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Iron in PDB 3om3: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation in the Reduced State

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation in the Reduced State, PDB code: 3om3 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) 40.46 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.650, 132.365, 178.006, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 22.9

Other elements in 3om3:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation in the Reduced State 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 in the Reduced State (pdb code 3om3). 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 in the Reduced State, PDB code: 3om3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3om3

Go back to Iron Binding Sites List in 3om3
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 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 K362M Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1

b:32.9
occ:1.00
FE A:HEA1 0.0 32.9 1.0
NE2 A:HIS102 2.0 31.3 1.0
NB A:HEA1 2.0 35.2 1.0
NC A:HEA1 2.1 36.5 1.0
ND A:HEA1 2.1 36.1 1.0
NA A:HEA1 2.1 34.7 1.0
NE2 A:HIS421 2.2 36.7 1.0
CE1 A:HIS102 2.9 31.8 1.0
C4B A:HEA1 3.0 35.9 1.0
CD2 A:HIS102 3.0 33.3 1.0
C1B A:HEA1 3.0 34.3 1.0
CE1 A:HIS421 3.0 39.1 1.0
C1C A:HEA1 3.1 36.3 1.0
C4D A:HEA1 3.1 36.3 1.0
C4A A:HEA1 3.1 34.8 1.0
C1D A:HEA1 3.1 36.9 1.0
C1A A:HEA1 3.1 34.4 1.0
C4C A:HEA1 3.1 36.4 1.0
CD2 A:HIS421 3.2 37.6 1.0
CHC A:HEA1 3.4 35.2 1.0
CHB A:HEA1 3.4 35.4 1.0
CHA A:HEA1 3.5 35.5 1.0
CHD A:HEA1 3.5 35.6 1.0
ND1 A:HIS102 4.0 33.0 1.0
CG A:HIS102 4.1 33.2 1.0
ND1 A:HIS421 4.2 39.5 1.0
C3B A:HEA1 4.2 36.0 1.0
C2B A:HEA1 4.2 35.1 1.0
C2C A:HEA1 4.3 37.2 1.0
CG A:HIS421 4.3 38.4 1.0
C3D A:HEA1 4.3 36.3 1.0
C3A A:HEA1 4.3 34.2 1.0
C2A A:HEA1 4.3 34.5 1.0
C2D A:HEA1 4.3 36.5 1.0
C3C A:HEA1 4.3 36.3 1.0
CG2 A:THR48 4.5 35.3 1.0

Iron binding site 2 out of 4 in 3om3

Go back to Iron Binding Sites List in 3om3
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 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 K362M Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2

b:46.7
occ:1.00
FE A:HEA2 0.0 46.7 1.0
ND A:HEA2 2.1 44.0 1.0
NE2 A:HIS419 2.1 37.1 1.0
NA A:HEA2 2.1 47.7 1.0
NC A:HEA2 2.1 47.6 1.0
NB A:HEA2 2.2 50.4 1.0
C4D A:HEA2 3.0 45.3 1.0
CE1 A:HIS419 3.1 37.6 1.0
C1D A:HEA2 3.1 45.1 1.0
CD2 A:HIS419 3.1 37.3 1.0
C1A A:HEA2 3.1 47.2 1.0
C1C A:HEA2 3.1 48.0 1.0
C4C A:HEA2 3.2 47.7 1.0
C4A A:HEA2 3.2 48.8 1.0
C4B A:HEA2 3.2 50.4 1.0
C1B A:HEA2 3.2 51.1 1.0
CHA A:HEA2 3.4 46.4 1.0
CHD A:HEA2 3.5 46.7 1.0
CHC A:HEA2 3.5 49.3 1.0
CHB A:HEA2 3.5 49.1 1.0
ND1 A:HIS419 4.2 37.4 1.0
CG A:HIS419 4.2 36.4 1.0
C3D A:HEA2 4.3 44.4 1.0
C2D A:HEA2 4.3 44.3 1.0
C2A A:HEA2 4.4 48.0 1.0
C2C A:HEA2 4.4 47.9 1.0
C3C A:HEA2 4.4 47.6 1.0
C3A A:HEA2 4.4 48.9 1.0
C2B A:HEA2 4.4 51.7 1.0
C3B A:HEA2 4.4 52.3 1.0
CG1 A:VAL423 4.7 42.8 1.0
CA A:GLY398 4.9 48.9 1.0

Iron binding site 3 out of 4 in 3om3

Go back to Iron Binding Sites List in 3om3
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 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 K362M Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1

b:47.9
occ:1.00
FE C:HEA1 0.0 47.9 1.0
NB C:HEA1 2.0 45.0 1.0
NE2 C:HIS102 2.0 52.7 1.0
ND C:HEA1 2.0 45.5 1.0
NC C:HEA1 2.1 46.7 1.0
NE2 C:HIS421 2.1 47.9 1.0
NA C:HEA1 2.2 46.8 1.0
C4B C:HEA1 3.0 47.2 1.0
CE1 C:HIS102 3.0 52.3 1.0
CD2 C:HIS102 3.0 53.1 1.0
CE1 C:HIS421 3.0 48.7 1.0
C1D C:HEA1 3.0 46.4 1.0
C1B C:HEA1 3.1 46.3 1.0
C1C C:HEA1 3.1 47.0 1.0
C4C C:HEA1 3.1 45.9 1.0
C4D C:HEA1 3.1 46.0 1.0
C4A C:HEA1 3.2 46.2 1.0
C1A C:HEA1 3.2 45.9 1.0
CD2 C:HIS421 3.2 48.6 1.0
CHC C:HEA1 3.4 46.6 1.0
CHD C:HEA1 3.4 46.4 1.0
CHB C:HEA1 3.5 46.5 1.0
CHA C:HEA1 3.5 46.0 1.0
ND1 C:HIS102 4.1 52.7 1.0
CG C:HIS102 4.2 53.0 1.0
ND1 C:HIS421 4.2 49.9 1.0
C3B C:HEA1 4.2 48.5 1.0
C2B C:HEA1 4.3 47.5 1.0
C2D C:HEA1 4.3 46.5 1.0
C3D C:HEA1 4.3 46.3 1.0
CG C:HIS421 4.3 48.9 1.0
C3C C:HEA1 4.3 46.2 1.0
C2C C:HEA1 4.3 47.5 1.0
C3A C:HEA1 4.4 46.1 1.0
C2A C:HEA1 4.4 46.3 1.0
CG2 C:THR48 4.7 56.1 1.0

Iron binding site 4 out of 4 in 3om3

Go back to Iron Binding Sites List in 3om3
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 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 K362M Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe2

b:49.7
occ:1.00
FE C:HEA2 0.0 49.7 1.0
ND C:HEA2 2.0 52.1 1.0
NA C:HEA2 2.1 51.3 1.0
NE2 C:HIS419 2.1 46.5 1.0
NC C:HEA2 2.2 54.6 1.0
NB C:HEA2 2.2 53.6 1.0
C4D C:HEA2 3.0 51.9 1.0
C1D C:HEA2 3.0 52.6 1.0
C1A C:HEA2 3.0 49.9 1.0
CE1 C:HIS419 3.1 47.2 1.0
C4A C:HEA2 3.1 52.1 1.0
C4C C:HEA2 3.1 53.8 1.0
CD2 C:HIS419 3.2 47.0 1.0
C1B C:HEA2 3.2 54.1 1.0
C1C C:HEA2 3.2 54.0 1.0
C4B C:HEA2 3.2 54.4 1.0
CHA C:HEA2 3.3 51.5 1.0
CHD C:HEA2 3.4 53.1 1.0
CHB C:HEA2 3.5 52.9 1.0
CHC C:HEA2 3.6 53.9 1.0
C3D C:HEA2 4.2 51.5 1.0
ND1 C:HIS419 4.2 46.9 1.0
C2D C:HEA2 4.2 52.5 1.0
CG C:HIS419 4.3 47.4 1.0
C2A C:HEA2 4.3 50.5 1.0
C3A C:HEA2 4.3 51.0 1.0
C3C C:HEA2 4.4 54.1 1.0
C2C C:HEA2 4.4 54.3 1.0
C2B C:HEA2 4.4 54.7 1.0
C3B C:HEA2 4.5 55.3 1.0
CG1 C:VAL423 4.7 53.1 1.0
CA C:GLY398 4.9 52.2 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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