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

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 in the Reduced State, PDB code: 3fye was solved by L.Qin, D.A.Mills, D.A.Proshlyakov, C.Hiser, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.613, 131.472, 176.192, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.1

Other elements in 3fye:

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

Iron binding site 1 out of 4 in 3fye

Go back to Iron Binding Sites List in 3fye
Iron binding site 1 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe567

b:26.8
occ:1.00
 FE A:HEA567 0.0 26.8 1.0
NB A:HEA567 2.0 28.7 1.0
NC A:HEA567 2.0 26.9 1.0
ND A:HEA567 2.0 28.2 1.0
NA A:HEA567 2.0 27.1 1.0
NE2 A:HIS102 2.0 25.6 1.0
NE2 A:HIS421 2.1 31.3 1.0
CE1 A:HIS421 2.9 30.3 1.0
CE1 A:HIS102 3.0 27.0 1.0
C4B A:HEA567 3.0 27.1 1.0
C1B A:HEA567 3.0 26.0 1.0
C1C A:HEA567 3.0 26.3 1.0
C4C A:HEA567 3.0 27.4 1.0
C1D A:HEA567 3.0 26.7 1.0
CD2 A:HIS102 3.0 24.9 1.0
C4A A:HEA567 3.0 27.0 1.0
C4D A:HEA567 3.0 26.3 1.0
C1A A:HEA567 3.0 26.5 1.0
CD2 A:HIS421 3.1 29.9 1.0
CHC A:HEA567 3.4 25.4 1.0
CHB A:HEA567 3.4 25.3 1.0
CHD A:HEA567 3.4 25.6 1.0
CHA A:HEA567 3.4 25.0 1.0
ND1 A:HIS102 4.1 24.4 1.0
ND1 A:HIS421 4.1 28.0 1.0
CG A:HIS102 4.1 25.4 1.0
C3B A:HEA567 4.2 26.7 1.0
C2B A:HEA567 4.2 27.4 1.0
CG A:HIS421 4.2 29.9 1.0
C2D A:HEA567 4.2 26.7 1.0
C3C A:HEA567 4.2 26.4 1.0
C3D A:HEA567 4.2 26.9 1.0
C2C A:HEA567 4.2 26.9 1.0
C3A A:HEA567 4.3 26.6 1.0
C2A A:HEA567 4.3 27.6 1.0
CG2 A:THR48 4.5 25.8 1.0

Iron binding site 2 out of 4 in 3fye

Go back to Iron Binding Sites List in 3fye
Iron binding site 2 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe568

b:38.1
occ:1.00
 FE A:HEA568 0.0 38.1 1.0
ND A:HEA568 2.0 32.2 1.0
NC A:HEA568 2.1 33.8 1.0
NB A:HEA568 2.2 39.4 1.0
NA A:HEA568 2.2 34.8 1.0
NE2 A:HIS419 2.2 32.5 1.0
C1C A:HEA568 3.0 32.4 1.0
C4D A:HEA568 3.0 34.9 1.0
C1D A:HEA568 3.1 34.1 1.0
C4C A:HEA568 3.1 32.5 1.0
C4B A:HEA568 3.1 39.3 1.0
CE1 A:HIS419 3.1 32.6 1.0
C1A A:HEA568 3.1 34.0 1.0
C4A A:HEA568 3.2 34.8 1.0
C1B A:HEA568 3.2 40.7 1.0
CD2 A:HIS419 3.2 30.8 1.0
O A:HOH601 3.3 55.7 1.0
CHC A:HEA568 3.4 36.2 1.0
CHA A:HEA568 3.4 33.1 1.0
CHD A:HEA568 3.5 33.8 1.0
CHB A:HEA568 3.6 36.2 1.0
C2C A:HEA568 4.3 35.9 1.0
ND1 A:HIS419 4.3 32.4 1.0
C3D A:HEA568 4.3 32.5 1.0
C3C A:HEA568 4.3 34.2 1.0
C2D A:HEA568 4.3 32.4 1.0
CG A:HIS419 4.4 30.5 1.0
C3B A:HEA568 4.4 40.9 1.0
C2A A:HEA568 4.4 34.7 1.0
C3A A:HEA568 4.4 34.8 1.0
C2B A:HEA568 4.4 39.3 1.0
CG1 A:VAL423 4.5 32.9 1.0
CA A:GLY398 4.9 37.9 1.0

Iron binding site 3 out of 4 in 3fye

Go back to Iron Binding Sites List in 3fye
Iron binding site 3 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe567

b:36.6
occ:1.00
 FE C:HEA567 0.0 36.6 1.0
NB C:HEA567 1.9 35.1 1.0
ND C:HEA567 2.0 33.5 1.0
NC C:HEA567 2.0 36.6 1.0
NA C:HEA567 2.0 35.5 1.0
NE2 C:HIS421 2.0 37.4 1.0
NE2 C:HIS102 2.1 41.6 1.0
CE1 C:HIS421 2.9 36.4 1.0
C4B C:HEA567 3.0 35.7 1.0
C1C C:HEA567 3.0 35.2 1.0
C1A C:HEA567 3.0 33.3 1.0
C1B C:HEA567 3.0 35.8 1.0
C4D C:HEA567 3.0 35.1 1.0
C1D C:HEA567 3.0 35.4 1.0
C4A C:HEA567 3.0 35.7 1.0
C4C C:HEA567 3.0 34.8 1.0
CE1 C:HIS102 3.1 40.4 1.0
CD2 C:HIS102 3.1 41.8 1.0
CD2 C:HIS421 3.1 37.1 1.0
CHC C:HEA567 3.4 34.6 1.0
CHA C:HEA567 3.4 34.1 1.0
CHD C:HEA567 3.4 35.0 1.0
CHB C:HEA567 3.4 33.3 1.0
ND1 C:HIS421 4.1 36.1 1.0
ND1 C:HIS102 4.2 40.8 1.0
C3B C:HEA567 4.2 35.2 1.0
CG C:HIS421 4.2 37.0 1.0
CG C:HIS102 4.2 41.2 1.0
C2B C:HEA567 4.2 34.5 1.0
C2A C:HEA567 4.2 35.3 1.0
C2D C:HEA567 4.2 32.7 1.0
C3D C:HEA567 4.2 34.3 1.0
C2C C:HEA567 4.2 36.9 1.0
C3A C:HEA567 4.2 34.7 1.0
C3C C:HEA567 4.3 35.3 1.0
CG2 C:THR48 4.7 39.4 1.0
OG C:SER425 5.0 45.7 1.0

Iron binding site 4 out of 4 in 3fye

Go back to Iron Binding Sites List in 3fye
Iron binding site 4 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe568

b:42.1
occ:1.00
 FE C:HEA568 0.0 42.1 1.0
ND C:HEA568 2.0 36.3 1.0
NA C:HEA568 2.1 39.9 1.0
NC C:HEA568 2.2 44.4 1.0
NE2 C:HIS419 2.2 36.1 1.0
NB C:HEA568 2.2 45.6 1.0
C4D C:HEA568 3.0 39.3 1.0
C1A C:HEA568 3.0 37.8 1.0
C1D C:HEA568 3.1 40.2 1.0
C1C C:HEA568 3.2 43.2 1.0
CE1 C:HIS419 3.2 38.1 1.0
C4C C:HEA568 3.2 42.3 1.0
C4A C:HEA568 3.2 40.9 1.0
CD2 C:HIS419 3.2 36.4 1.0
O C:HOH1601 3.2 48.2 1.0
C4B C:HEA568 3.2 46.9 1.0
C1B C:HEA568 3.3 45.7 1.0
CHA C:HEA568 3.3 38.5 1.0
CHD C:HEA568 3.5 41.4 1.0
CHC C:HEA568 3.5 44.3 1.0
CHB C:HEA568 3.6 42.3 1.0
C3D C:HEA568 4.2 38.1 1.0
C2D C:HEA568 4.3 38.7 1.0
ND1 C:HIS419 4.3 38.2 1.0
C2A C:HEA568 4.3 38.9 1.0
CG C:HIS419 4.3 35.6 1.0
C3A C:HEA568 4.4 38.7 1.0
C3C C:HEA568 4.4 43.3 1.0
C2C C:HEA568 4.4 44.4 1.0
C2B C:HEA568 4.5 45.9 1.0
C3B C:HEA568 4.5 47.6 1.0
CG1 C:VAL423 4.7 42.4 1.0
CA C:GLY398 5.0 42.7 1.0

Reference:

L.Qin, J.Liu, D.Mills, D.A.Proshlyakov, C.Hiser, S.Ferguson-Miller. Redox Dependent Conformational Changes in Cytochrome C Oxidase Suggest A Gating Mechanism For Proton Uptake. Biochemistry V. 48 5121 2009.
ISSN: ISSN 0006-2960
PubMed: 19397279
DOI: 10.1021/BI9001387
Page generated: Sun Aug 4 10:21:06 2024

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