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Zinc in PDB 5zcp: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days

Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days

All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days:
1.9.3.1;

Protein crystallography data

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5zcp was solved by A.Shimada, K.Hatano, H.Tadehara, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.320, 206.171, 177.625, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.7

Other elements in 5zcp:

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days (pdb code 5zcp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5zcp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5zcp

Go back to Zinc Binding Sites List in 5zcp
Zinc binding site 1 out of 2 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:31.6
occ:1.00
SG F:CYS82 2.3 31.1 1.0
SG F:CYS60 2.3 31.7 1.0
SG F:CYS85 2.3 31.8 1.0
SG F:CYS62 2.4 32.7 1.0
CB F:CYS82 3.1 31.1 1.0
CB F:CYS60 3.3 32.6 1.0
CB F:CYS62 3.3 32.4 1.0
CB F:CYS85 3.4 33.1 1.0
CA F:CYS62 3.6 33.2 1.0
N F:CYS85 3.8 31.8 1.0
CA F:CYS85 4.1 32.8 1.0
N F:CYS62 4.2 31.8 1.0
O F:CYS60 4.4 29.0 1.0
C F:CYS60 4.4 29.7 1.0
CB F:SER84 4.4 30.9 1.0
CA F:CYS60 4.4 30.3 1.0
O F:HOH209 4.6 47.2 1.0
OG1 F:THR87 4.6 33.6 0.5
CA F:CYS82 4.6 30.3 1.0
OG1 F:THR87 4.6 32.1 0.5
O A:HOH702 4.7 0.7 1.0
OG F:SER84 4.7 41.2 1.0
C F:SER84 4.8 34.8 1.0
C F:CYS85 4.8 34.4 1.0
N F:GLY86 4.9 31.4 1.0
C F:ILE61 4.9 32.6 1.0
CB F:ILE70 4.9 27.2 1.0
C F:CYS62 5.0 40.5 1.0
CG1 F:ILE70 5.0 29.5 1.0

Zinc binding site 2 out of 2 in 5zcp

Go back to Zinc Binding Sites List in 5zcp
Zinc binding site 2 out of 2 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:33.2
occ:1.00
SG S:CYS82 2.3 32.4 1.0
SG S:CYS60 2.3 32.1 1.0
SG S:CYS62 2.3 33.8 1.0
SG S:CYS85 2.4 34.3 1.0
CB S:CYS82 3.1 31.6 1.0
CB S:CYS60 3.3 37.1 1.0
CB S:CYS62 3.3 31.9 1.0
CB S:CYS85 3.5 36.1 1.0
CA S:CYS62 3.6 32.8 1.0
N S:CYS85 3.8 33.2 1.0
CA S:CYS85 4.1 33.0 1.0
N S:CYS62 4.2 34.7 1.0
CG2 S:THR87 4.4 34.2 0.5
CB S:SER84 4.4 34.1 1.0
C S:CYS60 4.4 29.3 1.0
O S:CYS60 4.4 29.8 1.0
CA S:CYS60 4.4 31.2 1.0
O S:HOH212 4.6 52.7 1.0
CA S:CYS82 4.6 30.5 1.0
C S:SER84 4.7 35.6 1.0
OG S:SER84 4.8 38.6 1.0
CG2 S:THR87 4.8 30.5 0.5
C S:CYS85 4.9 33.9 1.0
C S:ILE61 4.9 34.5 1.0
N S:SER84 4.9 33.4 1.0
CB S:ILE70 5.0 28.7 1.0
CG1 S:ILE70 5.0 28.9 1.0
N S:GLY86 5.0 34.5 1.0
C S:CYS62 5.0 36.9 1.0
CA S:SER84 5.0 33.5 1.0

Reference:

A.Shimada, K.Hatano, H.Tadehara, N.Yano, K.Shinzawa-Itoh, E.Yamashita, K.Muramoto, 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 1083-351X
PubMed: 30077971
DOI: 10.1074/JBC.RA118.003123
Page generated: Mon Oct 28 16:39:13 2024

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