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Magnesium in PDB 3oma: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation, PDB code: 3oma 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) 50.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.019, 131.579, 176.626, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.9

Other elements in 3oma:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation also contains other interesting chemical elements:

Cadmium (Cd) 4 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 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 K362M Mutation (pdb code 3oma). 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 K362M Mutation, PDB code: 3oma:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3oma

Go back to Magnesium Binding Sites List in 3oma
Magnesium binding site 1 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg6

b:20.3
occ:1.00
 O B:HOH744 1.7 32.4 1.0
O B:HOH750 2.0 34.0 1.0
OE1 B:GLU254 2.0 33.8 1.0
NE2 A:HIS411 2.1 27.8 1.0
OD2 A:ASP412 2.2 33.5 1.0
O B:HOH738 2.2 27.0 1.0
CE1 A:HIS411 3.0 27.2 1.0
CD2 A:HIS411 3.2 27.8 1.0
CD B:GLU254 3.2 33.8 1.0
CG A:ASP412 3.4 31.7 1.0
OE2 B:GLU254 3.8 32.6 1.0
O A:HOH763 3.9 32.6 1.0
O B:SER253 3.9 29.6 1.0
OD1 B:ASP229 4.1 39.7 1.0
CB A:ASP412 4.2 29.5 1.0
ND1 A:HIS411 4.2 25.9 1.0
CG A:HIS411 4.3 27.9 1.0
OD2 B:ASP229 4.3 36.1 1.0
OD1 A:ASP412 4.3 32.9 1.0
CG B:GLU254 4.3 29.2 1.0
O A:HOH740 4.4 37.0 1.0
CB B:GLU254 4.5 27.6 1.0
O A:HOH751 4.5 34.5 1.0
O B:HOH768 4.6 38.1 1.0
CG B:ASP229 4.6 36.7 1.0
OG1 A:THR337 4.6 36.5 1.0
O A:HOH745 4.6 26.5 1.0
O A:HOH14 4.6 29.6 1.0
CA B:GLU254 4.8 27.8 1.0
CE2 A:TYR175 4.9 29.6 1.0

Magnesium binding site 2 out of 2 in 3oma

Go back to Magnesium Binding Sites List in 3oma
Magnesium binding site 2 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg6

b:20.4
occ:1.00
 O C:HOH585 1.8 32.6 1.0
OE1 D:GLU254 2.0 38.5 1.0
OD2 C:ASP412 2.0 34.1 1.0
O D:HOH327 2.0 34.2 1.0
NE2 C:HIS411 2.1 32.8 1.0
O D:HOH316 2.2 32.4 1.0
CE1 C:HIS411 3.0 31.6 1.0
CD2 C:HIS411 3.2 32.4 1.0
CD D:GLU254 3.2 39.3 1.0
CG C:ASP412 3.2 35.5 1.0
OE2 D:GLU254 3.8 40.0 1.0
O D:SER253 3.9 35.0 1.0
O C:HOH591 4.0 38.3 1.0
CB C:ASP412 4.1 32.8 1.0
ND1 C:HIS411 4.2 31.3 1.0
OD1 C:ASP412 4.2 39.9 1.0
OD1 D:ASP229 4.2 42.2 1.0
CG C:HIS411 4.2 32.5 1.0
O C:HOH568 4.3 40.6 1.0
CG D:GLU254 4.3 36.3 1.0
OD2 D:ASP229 4.3 41.8 1.0
O C:HOH14 4.5 42.3 1.0
O C:HOH578 4.5 39.8 1.0
CB D:GLU254 4.5 35.2 1.0
O C:HOH573 4.6 33.9 1.0
CG D:ASP229 4.7 40.4 1.0
O D:HOH343 4.7 40.1 1.0
OG1 C:THR337 4.7 40.5 1.0
CA D:GLU254 4.8 35.1 1.0
C D:SER253 5.0 35.0 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: Thu Aug 15 08:26:22 2024

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