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Sodium in PDB 5z85: The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days

Enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days

All present enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days:
1.9.3.1;

Protein crystallography data

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5z85 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 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.126, 205.893, 177.576, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.9

Other elements in 5z85:

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days (pdb code 5z85). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5z85:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5z85

Go back to Sodium Binding Sites List in 5z85
Sodium binding site 1 out of 2 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:28.2
occ:1.00
O A:GLY45 2.3 29.8 1.0
O A:SER441 2.3 26.2 1.0
OE1 A:GLU40 2.3 29.2 1.0
O A:GLU40 2.3 27.9 1.0
O A:HOH858 2.3 28.2 1.0
CD A:GLU40 3.3 28.7 1.0
C A:GLU40 3.4 28.3 1.0
O A:HOH746 3.4 36.8 1.0
CG A:GLU40 3.5 27.5 1.0
C A:GLY45 3.5 31.1 1.0
C A:SER441 3.5 26.2 1.0
CA A:ASP442 4.0 26.1 1.0
O A:GLN43 4.0 29.4 1.0
CA A:THR46 4.0 30.6 1.0
CB A:ASP442 4.0 26.6 1.0
CG A:ASP442 4.1 29.4 1.0
OD1 A:ASP442 4.1 29.3 1.0
N A:THR46 4.2 31.7 1.0
N A:ASP442 4.2 26.5 1.0
CA A:GLU40 4.2 27.5 1.0
N A:LEU41 4.3 25.7 1.0
CA A:LEU41 4.3 25.6 1.0
N A:LEU47 4.3 31.7 1.0
CB A:GLU40 4.4 25.0 1.0
OE2 A:GLU40 4.5 31.2 1.0
N A:GLY45 4.5 28.6 1.0
CA A:GLY45 4.6 31.1 1.0
C A:THR46 4.6 35.0 1.0
CA A:SER441 4.6 26.5 1.0
CD2 A:LEU41 4.7 26.7 1.0
CB A:SER441 4.9 26.7 1.0
OD2 A:ASP442 4.9 28.5 1.0

Sodium binding site 2 out of 2 in 5z85

Go back to Sodium Binding Sites List in 5z85
Sodium binding site 2 out of 2 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:35.6
occ:1.00
OE1 N:GLU40 2.3 35.9 1.0
O N:SER441 2.3 34.8 1.0
O N:GLY45 2.3 37.3 1.0
O N:HOH862 2.3 33.9 1.0
O N:GLU40 2.3 36.5 1.0
CD N:GLU40 3.2 37.9 1.0
C N:GLU40 3.4 34.4 1.0
CG N:GLU40 3.4 34.0 1.0
O N:HOH730 3.5 39.5 1.0
C N:GLY45 3.5 42.8 1.0
C N:SER441 3.5 33.7 1.0
OD1 N:ASP442 3.9 36.5 1.0
CA N:THR46 4.0 40.4 1.0
O N:GLN43 4.0 35.9 1.0
CA N:ASP442 4.0 35.8 1.0
CB N:ASP442 4.0 33.8 1.0
CG N:ASP442 4.1 38.4 1.0
N N:THR46 4.2 40.6 1.0
N N:ASP442 4.2 35.5 1.0
CA N:GLU40 4.3 35.0 1.0
N N:LEU41 4.3 33.1 1.0
N N:LEU47 4.3 40.5 1.0
OE2 N:GLU40 4.4 36.9 1.0
CA N:LEU41 4.4 31.7 1.0
CB N:GLU40 4.4 33.8 1.0
N N:GLY45 4.4 37.6 1.0
CA N:GLY45 4.6 36.5 1.0
C N:THR46 4.6 43.9 1.0
CA N:SER441 4.6 33.8 1.0
CD2 N:LEU41 4.7 31.6 1.0
OD2 N:ASP442 4.9 36.3 1.0
CB N:SER441 4.9 35.6 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: Tue Oct 8 01:29:21 2024

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