Atomistry » Sodium » PDB 8g2e-8h58 » 8gvm
Atomistry »
  Sodium »
    PDB 8g2e-8h58 »
      8gvm »

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

Go back to Sodium Binding Sites List in 8gvm
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

Go back to Sodium Binding Sites List in 8gvm
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

Go back to Sodium Binding Sites List in 8gvm
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

Go back to Sodium Binding Sites List in 8gvm
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

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy