Zinc in PDB 7xma: Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso

Enzymatic activity of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso

All present enzymatic activity of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso:
7.1.1.9;

Protein crystallography data

The structure of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso, PDB code: 7xma was solved by Y.Nishida, K.Shinzawa-Itoh, N.Mizuno, T.Kumasaka, S.Yoshikawa, T.Tsukihara, S.Takashima, Y.Shintani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.97 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.8, 203.577, 177.859, 90, 90, 90
R / Rfree (%) 18.6 / 21.3

Other elements in 7xma:

The structure of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso (pdb code 7xma). 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 Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso, PDB code: 7xma:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7xma

Go back to Zinc Binding Sites List in 7xma
Zinc binding site 1 out of 2 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso


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 Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:21.5
occ:1.00
SG F:CYS82 2.3 35.1 1.0
SG F:CYS62 2.3 35.1 1.0
SG F:CYS85 2.3 35.9 1.0
SG F:CYS60 2.3 32.1 1.0
CB F:CYS82 3.2 40.0 1.0
CB F:CYS60 3.3 25.5 1.0
CB F:CYS62 3.3 34.1 1.0
CB F:CYS85 3.4 32.5 1.0
CA F:CYS62 3.6 44.9 1.0
N F:CYS85 3.7 43.4 1.0
N F:CYS62 4.0 30.2 1.0
CA F:CYS85 4.1 40.3 1.0
O F:CYS60 4.2 35.6 1.0
C F:CYS60 4.4 39.2 1.0
OG1 F:THR87 4.4 66.0 1.0
CA F:CYS60 4.4 31.2 1.0
CB F:SER84 4.4 35.2 1.0
O F:HOH209 4.5 48.5 1.0
OG F:SER84 4.6 42.0 1.0
CA F:CYS82 4.7 28.3 1.0
C F:SER84 4.7 31.8 1.0
CG1 F:ILE70 4.8 34.0 1.0
C F:ILE61 4.8 44.4 1.0
C F:CYS85 4.8 41.6 1.0
CB F:ILE70 4.8 36.6 1.0
N F:GLY86 4.9 34.7 1.0
CA F:SER84 4.9 37.6 1.0
N F:SER84 4.9 44.3 1.0
C F:CYS62 5.0 58.2 1.0

Zinc binding site 2 out of 2 in 7xma

Go back to Zinc Binding Sites List in 7xma
Zinc binding site 2 out of 2 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso


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 Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:21.6
occ:1.00
SG S:CYS60 2.3 31.4 1.0
SG S:CYS62 2.3 36.0 1.0
SG S:CYS85 2.3 33.7 1.0
SG S:CYS82 2.3 36.7 1.0
CB S:CYS82 3.2 36.5 1.0
CB S:CYS60 3.3 32.2 1.0
CB S:CYS62 3.3 37.8 1.0
CB S:CYS85 3.4 34.4 1.0
CA S:CYS62 3.6 39.4 1.0
N S:CYS85 3.8 40.5 1.0
N S:CYS62 4.0 36.9 1.0
CA S:CYS85 4.2 45.0 1.0
O S:CYS60 4.2 28.8 1.0
OG1 S:THR87 4.3 57.2 1.0
C S:CYS60 4.4 40.9 1.0
CA S:CYS60 4.4 33.2 1.0
CB S:SER84 4.5 26.2 1.0
O S:HOH203 4.5 42.6 1.0
OG S:SER84 4.6 43.6 1.0
CA S:CYS82 4.7 26.1 1.0
C S:SER84 4.7 29.4 1.0
C S:ILE61 4.8 33.8 1.0
CG1 S:ILE70 4.8 30.4 1.0
C S:CYS85 4.9 44.5 1.0
CB S:ILE70 4.9 33.3 1.0
N S:GLY86 4.9 33.7 1.0
C S:CYS62 4.9 47.1 1.0
CA S:SER84 5.0 34.8 1.0
N S:SER84 5.0 40.2 1.0

Reference:

Y.Nishida, S.Yanagisawa, R.Morita, H.Shigematsu, K.Shinzawa-Itoh, H.Yuki, S.Ogasawara, K.Shimuta, T.Iwamoto, C.Nakabayashi, W.Matsumura, H.Kato, C.Gopalasingam, T.Nagao, T.Qaqorh, Y.Takahashi, S.Yamazaki, K.Kamiya, R.Harada, N.Mizuno, H.Takahashi, Y.Akeda, M.Ohnishi, Y.Ishii, T.Kumasaka, T.Murata, K.Muramoto, T.Tosha, Y.Shiro, T.Honma, Y.Shigeta, M.Kubo, S.Takashima, Y.Shintani. Identifying Antibiotics Based on Structural Differences in the Conserved Allostery From Mitochondrial Heme-Copper Oxidases. Nat Commun V. 13 7591 2022.
ISSN: ESSN 2041-1723
PubMed: 36481732
DOI: 10.1038/S41467-022-34771-Y
Page generated: Sat Apr 8 05:56:40 2023

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