PDB 8gvm: The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days

Enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days

All present enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days:
7.1.1.9;

Protein crystallography data

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days, PDB code: 8gvm was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.97 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.405, 206.272, 177.609, 90, 90, 90
R / Rfree (%) 16.4 / 18.8

Other elements in 8gvm:

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days (pdb code 8gvm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days, PDB code: 8gvm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8gvm

Go back to Zinc Binding Sites List in 8gvm
Zinc binding site 1 out of 2 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:33.1
occ:1.00
 SG F:CYS85 2.3 36.5 1.0
SG F:CYS60 2.3 33.7 1.0
SG F:CYS82 2.3 33.8 1.0
SG F:CYS62 2.4 34.9 1.0
CB F:CYS82 3.1 34.9 1.0
CB F:CYS60 3.2 34.9 1.0
CB F:CYS62 3.3 36.1 1.0
CB F:CYS85 3.3 40.5 1.0
CA F:CYS62 3.6 41.3 1.0
N F:CYS85 3.7 34.7 1.0
CA F:CYS85 4.1 35.0 1.0
N F:CYS62 4.2 34.8 1.0
O F:CYS60 4.4 33.0 1.0
C F:CYS60 4.4 30.6 1.0
CA F:CYS60 4.4 32.9 1.0
O F:HOH211 4.5 47.2 1.0
CG2 F:THR87 4.5 53.0 0.5
CA F:CYS82 4.6 30.5 1.0
OG F:SER84 4.6 45.3 1.0
CB F:SER84 4.6 33.8 1.0
C F:SER84 4.7 40.1 1.0
OG1 F:THR87 4.8 43.0 0.5
C F:CYS85 4.8 38.7 1.0
CG2 F:THR87 4.9 32.1 0.5
C F:ILE61 4.9 34.4 1.0
N F:GLY86 4.9 34.2 1.0
C F:CYS62 4.9 42.8 1.0
CB F:ILE70 5.0 32.1 1.0
N F:SER84 5.0 35.1 1.0
CG1 F:ILE70 5.0 31.2 1.0
CA F:SER84 5.0 32.3 1.0

Zinc binding site 2 out of 2 in 8gvm

Go back to Zinc Binding Sites List in 8gvm
Zinc binding site 2 out of 2 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn102

b:35.7
occ:1.00
 SG S:CYS60 2.3 36.9 1.0
SG S:CYS62 2.3 38.2 1.0
SG S:CYS82 2.3 38.7 1.0
SG S:CYS85 2.3 39.4 1.0
CB S:CYS82 3.2 34.3 1.0
CB S:CYS60 3.2 42.0 1.0
CB S:CYS62 3.3 40.0 1.0
CB S:CYS85 3.4 45.2 1.0
CA S:CYS62 3.7 38.7 1.0
N S:CYS85 3.7 36.5 1.0
CA S:CYS85 4.1 39.0 1.0
N S:CYS62 4.2 38.8 1.0
CB S:SER84 4.4 38.5 1.0
O S:CYS60 4.4 33.6 1.0
CA S:CYS60 4.4 38.3 1.0
C S:CYS60 4.4 36.8 1.0
OG1 S:THR87 4.5 43.4 0.5
O S:HOH231 4.6 51.6 1.0
CA S:CYS82 4.6 36.3 1.0
C S:SER84 4.7 46.3 1.0
CG2 S:THR87 4.7 30.8 0.5
OG S:SER84 4.8 46.4 1.0
C S:CYS85 4.8 40.3 1.0
N S:GLY86 4.9 42.0 1.0
CA S:SER84 4.9 37.5 1.0
C S:ILE61 4.9 43.8 1.0
N S:SER84 4.9 36.4 1.0
CB S:ILE70 4.9 34.0 1.0
CG1 S:ILE70 4.9 33.4 1.0

Reference:

A.Shimada, K.Hatano, H.Tadehara, N.Yano, K.Sinzawa-Itoh, E.Yamashita, K.Mutamoto, T.Tsukihara, S.Yoshikawa. X-Ray Structural Analyses of Azide-Bound Cytochromecoxidases Reveal That the H-Pathway Is Critically Important For the Proton-Pumping Activity J. Biol. Chem. V. 293 14868 2018.
ISSN: ESSN ESSN 1083-351X
PubMed: 30077971
DOI: 10.1074/JBC.RA118.003123
Page generated: Wed Oct 30 21:06:04 2024

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