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Sodium in PDB 7xmb: Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113

Enzymatic activity of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113

All present enzymatic activity of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113:
7.1.1.9;

Protein crystallography data

The structure of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113, PDB code: 7xmb was solved by Y.Nishida, K.Shinzawa-Itoh, N.Mizuno, T.Kumasaka, S.Yoshikawa, T.Tsukihara, Y.Shintani, S.Takashima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.097, 204.337, 177.933, 90, 90, 90
R / Rfree (%) 17.8 / 20.4

Other elements in 7xmb:

The structure of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113 (pdb code 7xmb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113, PDB code: 7xmb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7xmb

Go back to Sodium Binding Sites List in 7xmb
Sodium binding site 1 out of 2 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:16.8
occ:1.00
 OE2 A:GLU40 2.3 30.5 1.0
O A:SER441 2.3 30.1 1.0
O A:GLU40 2.3 26.6 1.0
O A:GLY45 2.3 29.3 1.0
O A:HOH839 2.4 24.8 1.0
CD A:GLU40 3.3 32.7 1.0
C A:GLU40 3.4 31.2 1.0
C A:GLY45 3.5 35.3 1.0
O A:HOH794 3.5 37.9 1.0
C A:SER441 3.5 25.3 1.0
CG A:GLU40 3.5 32.1 1.0
CA A:ASP442 4.0 24.7 1.0
CA A:THR46 4.0 34.6 0.8
O A:GLN43 4.0 26.6 1.0
CA A:THR46 4.1 30.7 0.2
CB A:ASP442 4.1 28.7 1.0
OD1 A:ASP442 4.1 26.8 1.0
N A:THR46 4.2 28.2 0.8
N A:THR46 4.2 28.5 0.2
N A:ASP442 4.2 20.8 1.0
CG A:ASP442 4.2 29.1 1.0
CA A:GLU40 4.2 22.1 1.0
N A:LEU41 4.2 24.7 1.0
CA A:LEU41 4.3 21.9 1.0
N A:LEU47 4.4 37.9 0.2
OE1 A:GLU40 4.4 35.1 1.0
CB A:GLU40 4.4 31.3 1.0
N A:GLY45 4.5 38.0 1.0
CD2 A:LEU41 4.5 22.3 1.0
CA A:GLY45 4.6 24.2 1.0
N A:LEU47 4.6 34.4 0.8
CA A:SER441 4.6 33.6 1.0
C A:THR46 4.7 44.2 0.8
C A:THR46 4.7 33.8 0.2
OD2 A:ASP442 4.9 31.7 1.0
O A:HOH710 4.9 47.2 1.0
CB A:SER441 5.0 26.8 1.0

Sodium binding site 2 out of 2 in 7xmb

Go back to Sodium Binding Sites List in 7xmb
Sodium binding site 2 out of 2 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:20.0
occ:1.00
 OE2 N:GLU40 2.3 34.4 1.0
O N:SER441 2.3 34.0 1.0
O N:GLU40 2.3 29.5 1.0
O N:GLY45 2.3 32.9 1.0
O N:HOH901 2.4 29.8 1.0
CD N:GLU40 3.2 40.6 1.0
O N:HOH752 3.3 50.8 1.0
C N:GLU40 3.4 34.5 1.0
CG N:GLU40 3.5 33.7 1.0
C N:GLY45 3.5 43.1 1.0
C N:SER441 3.5 29.8 1.0
CA N:THR46 4.0 42.7 0.2
CA N:ASP442 4.1 20.4 1.0
O N:GLN43 4.1 32.5 1.0
CA N:THR46 4.1 38.5 0.8
CB N:ASP442 4.2 32.1 1.0
N N:THR46 4.2 42.0 0.2
N N:THR46 4.2 33.2 0.8
CA N:GLU40 4.2 37.1 1.0
OD1 N:ASP442 4.2 39.5 1.0
N N:ASP442 4.2 28.5 1.0
N N:LEU41 4.3 31.4 1.0
CG N:ASP442 4.3 40.3 1.0
CA N:LEU41 4.4 32.2 1.0
N N:LEU47 4.4 53.4 0.2
OE1 N:GLU40 4.4 36.8 1.0
CB N:GLU40 4.4 24.1 1.0
N N:LEU47 4.5 56.9 0.8
N N:GLY45 4.5 37.7 1.0
C N:THR46 4.6 48.9 0.2
CA N:GLY45 4.6 28.7 1.0
CA N:SER441 4.6 33.8 1.0
CD2 N:LEU41 4.6 25.7 1.0
C N:THR46 4.7 46.5 0.8
O N:HOH706 4.9 54.3 1.0
CB N:SER441 5.0 43.9 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: Wed Oct 9 09:49:35 2024

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