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Magnesium 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:

Zinc (Zn) 2 atoms
Iron (Fe) 6 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5zcp

Go back to Magnesium Binding Sites List in 5zcp
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg604

b:26.4
occ:1.00
OD2 A:ASP369 2.0 24.9 1.0
NE2 A:HIS368 2.1 22.2 1.0
OE1 B:GLU198 2.1 30.3 1.0
O B:HOH467 2.1 26.3 1.0
O B:HOH431 2.2 27.3 1.0
O A:HOH892 2.2 26.4 1.0
CD B:GLU198 3.1 30.8 1.0
CD2 A:HIS368 3.1 25.2 1.0
CE1 A:HIS368 3.1 23.3 1.0
CG A:ASP369 3.2 24.0 1.0
OE2 B:GLU198 3.4 33.4 1.0
O B:SER197 3.9 26.3 1.0
CB A:ASP369 3.9 24.9 1.0
O A:HOH895 4.0 26.4 1.0
OD1 A:ASP369 4.2 26.7 1.0
CG A:HIS368 4.3 24.2 1.0
O A:HOH756 4.3 25.3 1.0
ND1 A:HIS368 4.3 23.7 1.0
OD2 B:ASP173 4.3 28.3 1.0
OD1 B:ASP173 4.3 27.5 1.0
CG B:GLU198 4.4 27.0 1.0
OG1 A:THR294 4.4 27.3 1.0
O B:HOH479 4.5 25.2 0.4
O A:HOH850 4.5 26.0 1.0
O A:HOH722 4.5 25.3 1.0
O B:HOH531 4.5 30.8 0.6
O A:HOH849 4.6 24.9 1.0
CB B:GLU198 4.6 25.9 1.0
CG B:ASP173 4.7 24.6 1.0
CA B:GLU198 4.8 26.6 1.0
O A:HOH823 5.0 37.5 0.8
CA A:ASP369 5.0 25.4 1.0

Magnesium binding site 2 out of 2 in 5zcp

Go back to Magnesium Binding Sites List in 5zcp
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg605

b:31.3
occ:1.00
NE2 N:HIS368 2.1 26.9 1.0
OD2 N:ASP369 2.1 28.8 1.0
O O:HOH432 2.1 31.9 1.0
OE1 O:GLU198 2.1 35.9 1.0
O O:HOH410 2.1 31.5 1.0
O O:HOH483 2.2 31.8 1.0
CD2 N:HIS368 3.1 30.4 1.0
CE1 N:HIS368 3.1 27.7 1.0
CD O:GLU198 3.2 34.0 1.0
CG N:ASP369 3.3 29.8 1.0
OE2 O:GLU198 3.5 36.2 1.0
O O:SER197 3.9 31.6 1.0
CB N:ASP369 3.9 30.6 1.0
O N:HOH871 4.0 30.2 1.0
ND1 N:HIS368 4.2 28.9 1.0
CG N:HIS368 4.2 28.3 1.0
OD1 N:ASP369 4.2 31.8 1.0
O N:HOH784 4.3 28.7 1.0
OD2 O:ASP173 4.3 32.5 1.0
OD1 O:ASP173 4.4 31.7 1.0
OG1 N:THR294 4.4 30.7 1.0
CG O:GLU198 4.4 31.7 1.0
O N:HOH710 4.5 31.0 1.0
O O:HOH445 4.5 26.8 0.3
O N:HOH852 4.5 29.9 1.0
CB O:GLU198 4.6 29.3 1.0
O N:HOH848 4.6 29.5 1.0
O O:HOH488 4.6 37.0 0.6
CG O:ASP173 4.7 32.2 1.0
CA O:GLU198 4.9 31.7 1.0
O N:HOH778 4.9 36.0 0.7
CA N:ASP369 5.0 28.4 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: Mon Sep 30 11:51:35 2024

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