Sodium in PDB 8gvm: 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:
7.1.1.9;

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: 8gvm was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.97 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.405, 206.272, 177.609, 90, 90, 90
R / Rfree (%) 16.4 / 18.8

Other elements in 8gvm:

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:

Copper (Cu) 6 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 6 atoms
Magnesium (Mg) 2 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 8gvm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 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: 8gvm:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8gvm

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Sodium binding site 1 out of 4 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:30.6
occ:1.00
 O A:HOH869 2.2 30.3 1.0
OE1 A:GLU40 2.3 33.4 1.0
O A:GLY45 2.3 33.7 1.0
O A:SER441 2.3 29.8 1.0
O A:GLU40 2.4 30.6 1.0
CD A:GLU40 3.3 30.8 1.0
C A:GLU40 3.4 35.5 1.0
O A:HOH788 3.5 42.7 1.0
CG A:GLU40 3.5 27.1 1.0
C A:GLY45 3.5 38.2 1.0
C A:SER441 3.5 32.2 1.0
CA A:ASP442 3.9 28.5 1.0
O A:GLN43 4.0 32.4 1.0
CB A:ASP442 4.0 31.4 1.0
OD1 A:ASP442 4.1 34.4 1.0
CG A:ASP442 4.1 32.0 1.0
CA A:THR46 4.1 33.5 1.0
N A:ASP442 4.2 29.2 1.0
N A:LEU41 4.2 30.1 1.0
N A:THR46 4.2 33.4 1.0
CA A:GLU40 4.2 31.0 1.0
CA A:LEU41 4.3 34.3 1.0
N A:LEU47 4.4 34.2 1.0
N A:GLY45 4.5 31.6 1.0
CB A:GLU40 4.5 28.2 1.0
OE2 A:GLU40 4.5 34.6 1.0
CA A:GLY45 4.6 35.1 1.0
CD2 A:LEU41 4.6 29.3 1.0
CA A:SER441 4.7 26.2 1.0
C A:THR46 4.7 37.0 1.0
OD2 A:ASP442 4.9 33.0 1.0
CB A:SER441 5.0 29.4 1.0

Sodium binding site 2 out of 4 in 8gvm

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Sodium binding site 2 out of 4 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
C:Na303

b:41.1
occ:1.00
 NE2 C:HIS148 2.2 41.5 1.0
NE2 C:HIS232 2.4 36.8 1.0
CD2 C:HIS232 3.1 32.2 1.0
CE1 C:HIS148 3.2 56.9 1.0
CD2 C:HIS148 3.2 41.6 1.0
CG C:GLU236 3.2 44.3 1.0
CD C:GLU236 3.3 75.0 1.0
CE1 C:HIS232 3.6 38.5 1.0
OE2 C:GLU236 3.6 52.0 1.0
O C:HOH494 3.6 70.0 1.0
OE1 C:GLU236 3.7 48.1 1.0
CG C:MET152 4.2 34.7 1.0
SD C:MET152 4.2 45.3 1.0
ND1 C:HIS148 4.3 48.7 1.0
CG C:HIS148 4.3 44.2 1.0
CG C:HIS232 4.4 33.0 1.0
ND1 C:HIS232 4.5 35.1 1.0
CB C:GLU236 4.8 32.0 1.0
O C:HOH407 4.9 33.3 1.0

Sodium binding site 3 out of 4 in 8gvm

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Sodium binding site 3 out of 4 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 3 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:38.4
occ:1.00
 O N:HOH859 2.2 38.6 1.0
OE1 N:GLU40 2.3 45.6 1.0
O N:GLY45 2.3 41.0 1.0
O N:SER441 2.3 39.6 1.0
O N:GLU40 2.4 42.7 1.0
CD N:GLU40 3.2 53.9 1.0
O N:HOH718 3.3 44.3 1.0
C N:GLU40 3.4 46.2 1.0
CG N:GLU40 3.5 38.3 1.0
C N:GLY45 3.5 53.7 1.0
C N:SER441 3.5 39.1 1.0
CA N:ASP442 3.9 41.5 1.0
CB N:ASP442 4.0 39.6 1.0
O N:GLN43 4.0 39.1 1.0
OD1 N:ASP442 4.0 40.4 1.0
CA N:THR46 4.0 44.5 1.0
CG N:ASP442 4.1 46.8 1.0
N N:THR46 4.2 44.8 1.0
N N:ASP442 4.2 41.6 1.0
N N:LEU41 4.3 38.1 1.0
CA N:GLU40 4.3 37.1 1.0
OE2 N:GLU40 4.4 41.8 1.0
CA N:LEU41 4.4 40.3 1.0
N N:LEU47 4.4 45.6 1.0
N N:GLY45 4.4 43.7 1.0
CB N:GLU40 4.5 37.0 1.0
CA N:GLY45 4.6 42.6 1.0
CD2 N:LEU41 4.6 37.3 1.0
CA N:SER441 4.7 37.5 1.0
C N:THR46 4.7 58.4 1.0
OD2 N:ASP442 4.9 44.5 1.0
CB N:SER441 4.9 46.2 1.0

Sodium binding site 4 out of 4 in 8gvm

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Sodium binding site 4 out of 4 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 4 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
P:Na302

b:43.0
occ:1.00
 NE2 P:HIS148 2.3 44.7 1.0
NE2 P:HIS232 2.3 31.1 1.0
CD2 P:HIS232 3.1 35.8 1.0
CD P:GLU236 3.2 82.5 1.0
CE1 P:HIS148 3.2 52.0 1.0
CG P:GLU236 3.2 44.8 1.0
CD2 P:HIS148 3.3 39.2 1.0
OE1 P:GLU236 3.4 58.8 1.0
CE1 P:HIS232 3.5 36.8 1.0
OE2 P:GLU236 3.6 55.3 1.0
SD P:MET152 4.2 44.1 1.0
CG P:MET152 4.2 43.4 1.0
CG P:HIS232 4.3 39.5 1.0
ND1 P:HIS148 4.4 43.1 1.0
CG P:HIS148 4.4 40.8 1.0
ND1 P:HIS232 4.5 31.4 1.0
CB P:GLU236 4.8 31.9 1.0
O P:HOH439 4.9 34.2 1.0
O P:HOH484 5.0 70.3 1.0

Reference:

A.Shimada, K.Hatano, H.Tadehara, N.Yano, K.Sinzawa-Itoh, E.Yamashita, K.Mutamoto, 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 ESSN 1083-351X
PubMed: 30077971
DOI: 10.1074/JBC.RA118.003123
Page generated: Wed Oct 9 12:07:32 2024

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