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Magnesium in PDB 2gsm: Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides

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

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

Protein crystallography data

The structure of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides, PDB code: 2gsm was solved by L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.020, 131.639, 176.802, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 23.2

Other elements in 2gsm:

The structure of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 (pdb code 2gsm). 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, PDB code: 2gsm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2gsm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3006

b:10.7
occ:1.00
O B:HOH5055 1.8 29.3 1.0
O B:HOH5048 1.9 29.3 1.0
OE1 B:GLU254 1.9 27.6 1.0
O B:HOH5042 2.2 19.7 1.0
NE2 A:HIS411 2.2 22.8 1.0
OD2 A:ASP412 2.3 24.8 1.0
CD B:GLU254 3.1 27.6 1.0
CE1 A:HIS411 3.1 22.6 1.0
CD2 A:HIS411 3.2 21.8 1.0
CG A:ASP412 3.4 27.2 1.0
OE2 B:GLU254 3.7 28.9 1.0
O A:HOH6551 3.8 23.8 1.0
O B:SER253 3.9 23.2 1.0
CB A:ASP412 4.2 24.7 1.0
OD1 B:ASP229 4.2 27.5 1.0
ND1 A:HIS411 4.2 21.7 1.0
CG B:GLU254 4.3 24.3 1.0
OD2 B:ASP229 4.3 26.7 1.0
O A:HOH6529 4.3 25.4 1.0
CG A:HIS411 4.3 24.1 1.0
OD1 A:ASP412 4.4 25.6 1.0
O A:HOH6541 4.4 28.1 1.0
O B:HOH5072 4.5 29.6 1.0
CB B:GLU254 4.5 23.7 1.0
O A:HOH6514 4.6 22.6 1.0
OG1 A:THR337 4.6 26.4 1.0
O A:HOH6535 4.6 23.8 1.0
CG B:ASP229 4.7 25.6 1.0
CA B:GLU254 4.8 23.3 1.0
CE2 A:TYR175 4.9 21.1 1.0

Magnesium binding site 2 out of 2 in 2gsm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg4006

b:12.8
occ:1.00
O D:HOH1082 1.8 32.4 1.0
O D:HOH1094 1.8 28.3 1.0
OE1 D:GLU254 1.9 32.9 1.0
OD2 C:ASP412 2.1 26.2 1.0
NE2 C:HIS411 2.2 28.7 1.0
O D:HOH1071 2.2 26.6 1.0
CE1 C:HIS411 3.1 27.6 1.0
CD D:GLU254 3.1 33.9 1.0
CD2 C:HIS411 3.2 26.9 1.0
CG C:ASP412 3.4 28.3 1.0
OE2 D:GLU254 3.7 34.8 1.0
O D:SER253 4.0 28.4 1.0
O C:HOH1093 4.0 32.8 1.0
CB C:ASP412 4.2 27.0 1.0
ND1 C:HIS411 4.2 26.5 1.0
OD1 D:ASP229 4.2 33.0 1.0
CG D:GLU254 4.3 31.0 1.0
OD1 C:ASP412 4.3 30.0 1.0
CG C:HIS411 4.3 25.9 1.0
O C:HOH1041 4.3 32.5 1.0
OD2 D:ASP229 4.3 32.3 1.0
O C:HOH1014 4.4 26.0 1.0
O C:HOH1069 4.4 31.5 1.0
CB D:GLU254 4.5 27.9 1.0
O D:HOH1127 4.5 33.2 1.0
OG1 C:THR337 4.7 31.5 1.0
O C:HOH1051 4.7 25.9 1.0
CG D:ASP229 4.7 31.5 1.0
CA D:GLU254 4.8 28.3 1.0
CE2 C:TYR175 4.9 32.3 1.0

Reference:

L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, S.Ferguson-Miller. Identification of Conserved Lipid/Detergent-Binding Sites in A High-Resolution Structure of the Membrane Protein Cytochrome C Oxidase. Proc.Natl.Acad.Sci.Usa V. 103 16117 2006.
ISSN: ISSN 0027-8424
PubMed: 17050688
DOI: 10.1073/PNAS.0606149103
Page generated: Mon Dec 14 07:24:57 2020

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