Atomistry » Magnesium » PDB 3ohb-3otb » 3omi
Atomistry »
  Magnesium »
    PDB 3ohb-3otb »
      3omi »

Magnesium in PDB 3omi: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation:
1.9.3.1;

Protein crystallography data

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation, PDB code: 3omi was solved by J.Liu, L.Qin, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.84 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.064, 131.519, 175.674, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.5

Other elements in 3omi:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation also contains other interesting chemical elements:

Cadmium (Cd) 4 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms
Copper (Cu) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation (pdb code 3omi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation, PDB code: 3omi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3omi

Go back to Magnesium Binding Sites List in 3omi
Magnesium binding site 1 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg612

b:16.1
occ:1.00
O B:HOH428 1.9 30.3 1.0
O B:HOH518 2.0 27.4 1.0
OE1 B:GLU254 2.0 29.6 1.0
O B:HOH514 2.1 25.3 1.0
NE2 A:HIS411 2.2 18.5 1.0
OD2 A:ASP412 2.3 26.9 1.0
CE1 A:HIS411 3.1 17.9 1.0
CD2 A:HIS411 3.2 17.4 1.0
CD B:GLU254 3.2 29.2 1.0
CG A:ASP412 3.5 26.6 1.0
O A:HOH814 3.8 26.8 1.0
OE2 B:GLU254 3.9 30.4 1.0
O B:SER253 4.0 23.9 1.0
OD1 B:ASP229 4.1 31.3 1.0
ND1 A:HIS411 4.2 18.6 1.0
CB A:ASP412 4.2 23.5 1.0
OD2 B:ASP229 4.2 28.5 1.0
O A:HOH712 4.3 29.6 1.0
CG A:HIS411 4.3 20.6 1.0
CG B:GLU254 4.4 23.6 1.0
OD1 A:ASP412 4.4 30.9 1.0
O A:HOH721 4.5 26.5 1.0
CB B:GLU254 4.6 22.6 1.0
O B:HOH461 4.6 31.3 1.0
O A:HOH707 4.6 24.2 1.0
CG B:ASP229 4.6 28.3 1.0
OG1 A:THR337 4.6 25.9 1.0
O A:HOH802 4.7 21.2 1.0
CA B:GLU254 4.9 22.3 1.0
CE2 A:TYR175 4.9 23.4 1.0

Magnesium binding site 2 out of 2 in 3omi

Go back to Magnesium Binding Sites List in 3omi
Magnesium binding site 2 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg609

b:20.4
occ:1.00
O C:HOH721 1.9 33.7 1.0
O D:HOH438 2.0 35.4 1.0
OE1 D:GLU254 2.0 32.7 1.0
OD2 C:ASP412 2.1 29.0 1.0
NE2 C:HIS411 2.2 28.0 1.0
O D:HOH436 2.2 30.0 1.0
CE1 C:HIS411 3.1 26.6 1.0
CD D:GLU254 3.2 32.7 1.0
CD2 C:HIS411 3.2 27.4 1.0
CG C:ASP412 3.3 29.6 1.0
OE2 D:GLU254 3.8 34.7 1.0
O C:HOH755 4.0 33.5 1.0
O D:SER253 4.0 27.8 1.0
OD1 D:ASP229 4.2 37.9 1.0
CB C:ASP412 4.2 27.0 1.0
ND1 C:HIS411 4.2 27.4 1.0
OD1 C:ASP412 4.2 32.7 1.0
O C:HOH741 4.2 36.4 1.0
CG C:HIS411 4.3 26.8 1.0
CG D:GLU254 4.3 29.7 1.0
O C:HOH732 4.3 30.8 1.0
OD2 D:ASP229 4.4 36.4 1.0
CB D:GLU254 4.5 27.8 1.0
O C:HOH707 4.5 31.7 1.0
OG1 C:THR337 4.6 32.3 1.0
O C:HOH746 4.6 30.7 1.0
O D:HOH471 4.7 40.5 1.0
CG D:ASP229 4.7 33.1 1.0
CA D:GLU254 4.9 27.9 1.0
CE2 C:TYR175 4.9 34.4 1.0

Reference:

J.Liu, L.Qin, S.Ferguson-Miller. Crystallographic and Online Spectral Evidence For Role of Conformational Change and Conserved Water in Cytochrome Oxidase Proton Pump. Proc.Natl.Acad.Sci.Usa V. 108 1284 2011.
ISSN: ISSN 0027-8424
PubMed: 21205904
DOI: 10.1073/PNAS.1012846108
Page generated: Mon Dec 14 08:36:28 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