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Iron in PDB 3omi: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation:
1.9.3.1;

Protein crystallography data

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation, PDB code: 3omi was solved by J.Liu, L.Qin, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.84 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.064, 131.519, 175.674, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.5

Other elements in 3omi:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Cadmium (Cd) 4 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 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 with D132A Mutation (pdb code 3omi). 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 with D132A Mutation, PDB code: 3omi:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3omi

Go back to Iron Binding Sites List in 3omi
Iron binding site 1 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


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 with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe607

b:18.3
occ:1.00
 FE A:HEA607 0.0 18.3 1.0
NE2 A:HIS102 2.0 17.1 1.0
NE2 A:HIS421 2.0 19.1 1.0
NC A:HEA607 2.1 18.8 1.0
NB A:HEA607 2.1 19.4 1.0
ND A:HEA607 2.1 19.3 1.0
NA A:HEA607 2.1 17.1 1.0
CE1 A:HIS421 2.9 19.6 1.0
CE1 A:HIS102 3.0 18.3 1.0
C4C A:HEA607 3.0 19.4 1.0
C4B A:HEA607 3.1 18.4 1.0
C1D A:HEA607 3.1 19.4 1.0
CD2 A:HIS102 3.1 17.8 1.0
C1C A:HEA607 3.1 18.9 1.0
C1A A:HEA607 3.1 19.2 1.0
C4A A:HEA607 3.1 18.7 1.0
C4D A:HEA607 3.1 19.4 1.0
C1B A:HEA607 3.1 18.8 1.0
CD2 A:HIS421 3.1 19.9 1.0
CHD A:HEA607 3.4 18.2 1.0
CHC A:HEA607 3.4 17.2 1.0
CHB A:HEA607 3.5 16.7 1.0
CHA A:HEA607 3.5 16.8 1.0
ND1 A:HIS421 4.1 18.6 1.0
ND1 A:HIS102 4.1 15.2 1.0
CG A:HIS102 4.2 18.2 1.0
CG A:HIS421 4.2 20.3 1.0
C2C A:HEA607 4.3 19.0 1.0
C3C A:HEA607 4.3 18.1 1.0
C3B A:HEA607 4.3 19.5 1.0
C2D A:HEA607 4.3 19.9 1.0
C2A A:HEA607 4.3 18.3 1.0
C3A A:HEA607 4.3 17.8 1.0
C3D A:HEA607 4.3 19.9 1.0
C2B A:HEA607 4.3 18.5 1.0
CG2 A:THR48 4.5 17.9 1.0
CE1 A:PHE420 4.9 18.6 1.0

Iron binding site 2 out of 4 in 3omi

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Iron binding site 2 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


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 with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe608

b:24.3
occ:1.00
 FE A:HEA608 0.0 24.3 1.0
ND A:HEA608 2.0 21.7 1.0
NC A:HEA608 2.1 19.4 1.0
NB A:HEA608 2.1 25.3 1.0
NE2 A:HIS419 2.1 20.1 1.0
NA A:HEA608 2.1 24.4 1.0
O A:HOH744 2.1 18.4 1.0
C4D A:HEA608 3.1 21.8 1.0
C1D A:HEA608 3.1 23.2 1.0
C4B A:HEA608 3.1 23.2 1.0
CE1 A:HIS419 3.1 21.2 1.0
C4C A:HEA608 3.1 21.5 1.0
C1C A:HEA608 3.1 21.2 1.0
C1B A:HEA608 3.1 25.3 1.0
C1A A:HEA608 3.1 24.2 1.0
CD2 A:HIS419 3.1 20.8 1.0
C4A A:HEA608 3.1 24.3 1.0
CHC A:HEA608 3.4 21.6 1.0
CHA A:HEA608 3.4 21.8 1.0
CHD A:HEA608 3.4 21.7 1.0
CHB A:HEA608 3.5 23.6 1.0
O A:OH601 3.8 17.9 1.0
ND1 A:HIS419 4.2 20.6 1.0
CG A:HIS419 4.3 19.7 1.0
C3D A:HEA608 4.3 22.0 1.0
C2D A:HEA608 4.3 21.1 1.0
C3B A:HEA608 4.3 25.4 1.0
C2B A:HEA608 4.3 25.7 1.0
C2A A:HEA608 4.3 24.7 1.0
C2C A:HEA608 4.3 20.9 1.0
C3C A:HEA608 4.3 22.3 1.0
C3A A:HEA608 4.3 26.1 1.0
CU A:CU611 4.8 28.2 1.0
CG2 A:VAL423 5.0 23.4 1.0

Iron binding site 3 out of 4 in 3omi

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Iron binding site 3 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


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 with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe605

b:29.3
occ:1.00
 FE C:HEA605 0.0 29.3 1.0
NB C:HEA605 2.0 26.6 1.0
ND C:HEA605 2.0 25.6 1.0
NE2 C:HIS102 2.1 32.7 1.0
NE2 C:HIS421 2.1 30.2 1.0
NC C:HEA605 2.1 28.7 1.0
NA C:HEA605 2.1 26.3 1.0
C4B C:HEA605 3.0 28.8 1.0
CE1 C:HIS102 3.0 32.6 1.0
C1B C:HEA605 3.0 27.6 1.0
CE1 C:HIS421 3.0 29.7 1.0
C1C C:HEA605 3.0 28.2 1.0
C4D C:HEA605 3.0 27.1 1.0
C1D C:HEA605 3.1 28.3 1.0
CD2 C:HIS102 3.1 32.8 1.0
C1A C:HEA605 3.1 25.7 1.0
CD2 C:HIS421 3.1 29.0 1.0
C4A C:HEA605 3.1 27.3 1.0
C4C C:HEA605 3.1 28.9 1.0
CHC C:HEA605 3.3 27.2 1.0
CHA C:HEA605 3.4 25.4 1.0
CHB C:HEA605 3.5 26.3 1.0
CHD C:HEA605 3.5 28.3 1.0
ND1 C:HIS102 4.1 32.7 1.0
ND1 C:HIS421 4.2 28.5 1.0
C3B C:HEA605 4.2 28.4 1.0
CG C:HIS102 4.2 34.0 1.0
CG C:HIS421 4.2 28.9 1.0
C2B C:HEA605 4.2 26.3 1.0
C3D C:HEA605 4.3 27.1 1.0
C2D C:HEA605 4.3 26.1 1.0
C2C C:HEA605 4.3 29.6 1.0
C2A C:HEA605 4.3 26.6 1.0
C3C C:HEA605 4.3 28.9 1.0
C3A C:HEA605 4.3 26.6 1.0
CG2 C:THR48 4.6 33.5 1.0
CE1 C:PHE420 4.8 28.0 1.0

Iron binding site 4 out of 4 in 3omi

Go back to Iron Binding Sites List in 3omi
Iron binding site 4 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


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 with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe606

b:29.0
occ:1.00
 FE C:HEA606 0.0 29.0 1.0
NB C:HEA606 2.1 32.9 1.0
ND C:HEA606 2.1 29.4 1.0
NA C:HEA606 2.1 30.5 1.0
O C:HOH795 2.1 25.4 1.0
NE2 C:HIS419 2.2 26.7 1.0
NC C:HEA606 2.2 31.3 1.0
C4D C:HEA606 3.0 29.6 1.0
C4B C:HEA606 3.1 31.9 1.0
C1A C:HEA606 3.1 29.8 1.0
C1B C:HEA606 3.1 32.4 1.0
C1D C:HEA606 3.1 31.5 1.0
CD2 C:HIS419 3.1 27.4 1.0
C4A C:HEA606 3.1 32.1 1.0
C1C C:HEA606 3.1 31.5 1.0
CE1 C:HIS419 3.1 28.8 1.0
C4C C:HEA606 3.2 31.5 1.0
CHA C:HEA606 3.4 29.9 1.0
CHC C:HEA606 3.4 30.5 1.0
CHB C:HEA606 3.5 31.4 1.0
CHD C:HEA606 3.5 30.7 1.0
O C:OH601 3.7 27.1 1.0
ND1 C:HIS419 4.2 30.2 1.0
CG C:HIS419 4.3 28.2 1.0
C3D C:HEA606 4.3 29.7 1.0
C2A C:HEA606 4.3 30.5 1.0
C3B C:HEA606 4.3 32.0 1.0
C2B C:HEA606 4.3 31.8 1.0
C2D C:HEA606 4.3 30.0 1.0
C3A C:HEA606 4.3 30.3 1.0
C2C C:HEA606 4.4 32.7 1.0
C3C C:HEA606 4.4 32.9 1.0
CU C:CU608 4.8 35.5 1.0

Reference:

J.Liu, L.Qin, S.Ferguson-Miller. Crystallographic and Online Spectral Evidence For Role of Conformational Change and Conserved Water in Cytochrome Oxidase Proton Pump. Proc.Natl.Acad.Sci.Usa V. 108 1284 2011.
ISSN: ISSN 0027-8424
PubMed: 21205904
DOI: 10.1073/PNAS.1012846108
Page generated: Sun Aug 4 17:11:58 2024

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