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Zinc in PDB 5w97: Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature

Enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature

All present enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature:
1.9.3.1;

Protein crystallography data

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97 was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, N.A.Zatsepin, T.D.Grant, P.Fromme, R.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.86 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.300, 189.000, 209.000, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.2

Other elements in 5w97:

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature (pdb code 5w97). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5w97

Go back to Zinc Binding Sites List in 5w97
Zinc binding site 1 out of 2 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:45.4
occ:1.00
SG F:CYS82 2.3 37.6 1.0
SG F:CYS60 2.3 33.0 1.0
SG F:CYS62 2.3 39.4 1.0
SG F:CYS85 2.4 41.2 1.0
CB F:CYS82 3.2 40.0 1.0
CB F:CYS60 3.3 31.6 1.0
CB F:CYS85 3.4 37.4 1.0
CB F:CYS62 3.5 39.4 1.0
N F:CYS85 3.7 40.5 1.0
CA F:CYS62 3.7 44.4 1.0
N F:CYS62 4.0 41.3 1.0
CA F:CYS85 4.1 39.6 1.0
O F:CYS60 4.3 29.0 1.0
C F:CYS60 4.4 30.7 1.0
CA F:CYS60 4.4 29.8 1.0
CB F:SER84 4.4 40.0 1.0
O F:HOH247 4.4 57.0 1.0
CA F:CYS82 4.6 37.7 1.0
C F:SER84 4.7 38.9 1.0
OG F:SER84 4.8 42.0 1.0
C F:CYS85 4.9 38.3 1.0
C F:ILE61 4.9 39.2 1.0
CG2 F:THR87 4.9 39.5 1.0
CA F:SER84 5.0 38.4 1.0
CB F:ILE70 5.0 32.2 1.0
N F:GLY86 5.0 41.1 1.0
N F:ILE61 5.0 33.1 1.0

Zinc binding site 2 out of 2 in 5w97

Go back to Zinc Binding Sites List in 5w97
Zinc binding site 2 out of 2 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Zn101

b:52.7
occ:1.00
SG f:CYS60 2.3 45.6 1.0
SG f:CYS62 2.3 52.2 1.0
SG f:CYS85 2.3 46.2 1.0
SG f:CYS82 2.4 44.3 1.0
CB f:CYS82 3.2 46.6 1.0
CB f:CYS85 3.3 45.3 1.0
CB f:CYS60 3.4 41.9 1.0
CB f:CYS62 3.4 47.3 1.0
CA f:CYS62 3.6 48.3 1.0
CG2 f:THR87 3.9 62.4 1.0
N f:CYS85 4.0 52.0 1.0
N f:CYS62 4.0 45.2 1.0
O f:HOH214 4.2 55.4 1.0
CA f:CYS85 4.2 46.0 1.0
C f:CYS60 4.5 42.1 1.0
CA f:CYS60 4.5 39.7 1.0
O f:CYS60 4.5 42.7 1.0
CB f:SER84 4.6 53.5 1.0
CA f:CYS82 4.7 46.2 1.0
C f:ILE61 4.9 44.6 1.0
C f:CYS85 4.9 47.7 1.0
C f:SER84 5.0 54.7 1.0

Reference:

I.Ishigami, N.A.Zatsepin, M.Hikita, C.E.Conrad, G.Nelson, J.D.Coe, S.Basu, T.D.Grant, M.H.Seaberg, R.G.Sierra, M.S.Hunter, P.Fromme, R.Fromme, S.R.Yeh, D.L.Rousseau. Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature. Proc. Natl. Acad. Sci. V. 114 8011 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28698372
DOI: 10.1073/PNAS.1705628114
Page generated: Wed Dec 16 11:15:36 2020

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