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Zinc in PDB 6nkn: Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature

Enzymatic activity of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

Protein crystallography data

The structure of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature, PDB code: 6nkn was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.50 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.700, 189.800, 211.300, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.7

Other elements in 6nkn:

The structure of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature (pdb code 6nkn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature, PDB code: 6nkn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6nkn

Go back to Zinc Binding Sites List in 6nkn
Zinc binding site 1 out of 2 in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:58.5
occ:1.00
SG F:CYS82 2.3 52.1 1.0
SG F:CYS62 2.3 48.2 1.0
SG F:CYS60 2.3 51.6 1.0
SG F:CYS85 2.4 56.0 1.0
CB F:CYS82 3.2 52.6 1.0
CB F:CYS60 3.2 46.4 1.0
CB F:CYS62 3.4 46.6 1.0
CB F:CYS85 3.5 50.0 1.0
CA F:CYS62 3.7 48.0 1.0
N F:CYS85 3.9 51.1 1.0
N F:CYS62 4.2 49.2 1.0
O F:CYS60 4.2 41.4 1.0
CA F:CYS85 4.2 51.6 1.0
C F:CYS60 4.4 43.0 1.0
CA F:CYS60 4.4 43.4 1.0
OG F:SER84 4.6 53.7 1.0
CB F:SER84 4.6 53.0 1.0
CA F:CYS82 4.6 47.6 1.0
C F:SER84 4.8 54.7 1.0
C F:CYS85 4.9 48.7 1.0
CG1 F:ILE70 4.9 41.9 1.0
CG2 F:THR87 4.9 52.5 1.0
C F:ILE61 4.9 44.2 1.0
CB F:ILE70 4.9 43.9 1.0
N F:GLY86 5.0 46.9 1.0

Zinc binding site 2 out of 2 in 6nkn

Go back to Zinc Binding Sites List in 6nkn
Zinc binding site 2 out of 2 in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:64.5
occ:1.00
SG S:CYS60 2.3 53.0 1.0
SG S:CYS85 2.3 59.9 1.0
SG S:CYS62 2.3 62.1 1.0
SG S:CYS82 2.4 53.9 1.0
CB S:CYS82 3.2 55.2 1.0
CB S:CYS62 3.2 57.6 1.0
CB S:CYS60 3.3 56.6 1.0
CB S:CYS85 3.4 63.7 1.0
CA S:CYS62 3.5 56.0 1.0
N S:CYS85 3.7 55.9 1.0
OG1 S:THR87 4.0 82.1 1.0
N S:CYS62 4.1 53.8 1.0
CA S:CYS85 4.1 58.5 1.0
CB S:SER84 4.4 66.9 1.0
CA S:CYS60 4.5 53.6 1.0
C S:CYS60 4.5 56.6 1.0
CA S:CYS82 4.7 57.0 1.0
O S:CYS60 4.7 62.5 1.0
C S:CYS85 4.7 60.3 1.0
C S:SER84 4.7 61.2 1.0
C S:ILE61 4.8 54.9 1.0
OG S:SER84 4.9 70.7 1.0
N S:GLY86 4.9 64.0 1.0
C S:CYS62 4.9 63.4 1.0
CA S:SER84 4.9 63.4 1.0

Reference:

I.Ishigami, A.Lewis-Ballester, A.Echelmeier, G.Brehm, N.A.Zatsepin, T.D.Grant, J.D.Coe, S.Lisova, G.Nelson, S.Zhang, Z.F.Dobson, S.Boutet, R.G.Sierra, A.Batyuk, P.Fromme, R.Fromme, J.C.H.Spence, A.Ros, S.R.Yeh, D.L.Rousseau. Snapshot of An Oxygen Intermediate in the Catalytic Reaction of Cytochromecoxidase. Proc. Natl. Acad. Sci. V. 116 3572 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30808749
DOI: 10.1073/PNAS.1814526116
Page generated: Wed Dec 16 12:24:01 2020

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