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Iron 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:

Magnesium (Mg) 2 atoms
Cadmium (Cd) 4 atoms
Calcium (Ca) 2 atoms
Copper (Cu) 6 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides, PDB code: 2gsm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2gsm

Go back to Iron Binding Sites List in 2gsm
Iron binding site 1 out of 4 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 Iron with other atoms in the Fe 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:Fe2001

b:20.4
occ:1.00
 FE A:HEA2001 0.0 20.4 1.0
NC A:HEA2001 2.0 19.6 1.0
ND A:HEA2001 2.0 19.9 1.0
NA A:HEA2001 2.0 19.7 1.0
NB A:HEA2001 2.0 20.4 1.0
NE2 A:HIS102 2.1 17.6 1.0
NE2 A:HIS421 2.1 22.4 1.0
CE1 A:HIS421 3.0 22.6 1.0
C4C A:HEA2001 3.0 20.8 1.0
C1D A:HEA2001 3.0 21.2 1.0
C4A A:HEA2001 3.0 20.0 1.0
CD2 A:HIS102 3.0 18.1 1.0
C1B A:HEA2001 3.0 21.1 1.0
C4B A:HEA2001 3.0 20.3 1.0
C1A A:HEA2001 3.0 20.8 1.0
C4D A:HEA2001 3.0 19.6 1.0
C1C A:HEA2001 3.0 19.0 1.0
CE1 A:HIS102 3.1 18.9 1.0
CD2 A:HIS421 3.1 23.5 1.0
CHD A:HEA2001 3.4 20.3 1.0
CHB A:HEA2001 3.4 19.3 1.0
CHC A:HEA2001 3.4 19.6 1.0
CHA A:HEA2001 3.5 17.7 1.0
ND1 A:HIS421 4.1 21.8 1.0
ND1 A:HIS102 4.2 19.2 1.0
CG A:HIS102 4.2 19.7 1.0
C2D A:HEA2001 4.2 21.0 1.0
C3A A:HEA2001 4.2 20.6 1.0
CG A:HIS421 4.2 21.4 1.0
C3C A:HEA2001 4.2 20.7 1.0
C2A A:HEA2001 4.2 19.8 1.0
C3D A:HEA2001 4.2 21.5 1.0
C3B A:HEA2001 4.3 22.9 1.0
C2C A:HEA2001 4.3 20.2 1.0
C2B A:HEA2001 4.3 21.5 1.0
CG2 A:THR48 4.6 20.5 1.0
CE1 A:PHE420 4.9 23.0 1.0

Iron binding site 2 out of 4 in 2gsm

Go back to Iron Binding Sites List in 2gsm
Iron binding site 2 out of 4 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 Iron with other atoms in the Fe 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
A:Fe2002

b:24.2
occ:1.00
 FE A:HEA2002 0.0 24.2 1.0
NC A:HEA2002 2.1 22.7 1.0
ND A:HEA2002 2.1 23.4 1.0
NA A:HEA2002 2.1 25.6 1.0
NE2 A:HIS419 2.1 20.2 1.0
O A:HOH6506 2.1 24.5 1.0
NB A:HEA2002 2.1 27.8 1.0
CD2 A:HIS419 3.0 20.6 1.0
C1D A:HEA2002 3.1 24.5 1.0
C4C A:HEA2002 3.1 23.4 1.0
C1C A:HEA2002 3.1 23.0 1.0
C1A A:HEA2002 3.1 25.2 1.0
C4D A:HEA2002 3.1 25.1 1.0
C4A A:HEA2002 3.1 26.0 1.0
C4B A:HEA2002 3.1 26.9 1.0
C1B A:HEA2002 3.1 27.1 1.0
CE1 A:HIS419 3.2 22.2 1.0
CHD A:HEA2002 3.4 21.8 1.0
CHA A:HEA2002 3.5 24.1 1.0
CHC A:HEA2002 3.5 24.1 1.0
CHB A:HEA2002 3.5 26.7 1.0
O A:OH6501 4.0 26.7 1.0
CG A:HIS419 4.2 22.3 1.0
ND1 A:HIS419 4.2 23.4 1.0
C2C A:HEA2002 4.3 23.3 1.0
C2A A:HEA2002 4.3 26.4 1.0
C2D A:HEA2002 4.3 23.8 1.0
C3C A:HEA2002 4.3 23.7 1.0
C3A A:HEA2002 4.3 26.6 1.0
C3D A:HEA2002 4.3 24.3 1.0
C2B A:HEA2002 4.3 27.2 1.0
C3B A:HEA2002 4.4 26.7 1.0
CU A:CU3005 4.9 27.2 1.0
CG2 A:VAL423 5.0 24.5 1.0

Iron binding site 3 out of 4 in 2gsm

Go back to Iron Binding Sites List in 2gsm
Iron binding site 3 out of 4 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 Iron with other atoms in the Fe binding site number 3 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:Fe3001

b:29.2
occ:1.00
 FE C:HEA3001 0.0 29.2 1.0
NB C:HEA3001 2.0 28.8 1.0
ND C:HEA3001 2.0 29.6 1.0
NC C:HEA3001 2.0 30.1 1.0
NA C:HEA3001 2.0 28.5 1.0
NE2 C:HIS102 2.1 32.5 1.0
NE2 C:HIS421 2.1 29.2 1.0
C4B C:HEA3001 3.0 30.4 1.0
C1A C:HEA3001 3.0 28.6 1.0
C4D C:HEA3001 3.0 28.8 1.0
C1C C:HEA3001 3.0 28.6 1.0
C1D C:HEA3001 3.0 30.1 1.0
C1B C:HEA3001 3.0 29.8 1.0
C4C C:HEA3001 3.0 29.3 1.0
C4A C:HEA3001 3.0 28.8 1.0
CE1 C:HIS421 3.1 28.8 1.0
CD2 C:HIS102 3.1 32.4 1.0
CE1 C:HIS102 3.1 33.2 1.0
CD2 C:HIS421 3.2 29.9 1.0
CHA C:HEA3001 3.4 29.2 1.0
CHC C:HEA3001 3.4 28.7 1.0
CHD C:HEA3001 3.4 30.8 1.0
CHB C:HEA3001 3.4 27.6 1.0
ND1 C:HIS421 4.2 28.3 1.0
ND1 C:HIS102 4.2 32.6 1.0
CG C:HIS102 4.2 32.9 1.0
C2A C:HEA3001 4.2 28.4 1.0
C3B C:HEA3001 4.2 31.2 1.0
C2D C:HEA3001 4.2 27.8 1.0
C2C C:HEA3001 4.2 30.3 1.0
C3A C:HEA3001 4.2 27.4 1.0
C3D C:HEA3001 4.2 28.4 1.0
C2B C:HEA3001 4.2 29.7 1.0
C3C C:HEA3001 4.2 29.7 1.0
CG C:HIS421 4.3 29.2 1.0
CG2 C:THR48 4.6 30.4 1.0
CE1 C:PHE420 4.9 27.5 1.0

Iron binding site 4 out of 4 in 2gsm

Go back to Iron Binding Sites List in 2gsm
Iron binding site 4 out of 4 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 Iron with other atoms in the Fe binding site number 4 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:Fe3002

b:28.0
occ:1.00
 FE C:HEA3002 0.0 28.0 1.0
O C:HOH1006 2.0 27.8 1.0
ND C:HEA3002 2.1 28.4 1.0
NC C:HEA3002 2.1 31.6 1.0
NA C:HEA3002 2.1 28.7 1.0
NB C:HEA3002 2.1 29.6 1.0
NE2 C:HIS419 2.1 25.9 1.0
C4D C:HEA3002 3.1 29.5 1.0
C1A C:HEA3002 3.1 29.8 1.0
C1C C:HEA3002 3.1 30.9 1.0
CE1 C:HIS419 3.1 29.0 1.0
C1D C:HEA3002 3.1 31.1 1.0
C4B C:HEA3002 3.1 30.0 1.0
CD2 C:HIS419 3.1 27.7 1.0
C4C C:HEA3002 3.1 32.6 1.0
C1B C:HEA3002 3.1 30.3 1.0
C4A C:HEA3002 3.1 30.7 1.0
CHA C:HEA3002 3.4 28.9 1.0
CHC C:HEA3002 3.4 28.9 1.0
CHD C:HEA3002 3.5 31.9 1.0
CHB C:HEA3002 3.5 30.9 1.0
O C:OH7501 3.8 35.4 1.0
ND1 C:HIS419 4.2 29.1 1.0
CG C:HIS419 4.3 27.4 1.0
C3D C:HEA3002 4.3 30.1 1.0
C2A C:HEA3002 4.3 29.9 1.0
C2D C:HEA3002 4.3 29.4 1.0
C2C C:HEA3002 4.3 32.6 1.0
C3A C:HEA3002 4.3 29.6 1.0
C3B C:HEA3002 4.3 29.8 1.0
C3C C:HEA3002 4.4 32.8 1.0
C2B C:HEA3002 4.4 29.0 1.0
CU C:CU4005 4.9 33.8 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: Sun Dec 13 14:45:43 2020

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