Zinc in PDB 5z86: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days

Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days

All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 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 3 Days, PDB code: 5z86 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 (°) 183.490, 206.292, 177.617, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 19.6

Other elements in 5z86:

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 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 3 Days (pdb code 5z86). 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 3 Days, PDB code: 5z86:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5z86

Go back to Zinc Binding Sites List in 5z86
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 3 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 3 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:34.2
occ:1.00
SG F:CYS82 2.4 32.2 1.0
SG F:CYS62 2.4 33.7 1.0
SG F:CYS60 2.4 33.3 1.0
SG F:CYS85 2.4 33.7 1.0
CB F:CYS82 3.1 33.6 1.0
CB F:CYS60 3.2 32.7 1.0
CB F:CYS85 3.4 35.2 1.0
CB F:CYS62 3.4 33.8 1.0
CA F:CYS62 3.6 35.3 1.0
N F:CYS85 3.7 34.7 1.0
CA F:CYS85 4.1 35.5 1.0
N F:CYS62 4.1 34.1 1.0
OG1 F:THR87 4.3 38.1 0.5
O F:CYS60 4.4 31.0 1.0
C F:CYS60 4.4 31.1 1.0
CA F:CYS60 4.4 30.9 1.0
O F:HOH226 4.5 50.1 1.0
OG1 F:THR87 4.5 36.9 0.5
CB F:SER84 4.5 35.9 1.0
CA F:CYS82 4.6 33.8 1.0
OG F:SER84 4.7 40.8 1.0
C F:SER84 4.8 36.2 1.0
C F:CYS85 4.8 35.6 1.0
C F:ILE61 4.9 34.4 1.0
CG1 F:ILE70 4.9 30.5 1.0
N F:GLY86 4.9 35.0 1.0
CB F:ILE70 4.9 30.0 1.0
C F:CYS62 5.0 37.9 1.0

Zinc binding site 2 out of 2 in 5z86

Go back to Zinc Binding Sites List in 5z86
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 3 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 3 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:37.1
occ:1.00
SG S:CYS62 2.4 37.0 1.0
SG S:CYS82 2.4 35.1 1.0
SG S:CYS60 2.4 34.7 1.0
SG S:CYS85 2.4 37.9 1.0
CB S:CYS82 3.2 36.4 1.0
CB S:CYS60 3.3 35.4 1.0
CB S:CYS85 3.4 38.3 1.0
CB S:CYS62 3.4 37.2 1.0
CA S:CYS62 3.7 38.7 1.0
N S:CYS85 3.7 38.6 1.0
CA S:CYS85 4.1 38.6 1.0
N S:CYS62 4.1 37.3 1.0
OG1 S:THR87 4.3 42.1 0.5
O S:CYS60 4.4 34.0 1.0
CB S:SER84 4.4 38.7 1.0
C S:CYS60 4.5 35.3 1.0
CA S:CYS60 4.5 34.5 1.0
CG2 S:THR87 4.5 41.8 0.5
CA S:CYS82 4.6 37.1 1.0
O S:HOH214 4.6 52.4 1.0
C S:SER84 4.7 39.1 1.0
OG S:SER84 4.8 41.2 1.0
C S:CYS85 4.8 38.7 1.0
C S:ILE61 4.9 37.7 1.0
N S:GLY86 4.9 39.3 1.0
CG1 S:ILE70 4.9 32.8 1.0
CA S:SER84 4.9 39.0 1.0
CB S:ILE70 4.9 32.4 1.0
N S:SER84 4.9 39.1 1.0
C S:CYS62 5.0 41.0 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 11:25:27 2020

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