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Sodium in PDB 5zcq: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days

Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days

All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days, PDB code: 5zcq 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 (°) 182.330, 204.832, 177.691, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.2

Other elements in 5zcq:

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days (pdb code 5zcq). 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 10 Mm Azide Solution For 2 Days, PDB code: 5zcq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5zcq

Go back to Sodium Binding Sites List in 5zcq
Sodium binding site 1 out of 2 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:25.7
occ:1.00
OE1 A:GLU40 2.3 25.9 1.0
O A:GLY45 2.3 29.2 1.0
O A:SER441 2.3 24.6 1.0
O A:HOH860 2.3 25.4 1.0
O A:GLU40 2.4 25.1 1.0
CD A:GLU40 3.3 25.0 1.0
C A:GLU40 3.4 25.8 1.0
CG A:GLU40 3.4 23.6 1.0
O A:HOH802 3.4 34.9 1.0
C A:GLY45 3.5 28.4 1.0
C A:SER441 3.6 26.1 1.0
CB A:ASP442 4.0 24.4 1.0
CA A:ASP442 4.0 24.2 1.0
CA A:THR46 4.0 28.7 1.0
O A:GLN43 4.0 26.2 1.0
CG A:ASP442 4.2 26.6 1.0
CA A:GLU40 4.2 23.4 1.0
OD1 A:ASP442 4.2 27.2 1.0
N A:THR46 4.2 28.5 1.0
N A:ASP442 4.3 23.9 1.0
N A:LEU41 4.3 23.1 1.0
N A:LEU47 4.3 28.2 1.0
CA A:LEU41 4.3 22.9 1.0
CB A:GLU40 4.4 24.6 1.0
OE2 A:GLU40 4.4 29.7 1.0
N A:GLY45 4.5 26.3 1.0
CA A:GLY45 4.6 28.1 1.0
C A:THR46 4.6 30.1 1.0
CD2 A:LEU41 4.7 26.1 1.0
CA A:SER441 4.7 24.0 1.0
CB A:SER441 4.9 25.8 1.0
OD2 A:ASP442 5.0 25.8 1.0

Sodium binding site 2 out of 2 in 5zcq

Go back to Sodium Binding Sites List in 5zcq
Sodium binding site 2 out of 2 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:33.1
occ:1.00
OE1 N:GLU40 2.3 35.5 1.0
O N:GLY45 2.3 34.8 1.0
O N:SER441 2.3 30.7 1.0
O N:HOH868 2.4 32.5 1.0
O N:GLU40 2.4 34.4 1.0
CD N:GLU40 3.2 36.8 1.0
CG N:GLU40 3.4 31.2 1.0
C N:GLU40 3.4 33.9 1.0
O N:HOH792 3.5 41.7 1.0
C N:SER441 3.5 30.5 1.0
C N:GLY45 3.5 37.7 1.0
CA N:ASP442 4.0 30.8 1.0
CB N:ASP442 4.0 32.0 1.0
O N:GLN43 4.0 33.6 1.0
OD1 N:ASP442 4.1 33.6 1.0
CA N:THR46 4.1 37.5 1.0
CG N:ASP442 4.1 33.6 1.0
N N:ASP442 4.2 31.4 1.0
CA N:GLU40 4.2 32.1 1.0
N N:THR46 4.3 39.4 1.0
N N:LEU41 4.3 29.7 1.0
CA N:LEU41 4.3 30.2 1.0
OE2 N:GLU40 4.4 33.8 1.0
CB N:GLU40 4.4 32.0 1.0
N N:LEU47 4.4 37.5 1.0
N N:GLY45 4.5 34.6 1.0
CD2 N:LEU41 4.6 30.4 1.0
CA N:GLY45 4.6 37.2 1.0
CA N:SER441 4.6 30.3 1.0
C N:THR46 4.7 41.6 1.0
OD2 N:ASP442 4.9 34.2 1.0
CB N:SER441 4.9 32.6 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 Dec 15 11:52:40 2020

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