Magnesium in PDB 5weh: Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State

Enzymatic activity of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State

All present enzymatic activity of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State:
1.9.3.1;

Protein crystallography data

The structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 5weh was solved by J.Liu, F.Ferguson-Miller, Q.Ling, C.Hiser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.45 / 3.45
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 339.221, 339.221, 89.199, 90.00, 90.00, 120.00
R / Rfree (%) 22.3 / 26.2

Other elements in 5weh:

The structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms
Copper (Cu) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State (pdb code 5weh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 5weh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5weh

Go back to Magnesium Binding Sites List in 5weh
Magnesium binding site 1 out of 2 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:95.3
occ:1.00
OE1 B:GLU254 2.0 0.8 1.0
NE2 A:HIS411 2.3 0.2 1.0
OD2 A:ASP412 2.4 0.4 1.0
CD B:GLU254 3.1 0.8 1.0
CE1 A:HIS411 3.3 0.6 1.0
CD2 A:HIS411 3.3 0.6 1.0
OE2 B:GLU254 3.5 0.2 1.0
OD2 B:ASP229 3.6 1.0 1.0
CG A:ASP412 3.6 0.8 1.0
OG1 A:THR337 4.0 0.9 1.0
OD1 A:ASP412 4.2 0.3 1.0
O B:SER253 4.3 0.9 1.0
CG B:GLU254 4.4 96.1 1.0
CG B:ASP229 4.4 0.1 1.0
ND1 A:HIS411 4.4 0.7 1.0
OD1 B:ASP229 4.4 0.1 1.0
CG A:HIS411 4.5 0.4 1.0
CB A:ASP412 4.7 0.8 1.0
CE2 A:TYR175 4.9 85.6 1.0
CB B:GLU254 4.9 94.2 1.0
O A:HIS334 5.0 94.0 1.0

Magnesium binding site 2 out of 2 in 5weh

Go back to Magnesium Binding Sites List in 5weh
Magnesium binding site 2 out of 2 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg605

b:86.3
occ:1.00
OE1 H:GLU254 2.1 0.0 1.0
OD2 G:ASP412 2.3 0.1 1.0
NE2 G:HIS411 2.3 0.5 1.0
CD H:GLU254 3.2 0.1 1.0
CD2 G:HIS411 3.2 0.8 1.0
OD2 H:ASP229 3.4 0.3 1.0
CE1 G:HIS411 3.4 0.4 1.0
CG G:ASP412 3.5 0.2 1.0
OE2 H:GLU254 3.7 0.7 1.0
OG1 G:THR337 4.0 0.8 1.0
OD1 H:ASP229 4.1 0.8 1.0
CG H:ASP229 4.1 0.3 1.0
OD1 G:ASP412 4.2 0.4 1.0
O H:SER253 4.2 0.5 1.0
CG G:HIS411 4.4 0.6 1.0
CG H:GLU254 4.4 0.6 1.0
ND1 G:HIS411 4.5 0.5 1.0
NZ H:LYS227 4.5 0.1 1.0
CB G:ASP412 4.6 0.6 1.0
CB H:GLU254 4.9 0.8 1.0

Reference:

J.Liu, C.Hiser, S.Ferguson-Miller. Role of Conformational Change and K-Path Ligands in Controlling Cytochrome C Oxidase Activity. Biochem. Soc. Trans. V. 45 1087 2017.
ISSN: ISSN 1470-8752
PubMed: 28842531
DOI: 10.1042/BST20160138
Page generated: Mon Dec 14 21:21:00 2020

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