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Sodium in PDB 5z84: The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days

Enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days

All present enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days:
1.9.3.1;

Protein crystallography data

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days, PDB code: 5z84 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 (°) 183.405, 206.272, 177.609, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.9

Other elements in 5z84:

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 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 Crystals Exposed to 20 Mm Azide Solution For 4 Days (pdb code 5z84). 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 Crystals Exposed to 20 Mm Azide Solution For 4 Days, PDB code: 5z84:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5z84

Go back to Sodium Binding Sites List in 5z84
Sodium binding site 1 out of 2 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 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 Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:32.1
occ:1.00
OE1 A:GLU40 2.3 33.0 1.0
O A:HOH865 2.3 32.4 1.0
O A:GLY45 2.3 35.3 1.0
O A:SER441 2.3 30.4 1.0
O A:GLU40 2.3 32.4 1.0
CD A:GLU40 3.2 32.6 1.0
C A:GLU40 3.4 33.2 1.0
CG A:GLU40 3.4 30.6 1.0
O A:HOH795 3.4 42.1 1.0
C A:GLY45 3.5 35.8 1.0
C A:SER441 3.5 30.0 1.0
CA A:ASP442 3.9 30.7 1.0
CB A:ASP442 4.0 30.3 1.0
O A:GLN43 4.0 33.5 1.0
CA A:THR46 4.1 35.9 1.0
OD1 A:ASP442 4.1 33.1 1.0
CG A:ASP442 4.1 33.5 1.0
CA A:GLU40 4.2 31.5 1.0
N A:THR46 4.2 35.3 1.0
N A:ASP442 4.2 30.4 1.0
N A:LEU41 4.3 30.6 1.0
CA A:LEU41 4.3 31.9 1.0
N A:LEU47 4.3 37.2 1.0
CB A:GLU40 4.4 29.3 1.0
OE2 A:GLU40 4.4 35.6 1.0
N A:GLY45 4.5 31.8 1.0
CA A:GLY45 4.6 35.2 1.0
CD2 A:LEU41 4.6 31.0 1.0
CA A:SER441 4.6 29.9 1.0
C A:THR46 4.7 40.7 1.0
CB A:SER441 4.9 30.1 1.0
OD2 A:ASP442 5.0 32.6 1.0

Sodium binding site 2 out of 2 in 5z84

Go back to Sodium Binding Sites List in 5z84
Sodium binding site 2 out of 2 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 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 Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na606

b:39.3
occ:1.00
OE1 N:GLU40 2.2 42.2 1.0
O N:SER441 2.3 40.4 1.0
O N:HOH871 2.3 38.0 1.0
O N:GLY45 2.3 41.8 1.0
O N:GLU40 2.3 41.8 1.0
CD N:GLU40 3.2 44.4 1.0
O N:HOH719 3.4 42.2 1.0
C N:GLU40 3.4 41.0 1.0
CG N:GLU40 3.4 38.3 1.0
C N:SER441 3.5 38.1 1.0
C N:GLY45 3.5 48.2 1.0
CA N:THR46 4.0 44.1 1.0
CA N:ASP442 4.0 40.3 1.0
O N:GLN43 4.0 39.3 1.0
OD1 N:ASP442 4.0 38.6 1.0
CB N:ASP442 4.1 39.1 1.0
CG N:ASP442 4.1 44.8 1.0
N N:THR46 4.2 43.7 1.0
N N:ASP442 4.2 40.0 1.0
CA N:GLU40 4.3 39.2 1.0
N N:LEU41 4.3 37.4 1.0
OE2 N:GLU40 4.3 40.7 1.0
N N:LEU47 4.4 44.7 1.0
CA N:LEU41 4.4 38.2 1.0
N N:GLY45 4.4 42.1 1.0
CB N:GLU40 4.4 39.1 1.0
CA N:GLY45 4.6 41.3 1.0
C N:THR46 4.6 49.3 1.0
CA N:SER441 4.6 39.7 1.0
CD2 N:LEU41 4.7 37.3 1.0
OD2 N:ASP442 4.9 41.6 1.0
CB N:SER441 4.9 40.7 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 Dec 15 11:52:10 2020

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