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

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide:
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 Bound with Cyanide, PDB code: 3fyi 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.344, 131.877, 176.160, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.9

Other elements in 3fyi:

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

Magnesium binding site 1 out of 2 in 3fyi

Go back to Magnesium Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg570

b:17.0
occ:1.00
 O B:HOH327 1.9 27.9 1.0
OE1 B:GLU254 2.0 27.6 1.0
O B:HOH318 2.1 27.2 1.0
O B:HOH334 2.1 27.7 1.0
NE2 A:HIS411 2.1 23.1 1.0
OD2 A:ASP412 2.1 29.3 1.0
CE1 A:HIS411 3.0 23.2 1.0
CD B:GLU254 3.2 27.5 1.0
CD2 A:HIS411 3.2 23.0 1.0
CG A:ASP412 3.4 29.1 1.0
O A:HOH632 3.8 31.1 1.0
OE2 B:GLU254 3.9 26.6 1.0
O B:SER253 4.0 25.2 1.0
OD1 B:ASP229 4.1 33.1 1.0
CB A:ASP412 4.1 27.4 1.0
ND1 A:HIS411 4.1 23.4 1.0
O A:HOH610 4.1 32.2 1.0
OD2 B:ASP229 4.2 33.1 1.0
CG A:HIS411 4.3 24.2 1.0
O B:HOH520 4.3 50.3 1.0
OD1 A:ASP412 4.3 31.8 1.0
CG B:GLU254 4.3 24.9 1.0
O A:HOH616 4.6 25.7 1.0
O B:HOH349 4.6 35.3 1.0
CG B:ASP229 4.6 31.6 1.0
CB B:GLU254 4.6 24.6 1.0
OG1 A:THR337 4.6 31.6 1.0
O A:HOH594 4.7 27.9 1.0
O A:HOH622 4.7 30.7 1.0
CA B:GLU254 4.9 24.9 1.0
CE2 A:TYR175 4.9 28.6 1.0

Magnesium binding site 2 out of 2 in 3fyi

Go back to Magnesium Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg570

b:20.4
occ:1.00
 O D:HOH1082 1.9 31.1 1.0
OE1 D:GLU254 2.0 35.4 1.0
O D:HOH1094 2.0 38.4 1.0
OD2 C:ASP412 2.1 28.3 1.0
NE2 C:HIS411 2.2 31.9 1.0
O D:HOH1071 2.2 30.7 1.0
CE1 C:HIS411 3.0 31.8 1.0
CD D:GLU254 3.1 35.5 1.0
CD2 C:HIS411 3.3 30.7 1.0
CG C:ASP412 3.4 30.4 1.0
OE2 D:GLU254 3.8 35.1 1.0
O C:HOH1093 3.9 35.0 1.0
O D:SER253 4.0 30.6 1.0
OD1 D:ASP229 4.1 37.3 1.0
CB C:ASP412 4.1 29.6 1.0
ND1 C:HIS411 4.2 30.0 1.0
O C:HOH1041 4.2 42.3 1.0
CG D:GLU254 4.3 31.4 1.0
OD1 C:ASP412 4.3 32.8 1.0
CG C:HIS411 4.3 30.5 1.0
OD2 D:ASP229 4.4 36.8 1.0
O D:HOH1127 4.5 40.3 1.0
CB D:GLU254 4.5 30.8 1.0
O C:HOH1069 4.5 35.4 1.0
O C:HOH1051 4.6 31.2 1.0
OG1 C:THR337 4.6 37.3 1.0
CG D:ASP229 4.6 36.1 1.0
O C:HOH1014 4.7 33.9 1.0
CE2 C:TYR175 4.8 37.3 1.0
CA D:GLU254 4.9 30.7 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: Sun Aug 10 21:07:42 2025

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