Magnesium in PDB 5z85: The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days

Enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days

All present enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days:
1.9.3.1;

Protein crystallography data

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5z85 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 (°) 183.126, 205.893, 177.576, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.9

Other elements in 5z85:

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days (pdb code 5z85). 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 Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5z85:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5z85

Go back to Magnesium Binding Sites List in 5z85
Magnesium binding site 1 out of 2 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:24.6
occ:1.00
NE2 A:HIS368 2.1 19.8 1.0
OD2 A:ASP369 2.1 22.3 1.0
OE1 B:GLU198 2.1 28.1 1.0
O B:HOH441 2.1 24.4 1.0
O B:HOH508 2.2 24.4 1.0
O B:HOH415 2.2 26.8 1.0
CD2 A:HIS368 3.0 22.8 1.0
CE1 A:HIS368 3.1 22.2 1.0
CD B:GLU198 3.2 29.5 1.0
CG A:ASP369 3.2 24.6 1.0
OE2 B:GLU198 3.5 29.5 1.0
O B:SER197 3.9 22.9 1.0
CB A:ASP369 3.9 23.8 1.0
O A:HOH887 4.0 23.8 1.0
OD1 A:ASP369 4.2 24.7 1.0
CG A:HIS368 4.2 21.9 1.0
ND1 A:HIS368 4.3 20.4 1.0
O A:HOH753 4.3 23.3 1.0
OD1 B:ASP173 4.3 26.1 1.0
OD2 B:ASP173 4.3 26.9 1.0
O A:HOH720 4.4 22.6 1.0
OG1 A:THR294 4.5 23.5 1.0
CG B:GLU198 4.5 24.1 1.0
O A:HOH855 4.5 23.9 1.0
O B:HOH454 4.5 22.2 0.4
O B:HOH510 4.6 29.0 0.6
CB B:GLU198 4.6 26.1 1.0
O A:HOH849 4.6 24.0 1.0
CG B:ASP173 4.7 24.0 1.0
CA B:GLU198 4.9 24.2 1.0
O A:HOH809 4.9 30.6 0.8
CA A:ASP369 5.0 24.1 1.0

Magnesium binding site 2 out of 2 in 5z85

Go back to Magnesium Binding Sites List in 5z85
Magnesium binding site 2 out of 2 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg604

b:31.4
occ:1.00
O O:HOH442 2.0 29.7 1.0
NE2 N:HIS368 2.1 25.6 1.0
OE1 O:GLU198 2.1 34.1 1.0
OD2 N:ASP369 2.1 28.5 1.0
O O:HOH411 2.2 31.4 1.0
O N:HOH892 2.2 29.0 1.0
CD2 N:HIS368 3.0 27.9 1.0
CE1 N:HIS368 3.1 25.8 1.0
CD O:GLU198 3.2 32.5 1.0
CG N:ASP369 3.3 30.0 1.0
OE2 O:GLU198 3.5 35.5 1.0
O O:SER197 3.8 28.8 1.0
CB N:ASP369 3.9 32.2 1.0
O N:HOH885 4.0 28.5 1.0
CG N:HIS368 4.2 25.5 1.0
OD1 N:ASP369 4.2 29.1 1.0
ND1 N:HIS368 4.2 25.6 1.0
OD2 O:ASP173 4.3 32.1 1.0
O N:HOH710 4.3 28.3 1.0
O N:HOH780 4.4 27.1 1.0
OD1 O:ASP173 4.4 31.0 1.0
OG1 N:THR294 4.4 29.2 1.0
CG O:GLU198 4.5 30.3 1.0
O O:HOH439 4.5 22.6 0.3
CB O:GLU198 4.5 27.8 1.0
O O:HOH495 4.6 44.8 0.6
O N:HOH865 4.6 27.9 1.0
O N:HOH828 4.6 27.0 1.0
CG O:ASP173 4.7 31.4 1.0
CA O:GLU198 4.8 31.1 1.0
CA N:ASP369 4.9 30.0 1.0
C O:SER197 5.0 30.1 1.0
O N:HOH758 5.0 36.9 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: Mon Dec 14 22:16:38 2020

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