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

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide:
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 Bound with Cyanide, PDB code: 3fyi 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.344, 131.877, 176.160, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.9

Other elements in 3fyi:

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

Iron binding site 1 out of 4 in 3fyi

Go back to Iron Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe567

b:23.4
occ:1.00
 FE A:HEA567 0.0 23.4 1.0
NB A:HEA567 2.0 24.6 1.0
ND A:HEA567 2.0 24.3 1.0
NC A:HEA567 2.0 24.5 1.0
NA A:HEA567 2.0 23.5 1.0
NE2 A:HIS102 2.0 22.2 1.0
NE2 A:HIS421 2.1 26.6 1.0
CE1 A:HIS421 3.0 27.6 1.0
CE1 A:HIS102 3.0 23.5 1.0
C4B A:HEA567 3.0 24.1 1.0
C4D A:HEA567 3.0 23.2 1.0
C1D A:HEA567 3.0 24.0 1.0
C1C A:HEA567 3.0 23.7 1.0
C1A A:HEA567 3.0 23.1 1.0
C4C A:HEA567 3.0 24.5 1.0
C1B A:HEA567 3.0 23.3 1.0
C4A A:HEA567 3.0 23.6 1.0
CD2 A:HIS102 3.1 22.6 1.0
CD2 A:HIS421 3.2 26.4 1.0
CHC A:HEA567 3.4 22.9 1.0
CHA A:HEA567 3.4 21.0 1.0
CHD A:HEA567 3.4 21.9 1.0
CHB A:HEA567 3.4 22.3 1.0
ND1 A:HIS102 4.1 21.2 1.0
ND1 A:HIS421 4.1 26.4 1.0
CG A:HIS102 4.2 22.5 1.0
C3B A:HEA567 4.2 23.8 1.0
C2D A:HEA567 4.2 22.5 1.0
C3D A:HEA567 4.2 24.2 1.0
C2B A:HEA567 4.2 22.0 1.0
C2A A:HEA567 4.2 22.5 1.0
CG A:HIS421 4.2 27.0 1.0
C3A A:HEA567 4.2 22.5 1.0
C2C A:HEA567 4.2 24.4 1.0
C3C A:HEA567 4.3 23.8 1.0
CG2 A:THR48 4.6 23.3 1.0

Iron binding site 2 out of 4 in 3fyi

Go back to Iron Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe568

b:33.1
occ:1.00
 FE A:HEA568 0.0 33.1 1.0
ND A:HEA568 2.1 26.4 1.0
NB A:HEA568 2.1 32.4 1.0
NC A:HEA568 2.1 28.8 1.0
NA A:HEA568 2.2 30.9 1.0
C A:CYN572 2.2 31.7 1.0
NE2 A:HIS419 2.3 29.7 1.0
C4D A:HEA568 3.1 28.1 1.0
C1A A:HEA568 3.1 29.2 1.0
C4C A:HEA568 3.1 27.7 1.0
C1D A:HEA568 3.1 28.3 1.0
C1C A:HEA568 3.1 28.8 1.0
C4B A:HEA568 3.1 33.5 1.0
C1B A:HEA568 3.1 34.1 1.0
C4A A:HEA568 3.1 31.4 1.0
CE1 A:HIS419 3.2 28.4 1.0
CD2 A:HIS419 3.3 29.7 1.0
N A:CYN572 3.3 32.3 1.0
CHA A:HEA568 3.4 28.5 1.0
CHC A:HEA568 3.5 31.1 1.0
CHD A:HEA568 3.5 27.7 1.0
CHB A:HEA568 3.5 32.9 1.0
C3D A:HEA568 4.3 28.3 1.0
C3C A:HEA568 4.3 29.3 1.0
C2A A:HEA568 4.3 30.5 1.0
C2C A:HEA568 4.3 30.1 1.0
C2D A:HEA568 4.3 26.2 1.0
C3A A:HEA568 4.3 31.0 1.0
ND1 A:HIS419 4.3 29.1 1.0
C3B A:HEA568 4.4 33.6 1.0
C2B A:HEA568 4.4 33.2 1.0
CG A:HIS419 4.4 28.3 1.0
O A:HOH647 4.8 39.9 1.0
CG1 A:VAL423 4.8 28.4 1.0

Iron binding site 3 out of 4 in 3fyi

Go back to Iron Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe567

b:34.0
occ:1.00
 FE C:HEA567 0.0 34.0 1.0
NB C:HEA567 1.9 32.4 1.0
ND C:HEA567 2.0 32.5 1.0
NC C:HEA567 2.0 34.8 1.0
NA C:HEA567 2.0 33.7 1.0
NE2 C:HIS421 2.1 35.5 1.0
NE2 C:HIS102 2.1 41.1 1.0
CE1 C:HIS421 2.9 34.3 1.0
C4B C:HEA567 3.0 33.6 1.0
C4D C:HEA567 3.0 33.0 1.0
C1A C:HEA567 3.0 31.0 1.0
C1C C:HEA567 3.0 32.6 1.0
C1D C:HEA567 3.0 33.6 1.0
C1B C:HEA567 3.0 33.8 1.0
C4C C:HEA567 3.0 33.1 1.0
C4A C:HEA567 3.0 32.7 1.0
CE1 C:HIS102 3.1 40.4 1.0
CD2 C:HIS102 3.1 41.1 1.0
CD2 C:HIS421 3.2 34.2 1.0
CHC C:HEA567 3.4 33.4 1.0
CHA C:HEA567 3.4 30.9 1.0
CHD C:HEA567 3.4 32.8 1.0
CHB C:HEA567 3.4 32.7 1.0
ND1 C:HIS421 4.1 34.2 1.0
ND1 C:HIS102 4.2 39.8 1.0
C3B C:HEA567 4.2 33.8 1.0
C3D C:HEA567 4.2 32.7 1.0
C2D C:HEA567 4.2 31.7 1.0
C2B C:HEA567 4.2 32.7 1.0
C2A C:HEA567 4.2 33.0 1.0
CG C:HIS421 4.2 34.9 1.0
CG C:HIS102 4.2 39.7 1.0
C2C C:HEA567 4.2 34.6 1.0
C3A C:HEA567 4.2 32.7 1.0
C3C C:HEA567 4.3 33.2 1.0
CG2 C:THR48 4.7 39.7 1.0

Iron binding site 4 out of 4 in 3fyi

Go back to Iron Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe568

b:37.1
occ:1.00
 FE C:HEA568 0.0 37.1 1.0
ND C:HEA568 2.0 30.6 1.0
NA C:HEA568 2.1 32.5 1.0
NB C:HEA568 2.2 38.2 1.0
C C:CYN572 2.2 36.8 1.0
NC C:HEA568 2.2 37.8 1.0
NE2 C:HIS419 2.3 32.2 1.0
C4D C:HEA568 3.0 32.7 1.0
C1A C:HEA568 3.0 31.3 1.0
C1D C:HEA568 3.1 34.5 1.0
C4A C:HEA568 3.1 33.9 1.0
C4C C:HEA568 3.2 37.0 1.0
N C:CYN572 3.2 37.9 1.0
C1B C:HEA568 3.2 38.3 1.0
C1C C:HEA568 3.2 37.9 1.0
C4B C:HEA568 3.2 39.0 1.0
CE1 C:HIS419 3.2 33.2 1.0
CD2 C:HIS419 3.3 32.9 1.0
CHA C:HEA568 3.3 32.2 1.0
CHD C:HEA568 3.5 34.6 1.0
CHB C:HEA568 3.5 35.4 1.0
CHC C:HEA568 3.5 38.3 1.0
C2A C:HEA568 4.2 33.3 1.0
C3D C:HEA568 4.2 33.4 1.0
C3A C:HEA568 4.3 31.9 1.0
C2D C:HEA568 4.3 33.5 1.0
ND1 C:HIS419 4.3 33.1 1.0
C3C C:HEA568 4.4 38.3 1.0
C2C C:HEA568 4.4 39.0 1.0
CG C:HIS419 4.4 33.7 1.0
C2B C:HEA568 4.4 37.1 1.0
C3B C:HEA568 4.4 38.8 1.0
O C:HOH1122 4.8 44.1 1.0
CG1 C:VAL423 4.9 39.8 1.0
CU C:CU1569 5.0 42.5 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 Dec 13 15:06:07 2020

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