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Zinc in PDB 5z85: The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days

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

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

Protein crystallography data

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5z85 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 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.126, 205.893, 177.576, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.9

Other elements in 5z85:

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days (pdb code 5z85). 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 Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5z85:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5z85

Go back to Zinc Binding Sites List in 5z85
Zinc binding site 1 out of 2 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:30.9
occ:1.00
SG F:CYS62 2.3 30.7 1.0
SG F:CYS82 2.3 29.4 1.0
SG F:CYS60 2.3 29.7 1.0
SG F:CYS85 2.4 30.6 1.0
CB F:CYS82 3.2 30.5 1.0
CB F:CYS60 3.2 30.1 1.0
CB F:CYS62 3.3 27.2 1.0
CB F:CYS85 3.4 32.8 1.0
CA F:CYS62 3.6 33.7 1.0
N F:CYS85 3.7 33.1 1.0
CA F:CYS85 4.1 32.5 1.0
N F:CYS62 4.2 30.2 1.0
O F:CYS60 4.4 27.2 1.0
C F:CYS60 4.4 27.9 1.0
CA F:CYS60 4.4 26.6 1.0
CB F:SER84 4.5 31.4 1.0
O F:HOH223 4.5 48.1 1.0
OG1 F:THR87 4.5 32.5 0.5
OG F:SER84 4.6 39.4 1.0
OG1 F:THR87 4.6 36.4 0.5
CA F:CYS82 4.7 29.9 1.0
C F:SER84 4.7 34.0 1.0
C F:CYS85 4.9 33.8 1.0
C F:ILE61 4.9 33.9 1.0
CG1 F:ILE70 4.9 26.5 1.0
CB F:ILE70 4.9 26.6 1.0
N F:GLY86 4.9 28.7 1.0
C F:CYS62 5.0 38.9 1.0
NZ A:LYS514 5.0 45.7 1.0

Zinc binding site 2 out of 2 in 5z85

Go back to Zinc Binding Sites List in 5z85
Zinc binding site 2 out of 2 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:32.7
occ:1.00
SG S:CYS62 2.3 33.0 1.0
SG S:CYS82 2.3 32.0 1.0
SG S:CYS85 2.4 33.7 1.0
SG S:CYS60 2.4 30.3 1.0
CB S:CYS82 3.1 32.2 1.0
CB S:CYS60 3.2 33.9 1.0
CB S:CYS62 3.3 32.2 1.0
CB S:CYS85 3.4 36.0 1.0
CA S:CYS62 3.6 34.0 1.0
N S:CYS85 3.7 34.2 1.0
N S:CYS62 4.1 31.9 1.0
CA S:CYS85 4.2 32.8 1.0
CG2 S:THR87 4.3 34.5 0.5
C S:CYS60 4.4 31.8 1.0
CA S:CYS60 4.4 30.4 1.0
O S:CYS60 4.4 28.8 1.0
CB S:SER84 4.5 37.5 1.0
O S:HOH219 4.5 49.5 1.0
CA S:CYS82 4.6 33.1 1.0
CG2 S:THR87 4.6 30.4 0.5
OG S:SER84 4.7 39.6 1.0
C S:SER84 4.7 36.8 1.0
C S:CYS85 4.9 33.7 1.0
C S:ILE61 4.9 36.0 1.0
N S:SER84 4.9 32.1 1.0
CB S:ILE70 4.9 28.2 1.0
CG1 S:ILE70 4.9 28.6 1.0
N S:GLY86 4.9 36.0 1.0
C S:CYS62 5.0 37.9 1.0
CA S:SER84 5.0 35.5 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: Wed Dec 16 11:25:19 2020

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