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Magnesium in PDB 5z84: 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:
1.9.3.1;

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: 5z84 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 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.405, 206.272, 177.609, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.9

Other elements in 5z84:

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:

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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days (pdb code 5z84). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium 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: 5z84:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5z84

Go back to Magnesium Binding Sites List in 5z84
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg604

b:28.8
occ:1.00
 NE2 A:HIS368 2.1 24.2 1.0
OD2 A:ASP369 2.1 26.6 1.0
OE1 B:GLU198 2.1 31.7 1.0
O B:HOH447 2.1 29.6 1.0
O B:HOH417 2.2 31.5 1.0
O B:HOH509 2.2 29.6 1.0
CD2 A:HIS368 3.0 27.8 1.0
CE1 A:HIS368 3.1 26.7 1.0
CD B:GLU198 3.2 34.2 1.0
CG A:ASP369 3.2 28.2 1.0
OE2 B:GLU198 3.5 34.6 1.0
O B:SER197 3.9 27.1 1.0
CB A:ASP369 3.9 28.9 1.0
O A:HOH892 4.0 29.2 1.0
OD1 A:ASP369 4.2 28.2 1.0
CG A:HIS368 4.2 25.5 1.0
ND1 A:HIS368 4.3 23.7 1.0
OD1 B:ASP173 4.3 30.8 1.0
O A:HOH774 4.3 28.3 1.0
OD2 B:ASP173 4.3 31.7 1.0
OG1 A:THR294 4.4 28.3 1.0
CG B:GLU198 4.4 27.2 1.0
O A:HOH718 4.5 26.6 1.0
O A:HOH861 4.5 28.3 1.0
O B:HOH444 4.6 28.9 0.4
O A:HOH864 4.6 28.2 1.0
CB B:GLU198 4.6 28.6 1.0
O B:HOH510 4.6 32.5 0.6
CG B:ASP173 4.7 30.0 1.0
CA B:GLU198 4.8 28.9 1.0
O A:HOH813 4.9 37.7 0.8
CA A:ASP369 5.0 30.5 1.0

Magnesium binding site 2 out of 2 in 5z84

Go back to Magnesium Binding Sites List in 5z84
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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
N:Mg605

b:35.2
occ:1.00
 NE2 N:HIS368 2.1 29.4 1.0
O O:HOH454 2.1 34.8 1.0
OE1 O:GLU198 2.1 37.9 1.0
OD2 N:ASP369 2.1 32.3 1.0
O O:HOH498 2.2 34.6 1.0
O O:HOH410 2.2 35.9 1.0
CD2 N:HIS368 3.0 32.0 1.0
CE1 N:HIS368 3.1 30.6 1.0
CD O:GLU198 3.2 36.6 1.0
CG N:ASP369 3.3 34.7 1.0
OE2 O:GLU198 3.5 39.6 1.0
O O:SER197 3.9 33.1 1.0
CB N:ASP369 4.0 37.1 1.0
O N:HOH883 4.0 33.0 1.0
CG N:HIS368 4.2 30.8 1.0
OD1 N:ASP369 4.2 33.3 1.0
ND1 N:HIS368 4.2 30.3 1.0
O N:HOH795 4.3 32.0 1.0
OD2 O:ASP173 4.3 36.7 1.0
O N:HOH712 4.4 34.0 1.0
OD1 O:ASP173 4.4 35.5 1.0
OG1 N:THR294 4.4 33.6 1.0
CG O:GLU198 4.5 32.4 1.0
O O:HOH489 4.5 45.9 0.6
O O:HOH456 4.5 26.5 0.3
O N:HOH870 4.5 33.1 1.0
O N:HOH852 4.6 32.2 1.0
CB O:GLU198 4.6 32.2 1.0
CG O:ASP173 4.7 34.7 1.0
CA O:GLU198 4.9 33.9 1.0
CA N:ASP369 5.0 34.3 1.0
O N:HOH781 5.0 38.3 0.7

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: Wed Aug 13 01:18:17 2025

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