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Iron in PDB 1m56: Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)

Enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)

All present enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type):
1.9.3.1;

Protein crystallography data

The structure of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type), PDB code: 1m56 was solved by M.Svensson-Ek, J.Abramson, G.Larsson, S.Tornroth, P.Brezezinski, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 340.360, 340.360, 89.668, 90.00, 90.00, 120.00
R / Rfree (%) 23.6 / 27.5

Other elements in 1m56:

The structure of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Copper (Cu) 6 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) (pdb code 1m56). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type), PDB code: 1m56:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1m56

Go back to Iron Binding Sites List in 1m56
Iron binding site 1 out of 4 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:28.6
occ:1.00
 FE A:HEA1001 0.0 28.6 1.0
ND A:HEA1001 1.9 26.7 1.0
NA A:HEA1001 1.9 27.3 1.0
NC A:HEA1001 2.0 27.1 1.0
NB A:HEA1001 2.0 27.1 1.0
NE2 A:HIS102 2.1 13.7 1.0
NE2 A:HIS421 2.1 16.0 1.0
CD2 A:HIS102 2.7 14.4 1.0
C4D A:HEA1001 2.9 26.7 1.0
C1A A:HEA1001 2.9 28.6 1.0
C1D A:HEA1001 2.9 26.4 1.0
C4A A:HEA1001 3.0 28.1 1.0
C4C A:HEA1001 3.0 26.4 1.0
CE1 A:HIS421 3.0 17.6 1.0
CD2 A:HIS421 3.1 19.0 1.0
C1B A:HEA1001 3.1 27.4 1.0
C4B A:HEA1001 3.1 27.4 1.0
C1C A:HEA1001 3.1 27.0 1.0
CE1 A:HIS102 3.2 14.8 1.0
CHA A:HEA1001 3.2 27.4 1.0
CHD A:HEA1001 3.3 26.0 1.0
CHB A:HEA1001 3.4 27.8 1.0
CHC A:HEA1001 3.5 27.6 1.0
CG A:HIS102 4.0 16.4 1.0
C3D A:HEA1001 4.1 25.4 1.0
C2D A:HEA1001 4.1 24.7 1.0
C2A A:HEA1001 4.1 28.7 1.0
ND1 A:HIS102 4.2 15.4 1.0
ND1 A:HIS421 4.2 19.6 1.0
C3A A:HEA1001 4.2 28.7 1.0
CG A:HIS421 4.3 17.4 1.0
C3C A:HEA1001 4.3 25.7 1.0
C2C A:HEA1001 4.3 26.0 1.0
C2B A:HEA1001 4.4 26.8 1.0
C3B A:HEA1001 4.4 27.1 1.0

Iron binding site 2 out of 4 in 1m56

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Iron binding site 2 out of 4 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:20.6
occ:1.00
 FE A:HEA1002 0.0 20.6 1.0
ND A:HEA1002 1.9 14.7 1.0
NA A:HEA1002 1.9 14.9 1.0
NC A:HEA1002 2.0 14.9 1.0
NB A:HEA1002 2.0 14.7 1.0
NE2 A:HIS419 2.2 19.9 1.0
C4D A:HEA1002 2.9 14.9 1.0
C1A A:HEA1002 2.9 14.9 1.0
C1D A:HEA1002 2.9 14.9 1.0
C4C A:HEA1002 3.0 15.5 1.0
C4A A:HEA1002 3.0 15.8 1.0
CE1 A:HIS419 3.0 23.5 1.0
C1B A:HEA1002 3.1 14.4 1.0
C1C A:HEA1002 3.1 14.2 1.0
C4B A:HEA1002 3.1 16.0 1.0
CHA A:HEA1002 3.2 14.7 1.0
CD2 A:HIS419 3.3 21.3 1.0
CHD A:HEA1002 3.3 14.7 1.0
CHB A:HEA1002 3.4 15.2 1.0
CHC A:HEA1002 3.5 14.4 1.0
C3D A:HEA1002 4.1 14.7 1.0
C2D A:HEA1002 4.2 13.7 1.0
C2A A:HEA1002 4.2 12.9 1.0
ND1 A:HIS419 4.2 24.1 1.0
C3A A:HEA1002 4.2 14.4 1.0
C3C A:HEA1002 4.3 14.9 1.0
C2C A:HEA1002 4.3 13.5 1.0
C2B A:HEA1002 4.3 15.0 1.0
C3B A:HEA1002 4.3 15.1 1.0
CG A:HIS419 4.4 20.6 1.0
CU A:CU1005 4.8 26.9 1.0

Iron binding site 3 out of 4 in 1m56

Go back to Iron Binding Sites List in 1m56
Iron binding site 3 out of 4 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:30.0
occ:1.00
 FE G:HEA1001 0.0 30.0 1.0
ND G:HEA1001 1.9 26.1 1.0
NA G:HEA1001 1.9 27.4 1.0
NC G:HEA1001 2.0 27.1 1.0
NB G:HEA1001 2.0 27.5 1.0
NE2 G:HIS102 2.1 13.9 1.0
NE2 G:HIS421 2.2 16.9 1.0
CD2 G:HIS102 2.7 14.5 1.0
C4D G:HEA1001 2.9 26.6 1.0
C1D G:HEA1001 2.9 26.4 1.0
C1A G:HEA1001 2.9 28.7 1.0
C4A G:HEA1001 3.0 28.4 1.0
C4C G:HEA1001 3.0 27.0 1.0
C1C G:HEA1001 3.1 27.4 1.0
C4B G:HEA1001 3.1 27.5 1.0
C1B G:HEA1001 3.1 27.6 1.0
CE1 G:HIS421 3.1 17.1 1.0
CD2 G:HIS421 3.1 18.1 1.0
CE1 G:HIS102 3.2 14.5 1.0
CHA G:HEA1001 3.2 27.4 1.0
CHD G:HEA1001 3.3 25.8 1.0
CHC G:HEA1001 3.4 27.8 1.0
CHB G:HEA1001 3.4 27.9 1.0
CG G:HIS102 4.0 16.4 1.0
C3D G:HEA1001 4.1 25.2 1.0
C2D G:HEA1001 4.2 25.0 1.0
ND1 G:HIS102 4.2 16.0 1.0
C2A G:HEA1001 4.2 28.4 1.0
C3A G:HEA1001 4.2 29.0 1.0
ND1 G:HIS421 4.2 18.6 1.0
CG G:HIS421 4.3 17.4 1.0
C2C G:HEA1001 4.3 26.0 1.0
C3C G:HEA1001 4.3 25.8 1.0
C2B G:HEA1001 4.4 26.8 1.0
C3B G:HEA1001 4.4 26.9 1.0

Iron binding site 4 out of 4 in 1m56

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Iron binding site 4 out of 4 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1002

b:20.2
occ:1.00
 FE G:HEA1002 0.0 20.2 1.0
ND G:HEA1002 1.9 14.2 1.0
NA G:HEA1002 1.9 15.3 1.0
NC G:HEA1002 2.0 14.8 1.0
NB G:HEA1002 2.0 14.9 1.0
NE2 G:HIS419 2.1 21.3 1.0
C4D G:HEA1002 2.9 14.7 1.0
C1D G:HEA1002 2.9 14.1 1.0
C1A G:HEA1002 3.0 14.6 1.0
C4C G:HEA1002 3.0 14.8 1.0
C4A G:HEA1002 3.0 15.6 1.0
CE1 G:HIS419 3.0 24.3 1.0
C1B G:HEA1002 3.1 14.4 1.0
C4B G:HEA1002 3.1 16.4 1.0
C1C G:HEA1002 3.1 14.2 1.0
CD2 G:HIS419 3.2 21.7 1.0
CHB G:HEA1002 3.3 14.6 1.0
CHD G:HEA1002 3.3 14.5 1.0
CHA G:HEA1002 3.3 14.1 1.0
CHC G:HEA1002 3.6 13.8 1.0
C3D G:HEA1002 4.1 14.6 1.0
C2D G:HEA1002 4.1 13.8 1.0
ND1 G:HIS419 4.2 23.4 1.0
C3A G:HEA1002 4.2 13.6 1.0
C2A G:HEA1002 4.2 13.0 1.0
C3C G:HEA1002 4.3 14.4 1.0
CG G:HIS419 4.3 20.6 1.0
C2C G:HEA1002 4.3 13.3 1.0
C2B G:HEA1002 4.3 15.6 1.0
C3B G:HEA1002 4.3 15.1 1.0
CU G:CU1005 4.6 28.5 1.0

Reference:

M.Svensson-Ek, J.Abramson, G.Larsson, S.Tornroth, P.Brzezinski, S.Iwata. The X-Ray Crystal Structures of Wild-Type and Eq(I-286) Mutant Cytochrome C Oxidases From Rhodobacter Sphaeroides. J.Mol.Biol. V. 321 329 2002.
ISSN: ISSN 0022-2836
PubMed: 12144789
DOI: 10.1016/S0022-2836(02)00619-8
Page generated: Wed Jul 16 17:40:31 2025

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