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

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State:
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 in the Reduced State, PDB code: 3omn 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) 42.70 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.670, 132.033, 176.286, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 21.9

Other elements in 3omn:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State 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 in the Reduced State (pdb code 3omn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State, PDB code: 3omn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3omn

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Iron binding site 1 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1

b:24.8
occ:1.00
 FE A:HEA1 0.0 24.8 1.0
NE2 A:HIS102 2.0 21.7 1.0
ND A:HEA1 2.1 25.2 1.0
NB A:HEA1 2.1 25.7 1.0
NE2 A:HIS421 2.1 29.3 1.0
NC A:HEA1 2.1 24.9 1.0
NA A:HEA1 2.1 23.1 1.0
CE1 A:HIS421 2.9 29.8 1.0
CE1 A:HIS102 3.0 22.7 1.0
C4B A:HEA1 3.0 25.0 1.0
CD2 A:HIS102 3.0 21.6 1.0
C4D A:HEA1 3.1 25.8 1.0
C1C A:HEA1 3.1 23.8 1.0
C1D A:HEA1 3.1 25.3 1.0
C1A A:HEA1 3.1 23.9 1.0
C4C A:HEA1 3.1 25.1 1.0
C1B A:HEA1 3.1 25.1 1.0
C4A A:HEA1 3.1 24.2 1.0
CD2 A:HIS421 3.2 27.6 1.0
CHC A:HEA1 3.4 23.2 1.0
CHA A:HEA1 3.4 23.1 1.0
CHD A:HEA1 3.5 24.1 1.0
CHB A:HEA1 3.5 22.4 1.0
ND1 A:HIS421 4.1 27.7 1.0
ND1 A:HIS102 4.1 21.6 1.0
CG A:HIS102 4.2 23.7 1.0
CG A:HIS421 4.2 27.5 1.0
C3B A:HEA1 4.3 25.1 1.0
C3D A:HEA1 4.3 25.7 1.0
C2D A:HEA1 4.3 25.5 1.0
C2B A:HEA1 4.3 24.8 1.0
C2C A:HEA1 4.3 23.9 1.0
C2A A:HEA1 4.3 22.6 1.0
C3C A:HEA1 4.3 23.9 1.0
C3A A:HEA1 4.3 22.5 1.0
CG2 A:THR48 4.6 25.1 1.0

Iron binding site 2 out of 6 in 3omn

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Iron binding site 2 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2

b:22.1
occ:0.40
 FE A:HEA2 0.0 22.1 0.4
ND A:HEA2 1.0 33.9 0.6
FE A:HEA2 1.3 32.2 0.6
C1D A:HEA2 1.9 33.2 0.6
ND A:HEA2 2.0 22.3 0.4
NA A:HEA2 2.0 21.3 0.4
NC A:HEA2 2.1 33.5 0.6
NC A:HEA2 2.1 22.4 0.4
O A:HOH701 2.1 12.9 0.4
NB A:HEA2 2.2 24.6 0.4
C4D A:HEA2 2.3 33.5 0.6
NE2 A:HIS419 2.4 31.1 0.6
CHD A:HEA2 2.4 33.0 0.6
C4C A:HEA2 2.5 33.3 0.6
O A:HOH701 2.7 31.0 0.6
NA A:HEA2 2.7 33.2 0.6
NE2 A:HIS419 2.7 29.1 0.4
C4D A:HEA2 3.0 22.3 0.4
C1A A:HEA2 3.0 21.8 0.4
C1D A:HEA2 3.1 22.9 0.4
C4A A:HEA2 3.1 22.4 0.4
CHA A:HEA2 3.1 33.1 0.6
C4C A:HEA2 3.1 22.2 0.4
C2D A:HEA2 3.1 33.1 0.6
C1C A:HEA2 3.1 22.9 0.4
C1B A:HEA2 3.2 24.3 0.4
C4B A:HEA2 3.2 23.5 0.4
C1A A:HEA2 3.2 33.6 0.6
NB A:HEA2 3.3 34.9 0.6
C3D A:HEA2 3.3 33.4 0.6
CD2 A:HIS419 3.3 29.9 0.6
CHA A:HEA2 3.3 21.7 0.4
C1C A:HEA2 3.4 32.9 0.6
CE1 A:HIS419 3.4 31.1 0.6
CHD A:HEA2 3.5 23.0 0.4
CHB A:HEA2 3.5 23.0 0.4
CD2 A:HIS419 3.5 27.7 0.4
CHC A:HEA2 3.5 22.8 0.4
O A:OH802 3.7 8.4 0.4
CE1 A:HIS419 3.8 28.6 0.4
C3C A:HEA2 3.9 33.2 0.6
C4A A:HEA2 4.0 33.2 0.6
C4B A:HEA2 4.1 35.3 0.6
CHC A:HEA2 4.1 33.7 0.6
C3D A:HEA2 4.2 22.6 0.4
C2A A:HEA2 4.2 22.4 0.4
C2D A:HEA2 4.3 22.6 0.4
C2C A:HEA2 4.3 33.4 0.6
C3A A:HEA2 4.3 22.8 0.4
C1B A:HEA2 4.3 34.9 0.6
C3C A:HEA2 4.4 23.3 0.4
C2C A:HEA2 4.4 22.9 0.4
C2B A:HEA2 4.4 24.2 0.4
C3B A:HEA2 4.4 23.5 0.4
CG A:HIS419 4.5 28.2 0.6
ND1 A:HIS419 4.5 30.8 0.6
CMD A:HEA2 4.5 33.0 0.6
CHB A:HEA2 4.5 33.7 0.6
CG2 A:VAL423 4.6 29.5 0.6
C2A A:HEA2 4.6 33.2 0.6
CG A:HIS419 4.7 27.3 0.4
ND1 A:HIS419 4.8 28.3 0.4
CAD A:HEA2 4.8 33.0 0.6
CU A:CU15 4.8 37.3 1.0
CB A:PHE420 4.9 26.4 1.0
C3A A:HEA2 4.9 33.8 0.6

Iron binding site 3 out of 6 in 3omn

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Iron binding site 3 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2

b:32.2
occ:0.60
 FE A:HEA2 0.0 32.2 0.6
NB A:HEA2 1.3 24.6 0.4
FE A:HEA2 1.3 22.1 0.4
NA A:HEA2 2.0 21.3 0.4
C1B A:HEA2 2.0 24.3 0.4
NB A:HEA2 2.0 34.9 0.6
NC A:HEA2 2.1 33.5 0.6
NA A:HEA2 2.1 33.2 0.6
NE2 A:HIS419 2.1 29.1 0.4
NE2 A:HIS419 2.1 31.1 0.6
ND A:HEA2 2.2 33.9 0.6
CHB A:HEA2 2.4 23.0 0.4
C4A A:HEA2 2.5 22.4 0.4
C4B A:HEA2 2.5 23.5 0.4
CE1 A:HIS419 2.7 31.1 0.6
O A:HOH701 2.8 31.0 0.6
NC A:HEA2 2.9 22.4 0.4
O A:HOH701 2.9 12.9 0.4
CE1 A:HIS419 3.0 28.6 0.4
C4B A:HEA2 3.0 35.3 0.6
C1C A:HEA2 3.0 32.9 0.6
C1B A:HEA2 3.1 34.9 0.6
C4A A:HEA2 3.1 33.2 0.6
C4C A:HEA2 3.1 33.3 0.6
C1A A:HEA2 3.2 33.6 0.6
C4D A:HEA2 3.2 33.5 0.6
C2B A:HEA2 3.2 24.2 0.4
C1D A:HEA2 3.2 33.2 0.6
CD2 A:HIS419 3.2 27.7 0.4
ND A:HEA2 3.3 22.3 0.4
CHC A:HEA2 3.3 22.8 0.4
C1A A:HEA2 3.3 21.8 0.4
CD2 A:HIS419 3.3 29.9 0.6
CHC A:HEA2 3.3 33.7 0.6
CHB A:HEA2 3.4 33.7 0.6
C3B A:HEA2 3.4 23.5 0.4
C1C A:HEA2 3.4 22.9 0.4
CHD A:HEA2 3.5 33.0 0.6
CHA A:HEA2 3.5 33.1 0.6
C3A A:HEA2 3.9 22.8 0.4
ND1 A:HIS419 3.9 30.8 0.6
CHA A:HEA2 4.0 21.7 0.4
C4D A:HEA2 4.0 22.3 0.4
C4C A:HEA2 4.1 22.2 0.4
ND1 A:HIS419 4.2 28.3 0.4
CG A:HIS419 4.2 28.2 0.6
C2A A:HEA2 4.2 22.4 0.4
C3B A:HEA2 4.2 35.7 0.6
C2B A:HEA2 4.2 35.1 0.6
C2C A:HEA2 4.3 33.4 0.6
CG A:HIS419 4.3 27.3 0.4
C3C A:HEA2 4.3 33.2 0.6
C3A A:HEA2 4.3 33.8 0.6
C1D A:HEA2 4.4 22.9 0.4
C2A A:HEA2 4.4 33.2 0.6
C2D A:HEA2 4.4 33.1 0.6
C3D A:HEA2 4.4 33.4 0.6
CMB A:HEA2 4.6 24.0 0.4
CG2 A:VAL423 4.6 29.5 0.6
CA A:GLY398 4.6 38.4 1.0
CHD A:HEA2 4.7 23.0 0.4
O A:OH802 4.7 8.4 0.4
C2C A:HEA2 4.8 22.9 0.4
C11 A:HEA2 5.0 22.9 0.4

Iron binding site 4 out of 6 in 3omn

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Iron binding site 4 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1

b:35.3
occ:1.00
 FE C:HEA1 0.0 35.3 1.0
NB C:HEA1 2.0 34.2 1.0
ND C:HEA1 2.0 33.2 1.0
NE2 C:HIS421 2.1 36.5 1.0
NC C:HEA1 2.1 35.4 1.0
NE2 C:HIS102 2.1 40.6 1.0
NA C:HEA1 2.2 32.7 1.0
CE1 C:HIS421 2.9 35.9 1.0
C4B C:HEA1 3.0 35.1 1.0
C1C C:HEA1 3.0 34.4 1.0
C4D C:HEA1 3.0 33.2 1.0
C1B C:HEA1 3.1 35.2 1.0
C1D C:HEA1 3.1 34.2 1.0
CE1 C:HIS102 3.1 39.6 1.0
C1A C:HEA1 3.1 31.2 1.0
CD2 C:HIS102 3.1 40.3 1.0
C4C C:HEA1 3.1 34.6 1.0
C4A C:HEA1 3.2 33.3 1.0
CD2 C:HIS421 3.2 36.1 1.0
CHC C:HEA1 3.3 34.1 1.0
CHA C:HEA1 3.4 32.4 1.0
CHD C:HEA1 3.5 34.3 1.0
CHB C:HEA1 3.5 32.4 1.0
ND1 C:HIS421 4.1 35.8 1.0
ND1 C:HIS102 4.2 39.6 1.0
C3B C:HEA1 4.2 35.0 1.0
CG C:HIS102 4.2 39.9 1.0
CG C:HIS421 4.3 35.5 1.0
C2B C:HEA1 4.3 33.1 1.0
C3D C:HEA1 4.3 32.8 1.0
C2D C:HEA1 4.3 31.8 1.0
C2C C:HEA1 4.3 36.4 1.0
C2A C:HEA1 4.3 32.4 1.0
C3C C:HEA1 4.3 34.6 1.0
C3A C:HEA1 4.4 32.1 1.0
OG1 C:THR48 4.6 41.7 1.0
CE1 C:PHE420 5.0 34.8 1.0

Iron binding site 5 out of 6 in 3omn

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Iron binding site 5 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe2

b:27.4
occ:0.40
 FE C:HEA2 0.0 27.4 0.4
ND C:HEA2 1.0 39.3 0.6
FE C:HEA2 1.3 36.6 0.6
C1D C:HEA2 1.9 39.7 0.6
NA C:HEA2 2.0 28.6 0.4
NB C:HEA2 2.1 29.5 0.4
ND C:HEA2 2.1 27.4 0.4
O C:HOH701 2.1 10.1 0.4
NC C:HEA2 2.1 40.1 0.6
NC C:HEA2 2.1 28.1 0.4
C4D C:HEA2 2.2 39.5 0.6
CHD C:HEA2 2.5 39.4 0.6
C4C C:HEA2 2.6 40.1 0.6
NE2 C:HIS419 2.6 34.7 0.6
NE2 C:HIS419 2.6 34.7 0.4
NA C:HEA2 2.7 39.8 0.6
CHA C:HEA2 3.0 39.1 0.6
C1A C:HEA2 3.0 27.9 0.4
C4A C:HEA2 3.0 28.6 0.4
C1B C:HEA2 3.1 29.3 0.4
C4D C:HEA2 3.1 27.9 0.4
O C:OH802 3.1 21.9 0.4
C4B C:HEA2 3.1 28.9 0.4
C2D C:HEA2 3.1 39.1 0.6
C1D C:HEA2 3.1 28.4 0.4
C1C C:HEA2 3.1 28.3 0.4
C4C C:HEA2 3.1 28.0 0.4
C1A C:HEA2 3.2 39.4 0.6
C3D C:HEA2 3.3 38.9 0.6
NB C:HEA2 3.3 42.1 0.6
CHA C:HEA2 3.4 28.1 0.4
CHB C:HEA2 3.4 28.9 0.4
CD2 C:HIS419 3.4 35.0 0.6
C1C C:HEA2 3.4 40.0 0.6
CHC C:HEA2 3.5 28.2 0.4
CHD C:HEA2 3.5 27.9 0.4
CD2 C:HIS419 3.5 34.7 0.4
CE1 C:HIS419 3.6 36.1 0.6
CE1 C:HIS419 3.6 35.1 0.4
C4A C:HEA2 3.9 40.4 0.6
C3C C:HEA2 4.0 40.0 0.6
C4B C:HEA2 4.2 41.8 0.6
CHC C:HEA2 4.2 41.0 0.6
C2A C:HEA2 4.2 28.5 0.4
C3A C:HEA2 4.3 28.1 0.4
C2B C:HEA2 4.3 29.3 0.4
C3D C:HEA2 4.3 28.0 0.4
C1B C:HEA2 4.3 41.9 0.6
C3B C:HEA2 4.3 28.6 0.4
C2D C:HEA2 4.3 28.2 0.4
C2C C:HEA2 4.3 40.8 0.6
C2C C:HEA2 4.4 28.0 0.4
C3C C:HEA2 4.4 28.6 0.4
CMD C:HEA2 4.5 38.8 0.6
CHB C:HEA2 4.5 40.4 0.6
C2A C:HEA2 4.6 39.5 0.6
CG2 C:VAL423 4.6 37.5 0.6
CG C:HIS419 4.6 34.7 0.6
CU C:CU1553 4.7 45.1 1.0
CG C:HIS419 4.7 34.4 0.4
ND1 C:HIS419 4.7 36.5 0.6
CAD C:HEA2 4.7 38.1 0.6
ND1 C:HIS419 4.7 35.3 0.4
C3A C:HEA2 4.9 39.4 0.6
CB C:PHE420 5.0 34.5 1.0

Iron binding site 6 out of 6 in 3omn

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Iron binding site 6 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe2

b:36.6
occ:0.60
 FE C:HEA2 0.0 36.6 0.6
FE C:HEA2 1.3 27.4 0.4
NB C:HEA2 1.3 29.5 0.4
C1B C:HEA2 2.0 29.3 0.4
NA C:HEA2 2.0 28.6 0.4
NA C:HEA2 2.1 39.8 0.6
ND C:HEA2 2.1 39.3 0.6
NC C:HEA2 2.1 40.1 0.6
NE2 C:HIS419 2.1 34.7 0.4
NB C:HEA2 2.1 42.1 0.6
NE2 C:HIS419 2.2 34.7 0.6
CHB C:HEA2 2.5 28.9 0.4
C4B C:HEA2 2.5 28.9 0.4
C4A C:HEA2 2.5 28.6 0.4
O C:HOH701 2.5 10.1 0.4
NC C:HEA2 2.8 28.1 0.4
CE1 C:HIS419 2.9 35.1 0.4
CE1 C:HIS419 2.9 36.1 0.6
C1A C:HEA2 3.1 39.4 0.6
C4D C:HEA2 3.1 39.5 0.6
C4A C:HEA2 3.1 40.4 0.6
C1C C:HEA2 3.1 40.0 0.6
C1D C:HEA2 3.1 39.7 0.6
C4C C:HEA2 3.1 40.1 0.6
C1B C:HEA2 3.1 41.9 0.6
C4B C:HEA2 3.2 41.8 0.6
C2B C:HEA2 3.2 29.3 0.4
CD2 C:HIS419 3.3 35.0 0.6
CHC C:HEA2 3.3 28.2 0.4
ND C:HEA2 3.3 27.4 0.4
CD2 C:HIS419 3.3 34.7 0.4
C1A C:HEA2 3.3 27.9 0.4
CHA C:HEA2 3.4 39.1 0.6
C1C C:HEA2 3.4 28.3 0.4
C3B C:HEA2 3.4 28.6 0.4
CHC C:HEA2 3.5 41.0 0.6
CHB C:HEA2 3.5 40.4 0.6
CHD C:HEA2 3.5 39.4 0.6
C3A C:HEA2 3.9 28.1 0.4
O C:OH802 4.1 21.9 0.4
C4C C:HEA2 4.1 28.0 0.4
CHA C:HEA2 4.1 28.1 0.4
C4D C:HEA2 4.1 27.9 0.4
ND1 C:HIS419 4.1 36.5 0.6
ND1 C:HIS419 4.1 35.3 0.4
C2A C:HEA2 4.3 28.5 0.4
CG C:HIS419 4.3 34.7 0.6
C2A C:HEA2 4.3 39.5 0.6
C3A C:HEA2 4.3 39.4 0.6
CG C:HIS419 4.3 34.4 0.4
C3D C:HEA2 4.3 38.9 0.6
C2C C:HEA2 4.3 40.8 0.6
C2D C:HEA2 4.3 39.1 0.6
C1D C:HEA2 4.3 28.4 0.4
C3C C:HEA2 4.4 40.0 0.6
C2B C:HEA2 4.4 42.2 0.6
C3B C:HEA2 4.4 42.9 0.6
CMB C:HEA2 4.5 28.8 0.4
CA C:GLY398 4.6 41.8 1.0
CHD C:HEA2 4.6 27.9 0.4
CG2 C:VAL423 4.7 37.5 0.6
C2C C:HEA2 4.8 28.0 0.4
C11 C:HEA2 4.9 29.0 0.4

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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