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Iron in PDB 1m57: Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))

Enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))

All present enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)):
1.9.3.1;

Protein crystallography data

The structure of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)), PDB code: 1m57 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) 4.00 / 3.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 340.720, 340.720, 89.760, 90.00, 90.00, 120.00
R / Rfree (%) 29.3 / 32.9

Other elements in 1m57:

The structure of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)) 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 Rhodobacter Sphaeroides (Eq(I-286) Mutant)) (pdb code 1m57). 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 Rhodobacter Sphaeroides (Eq(I-286) Mutant)), PDB code: 1m57:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1m57

Go back to Iron Binding Sites List in 1m57
Iron binding site 1 out of 4 in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))


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 Rhodobacter Sphaeroides (Eq(I-286) Mutant)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:24.2
occ:1.00
FE A:HEA1001 0.0 24.2 1.0
ND A:HEA1001 1.8 22.6 1.0
NA A:HEA1001 1.9 24.2 1.0
NC A:HEA1001 1.9 22.8 1.0
NE2 A:HIS102 2.0 9.2 1.0
NB A:HEA1001 2.0 23.0 1.0
NE2 A:HIS421 2.0 17.1 1.0
CD2 A:HIS102 2.7 6.9 1.0
C4D A:HEA1001 2.9 23.0 1.0
C1D A:HEA1001 2.9 22.7 1.0
CE1 A:HIS421 2.9 18.3 1.0
C1A A:HEA1001 2.9 24.3 1.0
C4C A:HEA1001 2.9 22.1 1.0
C4A A:HEA1001 3.0 24.7 1.0
C1C A:HEA1001 3.0 23.5 1.0
CD2 A:HIS421 3.1 17.8 1.0
CE1 A:HIS102 3.1 10.0 1.0
C4B A:HEA1001 3.1 23.5 1.0
C1B A:HEA1001 3.1 23.8 1.0
CHA A:HEA1001 3.2 23.5 1.0
CHD A:HEA1001 3.3 22.4 1.0
CHB A:HEA1001 3.4 24.3 1.0
CHC A:HEA1001 3.5 23.4 1.0
CG A:HIS102 3.9 12.0 1.0
ND1 A:HIS102 4.0 12.7 1.0
ND1 A:HIS421 4.1 21.1 1.0
C3D A:HEA1001 4.1 22.6 1.0
CG A:HIS421 4.2 20.5 1.0
C2D A:HEA1001 4.2 22.3 1.0
C2A A:HEA1001 4.2 25.0 1.0
C3C A:HEA1001 4.2 21.7 1.0
C3A A:HEA1001 4.2 24.9 1.0
C2C A:HEA1001 4.3 22.8 1.0
C2B A:HEA1001 4.4 23.4 1.0
C3B A:HEA1001 4.4 23.1 1.0

Iron binding site 2 out of 4 in 1m57

Go back to Iron Binding Sites List in 1m57
Iron binding site 2 out of 4 in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))


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 Rhodobacter Sphaeroides (Eq(I-286) Mutant)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:14.6
occ:1.00
FE A:HEA1002 0.0 14.6 1.0
ND A:HEA1002 1.9 11.6 1.0
NA A:HEA1002 1.9 12.7 1.0
NC A:HEA1002 2.0 10.8 1.0
NB A:HEA1002 2.0 11.3 1.0
NE2 A:HIS419 2.2 17.1 1.0
C4D A:HEA1002 2.9 12.5 1.0
C1D A:HEA1002 2.9 11.1 1.0
C4C A:HEA1002 2.9 10.6 1.0
C1A A:HEA1002 3.0 12.7 1.0
CE1 A:HIS419 3.0 17.8 1.0
C4A A:HEA1002 3.0 13.0 1.0
C1C A:HEA1002 3.1 11.2 1.0
C4B A:HEA1002 3.1 11.0 1.0
C1B A:HEA1002 3.1 12.2 1.0
CHA A:HEA1002 3.2 12.9 1.0
CHD A:HEA1002 3.2 10.5 1.0
CD2 A:HIS419 3.3 17.8 1.0
CHB A:HEA1002 3.4 12.8 1.0
CHC A:HEA1002 3.4 11.2 1.0
C2D A:HEA1002 4.1 11.4 1.0
ND1 A:HIS419 4.1 17.2 1.0
C3D A:HEA1002 4.1 12.1 1.0
C3C A:HEA1002 4.2 11.2 1.0
C2A A:HEA1002 4.2 12.0 1.0
C2C A:HEA1002 4.3 11.2 1.0
C3A A:HEA1002 4.3 12.5 1.0
CG A:HIS419 4.3 16.2 1.0
C3B A:HEA1002 4.3 11.1 1.0
C2B A:HEA1002 4.4 11.8 1.0
CU A:CU1005 4.7 22.8 1.0

Iron binding site 3 out of 4 in 1m57

Go back to Iron Binding Sites List in 1m57
Iron binding site 3 out of 4 in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))


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 Rhodobacter Sphaeroides (Eq(I-286) Mutant)) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:24.7
occ:1.00
FE G:HEA1001 0.0 24.7 1.0
ND G:HEA1001 1.9 22.4 1.0
NC G:HEA1001 1.9 22.5 1.0
NA G:HEA1001 1.9 24.4 1.0
NB G:HEA1001 2.0 23.1 1.0
NE2 G:HIS102 2.0 9.4 1.0
NE2 G:HIS421 2.1 16.9 1.0
CD2 G:HIS102 2.7 7.8 1.0
C4D G:HEA1001 2.9 22.8 1.0
C1D G:HEA1001 2.9 22.1 1.0
C4C G:HEA1001 2.9 22.2 1.0
CE1 G:HIS421 2.9 18.1 1.0
C1A G:HEA1001 3.0 24.4 1.0
C4A G:HEA1001 3.0 25.0 1.0
C1C G:HEA1001 3.0 23.6 1.0
CD2 G:HIS421 3.1 17.7 1.0
C4B G:HEA1001 3.1 23.6 1.0
C1B G:HEA1001 3.1 23.6 1.0
CE1 G:HIS102 3.2 9.8 1.0
CHA G:HEA1001 3.2 23.6 1.0
CHD G:HEA1001 3.2 22.6 1.0
CHB G:HEA1001 3.4 24.8 1.0
CHC G:HEA1001 3.5 23.7 1.0
CG G:HIS102 3.9 12.5 1.0
ND1 G:HIS421 4.0 21.4 1.0
ND1 G:HIS102 4.1 12.5 1.0
C3D G:HEA1001 4.1 22.5 1.0
C2D G:HEA1001 4.1 22.0 1.0
CG G:HIS421 4.1 20.6 1.0
C3C G:HEA1001 4.2 21.7 1.0
C2A G:HEA1001 4.2 24.7 1.0
C2C G:HEA1001 4.2 22.9 1.0
C3A G:HEA1001 4.3 24.9 1.0
C3B G:HEA1001 4.4 23.0 1.0
C2B G:HEA1001 4.4 23.2 1.0
CE2 G:PHE420 4.9 14.5 1.0

Iron binding site 4 out of 4 in 1m57

Go back to Iron Binding Sites List in 1m57
Iron binding site 4 out of 4 in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))


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 Rhodobacter Sphaeroides (Eq(I-286) Mutant)) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1002

b:14.0
occ:1.00
FE G:HEA1002 0.0 14.0 1.0
ND G:HEA1002 1.9 11.8 1.0
NA G:HEA1002 1.9 12.8 1.0
NC G:HEA1002 2.0 11.2 1.0
NB G:HEA1002 2.0 11.5 1.0
NE2 G:HIS419 2.4 17.4 1.0
C1D G:HEA1002 2.9 11.4 1.0
C4D G:HEA1002 2.9 12.1 1.0
C4C G:HEA1002 2.9 11.0 1.0
C1A G:HEA1002 2.9 12.9 1.0
C4A G:HEA1002 3.0 13.1 1.0
C1C G:HEA1002 3.1 10.9 1.0
C4B G:HEA1002 3.1 11.0 1.0
C1B G:HEA1002 3.1 12.1 1.0
CE1 G:HIS419 3.2 18.4 1.0
CHD G:HEA1002 3.3 10.8 1.0
CHA G:HEA1002 3.3 12.6 1.0
CHB G:HEA1002 3.4 12.5 1.0
CD2 G:HIS419 3.4 18.2 1.0
CHC G:HEA1002 3.4 10.8 1.0
C2D G:HEA1002 4.1 11.5 1.0
C3D G:HEA1002 4.2 12.1 1.0
C3A G:HEA1002 4.2 12.9 1.0
C3C G:HEA1002 4.2 11.3 1.0
C2A G:HEA1002 4.2 12.4 1.0
C2C G:HEA1002 4.3 11.1 1.0
C3B G:HEA1002 4.3 11.1 1.0
C2B G:HEA1002 4.3 11.9 1.0
ND1 G:HIS419 4.4 17.1 1.0
CG G:HIS419 4.5 15.8 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: Sun Dec 13 14:23:02 2020

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