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

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

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

Protein crystallography data

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5zcp 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 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.320, 206.171, 177.625, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.7

Other elements in 5zcp:

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

Sodium binding site 1 out of 2 in 5zcp

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

b:30.0
occ:1.00
OE1 A:GLU40 2.3 31.1 1.0
O A:GLY45 2.3 31.8 1.0
O A:HOH871 2.3 29.2 1.0
O A:SER441 2.3 27.2 1.0
O A:GLU40 2.4 29.0 1.0
CD A:GLU40 3.2 28.8 1.0
C A:GLU40 3.4 29.6 1.0
CG A:GLU40 3.4 28.2 1.0
O A:HOH788 3.5 38.3 1.0
C A:GLY45 3.5 34.8 1.0
C A:SER441 3.5 29.4 1.0
CA A:ASP442 4.0 28.5 1.0
O A:GLN43 4.0 31.2 1.0
CB A:ASP442 4.0 29.0 1.0
CA A:THR46 4.1 31.9 1.0
CG A:ASP442 4.1 31.3 1.0
CA A:GLU40 4.2 27.4 1.0
N A:THR46 4.2 31.4 1.0
OD1 A:ASP442 4.2 31.2 1.0
N A:ASP442 4.2 27.9 1.0
N A:LEU41 4.3 27.4 1.0
CA A:LEU41 4.3 27.2 1.0
N A:LEU47 4.4 33.9 1.0
CB A:GLU40 4.4 27.2 1.0
OE2 A:GLU40 4.5 32.8 1.0
N A:GLY45 4.5 31.0 1.0
CA A:GLY45 4.6 32.1 1.0
CA A:SER441 4.6 27.1 1.0
C A:THR46 4.7 36.6 1.0
CD2 A:LEU41 4.7 28.6 1.0
OD2 A:ASP442 4.9 30.6 1.0
CB A:SER441 4.9 28.4 1.0

Sodium binding site 2 out of 2 in 5zcp

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

b:35.2
occ:1.00
OE1 N:GLU40 2.2 38.0 1.0
O N:HOH861 2.3 33.5 1.0
O N:SER441 2.3 33.3 1.0
O N:GLY45 2.3 39.0 1.0
O N:GLU40 2.3 36.2 1.0
CD N:GLU40 3.2 39.8 1.0
C N:GLU40 3.4 36.1 1.0
CG N:GLU40 3.4 34.1 1.0
O N:HOH716 3.4 40.9 1.0
C N:GLY45 3.5 44.2 1.0
C N:SER441 3.5 35.5 1.0
CB N:ASP442 4.0 34.1 1.0
CA N:ASP442 4.0 34.6 1.0
O N:GLN43 4.0 38.6 1.0
CA N:THR46 4.0 40.5 1.0
OD1 N:ASP442 4.1 37.1 1.0
CG N:ASP442 4.2 37.4 1.0
N N:THR46 4.2 39.1 1.0
N N:ASP442 4.2 35.6 1.0
CA N:GLU40 4.2 32.9 1.0
OE2 N:GLU40 4.3 37.5 1.0
N N:LEU41 4.3 31.8 1.0
CA N:LEU41 4.3 33.3 1.0
N N:LEU47 4.4 39.0 1.0
CB N:GLU40 4.4 34.3 1.0
N N:GLY45 4.5 36.3 1.0
CA N:GLY45 4.6 35.0 1.0
CA N:SER441 4.6 33.2 1.0
C N:THR46 4.6 44.1 1.0
CD2 N:LEU41 4.7 34.1 1.0
CB N:SER441 4.9 38.4 1.0
OD2 N:ASP442 5.0 37.8 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 11:52:39 2020

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