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Iron in PDB 3oma: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation, PDB code: 3oma 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) 50.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.019, 131.579, 176.626, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.9

Other elements in 3oma:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation 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 with K362M Mutation (pdb code 3oma). 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 K362M Mutation, PDB code: 3oma:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3oma

Go back to Iron Binding Sites List in 3oma
Iron binding site 1 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1

b:24.9
occ:1.00
 FE A:HEA1 0.0 24.9 1.0
NE2 A:HIS421 2.0 25.6 1.0
NB A:HEA1 2.0 25.1 1.0
NE2 A:HIS102 2.0 22.4 1.0
NC A:HEA1 2.1 26.9 1.0
ND A:HEA1 2.1 26.3 1.0
NA A:HEA1 2.1 28.0 1.0
CE1 A:HIS421 2.9 26.1 1.0
CD2 A:HIS102 3.0 24.6 1.0
C1B A:HEA1 3.0 27.1 1.0
C1D A:HEA1 3.0 26.8 1.0
C4B A:HEA1 3.0 26.0 1.0
C4C A:HEA1 3.1 26.7 1.0
C1C A:HEA1 3.1 25.4 1.0
C4A A:HEA1 3.1 26.8 1.0
CE1 A:HIS102 3.1 25.8 1.0
CD2 A:HIS421 3.1 26.9 1.0
C4D A:HEA1 3.1 26.1 1.0
C1A A:HEA1 3.1 26.4 1.0
CHD A:HEA1 3.4 25.1 1.0
CHB A:HEA1 3.4 25.0 1.0
CHC A:HEA1 3.4 25.5 1.0
CHA A:HEA1 3.5 25.7 1.0
ND1 A:HIS421 4.0 24.9 1.0
CG A:HIS102 4.1 24.1 1.0
ND1 A:HIS102 4.2 23.1 1.0
CG A:HIS421 4.2 26.9 1.0
C3B A:HEA1 4.3 26.8 1.0
C2B A:HEA1 4.3 26.1 1.0
C2D A:HEA1 4.3 26.7 1.0
C2C A:HEA1 4.3 25.9 1.0
C3A A:HEA1 4.3 26.9 1.0
C3C A:HEA1 4.3 25.2 1.0
C3D A:HEA1 4.3 26.8 1.0
C2A A:HEA1 4.3 26.4 1.0
CG2 A:THR48 4.5 26.0 1.0

Iron binding site 2 out of 4 in 3oma

Go back to Iron Binding Sites List in 3oma
Iron binding site 2 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2

b:32.2
occ:1.00
 FE A:HEA2 0.0 32.2 1.0
NE2 A:HIS419 2.0 29.6 1.0
ND A:HEA2 2.0 30.9 1.0
NB A:HEA2 2.1 34.8 1.0
NC A:HEA2 2.1 32.7 1.0
NA A:HEA2 2.1 31.6 1.0
O A:HOH727 2.2 32.8 1.0
CE1 A:HIS419 2.9 30.8 1.0
C4D A:HEA2 3.0 31.4 1.0
C4B A:HEA2 3.1 34.5 1.0
C1A A:HEA2 3.1 32.5 1.0
C1D A:HEA2 3.1 33.3 1.0
CD2 A:HIS419 3.1 30.0 1.0
C1C A:HEA2 3.1 31.7 1.0
C1B A:HEA2 3.1 34.4 1.0
C4C A:HEA2 3.2 33.3 1.0
C4A A:HEA2 3.2 32.1 1.0
CHA A:HEA2 3.4 32.4 1.0
CHC A:HEA2 3.4 32.9 1.0
CHD A:HEA2 3.5 32.7 1.0
CHB A:HEA2 3.5 33.0 1.0
ND1 A:HIS419 4.0 31.8 1.0
O A:OH706 4.1 36.1 1.0
CG A:HIS419 4.2 29.9 1.0
C3D A:HEA2 4.2 31.6 1.0
C2D A:HEA2 4.3 31.2 1.0
C3B A:HEA2 4.3 35.4 1.0
C2B A:HEA2 4.3 34.4 1.0
C2A A:HEA2 4.3 34.4 1.0
C2C A:HEA2 4.3 33.3 1.0
C3A A:HEA2 4.4 33.5 1.0
C3C A:HEA2 4.4 33.7 1.0
CG2 A:VAL423 4.9 34.0 1.0
CU A:CU5 5.0 35.2 1.0

Iron binding site 3 out of 4 in 3oma

Go back to Iron Binding Sites List in 3oma
Iron binding site 3 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1

b:36.8
occ:1.00
 FE C:HEA1 0.0 36.8 1.0
NE2 C:HIS421 1.9 38.8 1.0
NB C:HEA1 2.0 35.0 1.0
ND C:HEA1 2.0 33.5 1.0
NE2 C:HIS102 2.1 41.3 1.0
NA C:HEA1 2.1 34.0 1.0
NC C:HEA1 2.1 35.8 1.0
CE1 C:HIS421 2.8 37.3 1.0
C4B C:HEA1 3.0 36.0 1.0
C4D C:HEA1 3.0 33.6 1.0
C1B C:HEA1 3.0 35.9 1.0
C1A C:HEA1 3.1 33.0 1.0
CD2 C:HIS102 3.1 41.1 1.0
C1C C:HEA1 3.1 34.3 1.0
CD2 C:HIS421 3.1 37.8 1.0
CE1 C:HIS102 3.1 41.1 1.0
C4A C:HEA1 3.1 34.5 1.0
C1D C:HEA1 3.1 34.5 1.0
C4C C:HEA1 3.2 35.6 1.0
CHA C:HEA1 3.4 32.9 1.0
CHC C:HEA1 3.4 34.8 1.0
CHB C:HEA1 3.5 33.6 1.0
CHD C:HEA1 3.5 34.9 1.0
ND1 C:HIS421 3.9 36.8 1.0
CG C:HIS421 4.1 37.0 1.0
ND1 C:HIS102 4.2 40.6 1.0
CG C:HIS102 4.2 41.6 1.0
C3B C:HEA1 4.2 36.1 1.0
C2B C:HEA1 4.2 34.4 1.0
C3D C:HEA1 4.3 33.2 1.0
C2A C:HEA1 4.3 33.7 1.0
C3A C:HEA1 4.3 33.9 1.0
C2D C:HEA1 4.3 32.8 1.0
C2C C:HEA1 4.3 37.3 1.0
C3C C:HEA1 4.4 34.7 1.0
CG2 C:THR48 4.6 41.7 1.0

Iron binding site 4 out of 4 in 3oma

Go back to Iron Binding Sites List in 3oma
Iron binding site 4 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe2

b:34.6
occ:1.00
 FE C:HEA2 0.0 34.6 1.0
ND C:HEA2 2.1 38.6 1.0
NB C:HEA2 2.1 40.4 1.0
O C:HOH556 2.1 33.9 1.0
NA C:HEA2 2.1 36.6 1.0
NC C:HEA2 2.1 40.1 1.0
NE2 C:HIS419 2.3 35.3 1.0
C4D C:HEA2 3.0 38.2 1.0
C4B C:HEA2 3.0 39.5 1.0
C1A C:HEA2 3.1 37.0 1.0
C1C C:HEA2 3.1 39.5 1.0
C1B C:HEA2 3.1 40.4 1.0
CE1 C:HIS419 3.1 36.6 1.0
C1D C:HEA2 3.1 40.0 1.0
C4A C:HEA2 3.2 38.0 1.0
C4C C:HEA2 3.2 40.3 1.0
CD2 C:HIS419 3.3 35.8 1.0
CHA C:HEA2 3.4 37.7 1.0
CHC C:HEA2 3.4 38.7 1.0
CHB C:HEA2 3.5 38.5 1.0
CHD C:HEA2 3.6 38.7 1.0
O C:OH706 3.9 48.3 1.0
C3D C:HEA2 4.3 38.1 1.0
C3B C:HEA2 4.3 39.1 1.0
ND1 C:HIS419 4.3 37.2 1.0
C2A C:HEA2 4.3 37.2 1.0
C2D C:HEA2 4.3 37.3 1.0
C2B C:HEA2 4.3 38.3 1.0
C3A C:HEA2 4.3 36.8 1.0
C2C C:HEA2 4.4 40.7 1.0
C3C C:HEA2 4.4 41.0 1.0
CG C:HIS419 4.4 35.7 1.0
CU C:CU553 4.9 42.4 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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