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Magnesium in PDB 3fye: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State

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

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

Protein crystallography data

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 3fye was solved by L.Qin, D.A.Mills, D.A.Proshlyakov, C.Hiser, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.613, 131.472, 176.192, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.1

Other elements in 3fye:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State 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 in the Reduced State (pdb code 3fye). 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 in the Reduced State, PDB code: 3fye:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3fye

Go back to Magnesium Binding Sites List in 3fye
Magnesium binding site 1 out of 2 in the Catalytic Core Subunits (I and II) of 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 Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg571

b:9.9
occ:1.00
 O B:HOH332 1.8 32.8 1.0
OE1 B:GLU254 1.9 30.2 1.0
O B:HOH338 2.0 29.1 1.0
O B:HOH326 2.0 29.2 1.0
OD2 A:ASP412 2.1 28.9 1.0
NE2 A:HIS411 2.2 26.8 1.0
CE1 A:HIS411 3.1 26.7 1.0
CD B:GLU254 3.1 29.9 1.0
CD2 A:HIS411 3.2 26.8 1.0
CG A:ASP412 3.3 29.9 1.0
O A:HOH633 3.8 32.5 1.0
OE2 B:GLU254 3.8 30.5 1.0
O B:SER253 4.0 28.8 1.0
CB A:ASP412 4.0 28.6 1.0
OD1 B:ASP229 4.2 34.4 1.0
ND1 A:HIS411 4.2 23.5 1.0
CG B:GLU254 4.3 27.4 1.0
OD2 B:ASP229 4.3 32.1 1.0
OD1 A:ASP412 4.3 32.6 1.0
CG A:HIS411 4.3 26.3 1.0
O A:HOH611 4.3 30.9 1.0
O B:HOH356 4.4 33.2 1.0
CB B:GLU254 4.5 27.7 1.0
O A:HOH594 4.5 28.2 1.0
O A:HOH622 4.6 27.0 1.0
O A:HOH616 4.6 25.1 1.0
OG1 A:THR337 4.6 30.8 1.0
CG B:ASP229 4.7 32.8 1.0
CA B:GLU254 4.8 27.5 1.0
CE2 A:TYR175 4.9 30.5 1.0

Magnesium binding site 2 out of 2 in 3fye

Go back to Magnesium Binding Sites List in 3fye
Magnesium binding site 2 out of 2 in the Catalytic Core Subunits (I and II) of 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 Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg571

b:14.3
occ:1.00
 O C:HOH1082 1.8 32.2 1.0
OE1 D:GLU254 1.9 35.2 1.0
O D:HOH1094 2.0 42.2 1.0
O D:HOH1071 2.1 30.2 1.0
OD2 C:ASP412 2.1 31.1 1.0
NE2 C:HIS411 2.2 34.2 1.0
CD D:GLU254 3.1 36.6 1.0
CE1 C:HIS411 3.1 34.6 1.0
CD2 C:HIS411 3.1 33.5 1.0
CG C:ASP412 3.3 32.4 1.0
OE2 D:GLU254 3.8 33.9 1.0
O C:HOH1093 3.9 34.3 1.0
O D:SER253 3.9 33.6 1.0
CB C:ASP412 4.0 32.6 1.0
ND1 C:HIS411 4.2 31.8 1.0
CG D:GLU254 4.2 35.1 1.0
OD1 D:ASP229 4.2 38.2 1.0
CG C:HIS411 4.3 31.9 1.0
O C:HOH1041 4.3 35.1 1.0
OD1 C:ASP412 4.3 34.3 1.0
OD2 D:ASP229 4.3 39.1 1.0
CB D:GLU254 4.5 34.6 1.0
O C:HOH1014 4.5 31.2 1.0
OG1 C:THR337 4.5 37.4 1.0
O C:HOH1069 4.6 33.5 1.0
O C:HOH1051 4.7 33.0 1.0
CG D:ASP229 4.7 37.7 1.0
O D:HOH1127 4.7 42.9 1.0
CA D:GLU254 4.8 34.4 1.0
CE2 C:TYR175 4.9 40.3 1.0

Reference:

L.Qin, J.Liu, D.Mills, D.A.Proshlyakov, C.Hiser, S.Ferguson-Miller. Redox Dependent Conformational Changes in Cytochrome C Oxidase Suggest A Gating Mechanism For Proton Uptake. Biochemistry V. 48 5121 2009.
ISSN: ISSN 0006-2960
PubMed: 19397279
DOI: 10.1021/BI9001387
Page generated: Wed Aug 14 13:58:22 2024

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