Magnesium in PDB 5zcq: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days

Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days

All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days, PDB code: 5zcq 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 (°) 182.330, 204.832, 177.691, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.2

Other elements in 5zcq:

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days (pdb code 5zcq). 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 10 Mm Azide Solution For 2 Days, PDB code: 5zcq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5zcq

Go back to Magnesium Binding Sites List in 5zcq
Magnesium binding site 1 out of 2 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:23.4
occ:1.00
OD2 A:ASP369 2.0 22.3 1.0
NE2 A:HIS368 2.1 20.0 1.0
OE1 B:GLU198 2.1 26.8 1.0
O B:HOH483 2.1 21.8 1.0
O A:HOH884 2.2 23.2 1.0
O B:HOH426 2.2 23.5 1.0
CD2 A:HIS368 3.1 21.6 1.0
CD B:GLU198 3.1 26.4 1.0
CE1 A:HIS368 3.1 20.7 1.0
CG A:ASP369 3.2 22.7 1.0
OE2 B:GLU198 3.4 29.4 1.0
O B:SER197 3.9 21.6 1.0
CB A:ASP369 3.9 22.9 1.0
O A:HOH883 4.0 22.6 1.0
OD1 A:ASP369 4.2 23.6 1.0
CG A:HIS368 4.2 21.0 1.0
ND1 A:HIS368 4.3 20.4 1.0
O A:HOH761 4.3 22.0 1.0
OD1 B:ASP173 4.3 22.2 1.0
OD2 B:ASP173 4.3 24.9 1.0
CG B:GLU198 4.4 22.8 1.0
OG1 A:THR294 4.4 22.9 1.0
O A:HOH720 4.5 21.8 1.0
O B:HOH445 4.5 21.2 0.4
O A:HOH840 4.5 22.5 1.0
O B:HOH532 4.5 24.5 0.6
O A:HOH857 4.6 21.9 1.0
CB B:GLU198 4.6 22.9 1.0
CG B:ASP173 4.7 22.9 1.0
CA B:GLU198 4.8 22.4 1.0
O A:HOH821 4.9 29.5 0.8

Magnesium binding site 2 out of 2 in 5zcq

Go back to Magnesium Binding Sites List in 5zcq
Magnesium binding site 2 out of 2 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 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 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg604

b:28.9
occ:1.00
OD2 N:ASP369 2.1 28.0 1.0
NE2 N:HIS368 2.1 25.7 1.0
O O:HOH434 2.1 28.8 1.0
OE1 O:GLU198 2.1 34.7 1.0
O O:HOH408 2.1 28.9 1.0
O O:HOH487 2.1 26.3 1.0
CD2 N:HIS368 3.1 27.1 1.0
CE1 N:HIS368 3.1 25.7 1.0
CD O:GLU198 3.1 32.0 1.0
CG N:ASP369 3.3 28.3 1.0
OE2 O:GLU198 3.5 35.3 1.0
O O:SER197 3.9 27.7 1.0
CB N:ASP369 4.0 26.9 1.0
O N:HOH875 4.0 26.5 1.0
O N:HOH787 4.2 25.7 1.0
CG N:HIS368 4.2 25.3 1.0
OD2 O:ASP173 4.3 29.6 1.0
ND1 N:HIS368 4.3 26.1 1.0
OD1 N:ASP369 4.3 28.4 1.0
OD1 O:ASP173 4.4 28.6 1.0
OG1 N:THR294 4.4 27.7 1.0
O O:HOH447 4.4 24.6 0.3
O N:HOH710 4.4 26.0 1.0
CG O:GLU198 4.4 28.1 1.0
O N:HOH857 4.5 25.8 1.0
O N:HOH840 4.6 25.4 1.0
O O:HOH489 4.6 33.6 0.6
CB O:GLU198 4.6 26.0 1.0
CG O:ASP173 4.7 30.0 1.0
O N:HOH766 4.8 31.0 0.7
CA O:GLU198 4.9 27.5 1.0
CA N:ASP369 5.0 26.0 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 Dec 14 22:17:08 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy