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Zinc in PDB 5zcq: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days

Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days

All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days, PDB code: 5zcq 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 (°) 182.330, 204.832, 177.691, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.2

Other elements in 5zcq:

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days (pdb code 5zcq). 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 10 Mm Azide Solution For 2 Days, PDB code: 5zcq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5zcq

Go back to Zinc Binding Sites List in 5zcq
Zinc binding site 1 out of 2 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:28.4
occ:1.00
SG F:CYS62 2.3 28.9 1.0
SG F:CYS60 2.3 27.6 1.0
SG F:CYS85 2.4 29.2 1.0
SG F:CYS82 2.4 27.6 1.0
CB F:CYS82 3.2 28.1 1.0
CB F:CYS60 3.2 28.7 1.0
CB F:CYS62 3.4 26.5 1.0
CB F:CYS85 3.4 29.4 1.0
CA F:CYS62 3.6 29.8 1.0
N F:CYS85 3.7 28.2 1.0
CA F:CYS85 4.1 28.9 1.0
N F:CYS62 4.2 28.9 1.0
O F:CYS60 4.4 25.6 1.0
C F:CYS60 4.4 28.0 1.0
CB F:SER84 4.4 29.3 1.0
CA F:CYS60 4.4 27.6 1.0
O F:HOH216 4.6 44.8 1.0
CA F:CYS82 4.6 28.4 1.0
OG1 F:THR87 4.7 44.6 1.0
OG F:SER84 4.7 35.1 1.0
CG2 F:THR87 4.7 39.3 1.0
C F:SER84 4.7 32.3 1.0
C F:CYS85 4.8 30.4 1.0
N F:GLY86 4.9 28.7 1.0
C F:ILE61 4.9 31.2 1.0
CB F:ILE70 4.9 22.6 1.0
C F:CYS62 4.9 33.6 1.0
CG1 F:ILE70 5.0 23.7 1.0

Zinc binding site 2 out of 2 in 5zcq

Go back to Zinc Binding Sites List in 5zcq
Zinc binding site 2 out of 2 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:29.4
occ:1.00
SG S:CYS82 2.3 29.3 1.0
SG S:CYS60 2.3 28.0 1.0
SG S:CYS62 2.3 29.9 1.0
SG S:CYS85 2.4 30.3 1.0
CB S:CYS82 3.1 30.8 1.0
CB S:CYS60 3.3 33.4 1.0
CB S:CYS62 3.3 31.2 1.0
CB S:CYS85 3.5 31.3 1.0
CA S:CYS62 3.6 29.0 1.0
N S:CYS85 3.8 30.9 1.0
OG1 S:THR87 3.9 38.9 0.5
CA S:CYS85 4.2 31.0 1.0
N S:CYS62 4.2 28.5 1.0
C S:CYS60 4.4 24.9 1.0
CA S:CYS60 4.4 28.3 1.0
O S:CYS60 4.4 24.8 1.0
CB S:SER84 4.5 31.6 1.0
O S:HOH223 4.6 45.3 1.0
CA S:CYS82 4.6 30.4 1.0
OG S:SER84 4.7 37.0 1.0
C S:SER84 4.7 32.9 1.0
CG2 S:THR87 4.8 27.8 0.5
C S:ILE61 4.9 31.4 1.0
C S:CYS85 4.9 32.7 1.0
C S:CYS62 4.9 35.0 1.0
N S:GLY86 5.0 30.5 1.0
CB S:ILE70 5.0 23.7 1.0
CB S:THR87 5.0 33.4 0.5
N S:SER84 5.0 30.0 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: Mon Oct 28 16:39:13 2024

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