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Magnesium in PDB 3dtu: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid

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

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

Protein crystallography data

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

Resolution Low / High (Å) 40.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.243, 132.052, 167.966, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.2

Other elements in 3dtu:

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

Cadmium (Cd) 5 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 Complexed with Deoxycholic Acid (pdb code 3dtu). 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 Complexed with Deoxycholic Acid, PDB code: 3dtu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3dtu

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


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 Complexed with Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1006

b:16.4
occ:1.00
 OE1 B:GLU254 1.9 33.7 1.0
O B:HOH1070 2.0 29.8 1.0
OD2 A:ASP412 2.0 25.9 1.0
O B:HOH1064 2.1 26.4 1.0
NE2 A:HIS411 2.1 27.1 1.0
O B:HOH1077 2.1 29.9 1.0
CE1 A:HIS411 3.0 27.2 1.0
CD B:GLU254 3.1 33.2 1.0
CD2 A:HIS411 3.2 26.2 1.0
CG A:ASP412 3.3 29.3 1.0
OE2 B:GLU254 3.7 34.0 1.0
O B:SER253 3.9 30.3 1.0
O A:HOH1554 3.9 31.2 1.0
ND1 A:HIS411 4.1 26.7 1.0
OD1 A:ASP412 4.2 31.6 1.0
CB A:ASP412 4.2 28.6 1.0
OD1 B:ASP229 4.2 34.8 1.0
CG A:HIS411 4.2 25.9 1.0
CG B:GLU254 4.3 31.3 1.0
O A:HOH1532 4.3 37.3 1.0
OD2 B:ASP229 4.4 30.7 1.0
O A:HOH1544 4.4 28.2 1.0
CB B:GLU254 4.5 30.3 1.0
OG1 A:THR337 4.6 32.0 1.0
O A:HOH1519 4.6 30.4 1.0
O B:HOH1093 4.6 39.0 1.0
O A:HOH1538 4.6 35.2 1.0
CG B:ASP229 4.7 31.0 1.0
CA B:GLU254 4.8 30.4 1.0
CE2 A:TYR175 4.9 31.1 1.0

Magnesium binding site 2 out of 2 in 3dtu

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


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 Complexed with Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg570

b:15.2
occ:1.00
 O C:HOH628 1.8 28.1 1.0
O D:HOH333 2.0 24.6 1.0
OE1 D:GLU254 2.0 29.4 1.0
OD2 C:ASP412 2.2 24.7 1.0
O D:HOH321 2.2 28.2 1.0
NE2 C:HIS411 2.2 23.3 1.0
CE1 C:HIS411 3.2 22.4 1.0
CD2 C:HIS411 3.2 23.8 1.0
CD D:GLU254 3.2 32.2 1.0
CG C:ASP412 3.4 25.6 1.0
O C:HOH633 3.9 32.4 1.0
OE2 D:GLU254 3.9 32.2 1.0
O D:SER253 3.9 28.2 1.0
OD1 D:ASP229 4.2 34.8 1.0
CB C:ASP412 4.2 24.7 1.0
O C:HOH610 4.3 33.5 1.0
ND1 C:HIS411 4.3 22.8 1.0
OD1 C:ASP412 4.3 27.7 1.0
OD2 D:ASP229 4.3 30.2 1.0
CG C:HIS411 4.3 23.0 1.0
CG D:GLU254 4.4 28.6 1.0
O C:HOH622 4.4 27.1 1.0
CB D:GLU254 4.5 28.2 1.0
O C:HOH616 4.5 26.3 1.0
O C:HOH597 4.6 26.9 1.0
OG1 C:THR337 4.6 27.1 1.0
O D:HOH349 4.7 33.9 1.0
CG D:ASP229 4.7 30.5 1.0
CA D:GLU254 4.8 28.3 1.0
CE2 C:TYR175 4.9 29.3 1.0

Reference:

L.Qin, D.A.Mills, L.Buhrow, C.Hiser, S.Ferguson-Miller. A Conserved Steroid Binding Site in Cytochrome C Oxidase. Biochemistry V. 47 9931 2008.
ISSN: ISSN 0006-2960
PubMed: 18759498
DOI: 10.1021/BI8013483
Page generated: Wed Aug 14 12:41:58 2024

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