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Iron in PDB 6ci0: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation, PDB code: 6ci0 was solved by J.Liu, C.Hiser, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.09 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.916, 130.969, 177.788, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.4

Other elements in 6ci0:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 1 atom
Cadmium (Cd) 2 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 E101A (II) Mutation (pdb code 6ci0). 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 E101A (II) Mutation, PDB code: 6ci0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6ci0

Go back to Iron Binding Sites List in 6ci0
Iron binding site 1 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe617

b:38.6
occ:1.00
 FE A:HEA617 0.0 38.6 1.0
NA A:HEA617 2.0 44.7 1.0
NC A:HEA617 2.0 45.1 1.0
NB A:HEA617 2.1 39.9 1.0
ND A:HEA617 2.1 41.1 1.0
NE2 A:HIS421 2.3 33.7 1.0
NE2 A:HIS102 2.3 31.5 1.0
C4A A:HEA617 3.0 35.8 1.0
C1A A:HEA617 3.0 36.5 1.0
C4C A:HEA617 3.0 46.3 1.0
C4B A:HEA617 3.0 43.5 1.0
C1B A:HEA617 3.1 34.5 1.0
C1C A:HEA617 3.1 42.1 1.0
C1D A:HEA617 3.1 44.9 1.0
C4D A:HEA617 3.1 39.9 1.0
CD2 A:HIS421 3.2 40.6 1.0
CD2 A:HIS102 3.2 36.4 1.0
CE1 A:HIS421 3.3 42.2 1.0
CE1 A:HIS102 3.4 40.8 1.0
CHB A:HEA617 3.4 36.4 1.0
CHC A:HEA617 3.4 37.4 1.0
CHD A:HEA617 3.4 45.2 1.0
CHA A:HEA617 3.4 39.8 1.0
C3A A:HEA617 4.1 37.3 1.0
C2A A:HEA617 4.2 35.3 1.0
C3C A:HEA617 4.3 41.9 1.0
C3B A:HEA617 4.3 42.5 1.0
C2B A:HEA617 4.3 35.9 1.0
C2C A:HEA617 4.4 46.4 1.0
CG A:HIS421 4.4 45.9 1.0
C2D A:HEA617 4.4 51.3 1.0
ND1 A:HIS421 4.4 43.2 1.0
CG A:HIS102 4.4 37.9 1.0
C3D A:HEA617 4.4 40.2 1.0
ND1 A:HIS102 4.4 41.6 1.0
CG2 A:THR48 4.7 35.1 1.0
CE1 A:PHE420 4.9 40.4 1.0

Iron binding site 2 out of 4 in 6ci0

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Iron binding site 2 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe618

b:46.5
occ:1.00
 FE A:HEA618 0.0 46.5 1.0
NA A:HEA618 2.1 57.6 1.0
NC A:HEA618 2.1 47.7 1.0
ND A:HEA618 2.1 47.6 1.0
NB A:HEA618 2.1 48.3 1.0
NE2 A:HIS419 2.4 42.8 1.0
O A:HOH770 2.5 47.0 1.0
C1A A:HEA618 3.0 42.8 1.0
C4A A:HEA618 3.0 44.0 1.0
C1C A:HEA618 3.0 45.0 1.0
C4C A:HEA618 3.1 41.2 1.0
C1D A:HEA618 3.1 44.6 1.0
C4D A:HEA618 3.1 39.7 1.0
C1B A:HEA618 3.1 48.6 1.0
C4B A:HEA618 3.1 48.2 1.0
CD2 A:HIS419 3.3 46.0 1.0
CE1 A:HIS419 3.3 48.5 1.0
CHC A:HEA618 3.4 42.7 1.0
CHA A:HEA618 3.4 45.1 1.0
CHB A:HEA618 3.4 49.0 1.0
CHD A:HEA618 3.4 44.4 1.0
C3A A:HEA618 4.2 53.8 1.0
C2A A:HEA618 4.2 52.6 1.0
C3C A:HEA618 4.3 41.6 1.0
C2C A:HEA618 4.3 46.5 1.0
C2D A:HEA618 4.4 41.3 1.0
C3D A:HEA618 4.4 42.0 1.0
C2B A:HEA618 4.4 50.7 1.0
C3B A:HEA618 4.4 56.8 1.0
ND1 A:HIS419 4.5 45.6 1.0
CG A:HIS419 4.5 44.2 1.0
CU A:CU614 4.8 51.4 1.0
CG1 A:VAL287 4.9 45.0 1.0

Iron binding site 3 out of 4 in 6ci0

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Iron binding site 3 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe605

b:56.6
occ:1.00
 FE C:HEA605 0.0 56.6 1.0
NA C:HEA605 1.9 72.0 1.0
NC C:HEA605 2.1 67.9 1.0
NB C:HEA605 2.1 54.3 1.0
ND C:HEA605 2.1 64.4 1.0
NE2 C:HIS102 2.4 63.6 1.0
NE2 C:HIS421 2.5 59.8 1.0
C1A C:HEA605 2.9 51.1 1.0
C4A C:HEA605 3.0 57.1 1.0
C4C C:HEA605 3.1 53.1 1.0
C1D C:HEA605 3.1 62.7 1.0
C4B C:HEA605 3.1 63.0 1.0
C1C C:HEA605 3.1 52.6 1.0
C1B C:HEA605 3.1 60.0 1.0
C4D C:HEA605 3.1 61.5 1.0
CD2 C:HIS102 3.3 65.4 1.0
CHA C:HEA605 3.4 54.5 1.0
CHD C:HEA605 3.4 67.4 1.0
CD2 C:HIS421 3.4 63.0 1.0
CHC C:HEA605 3.4 57.6 1.0
CHB C:HEA605 3.4 65.3 1.0
CE1 C:HIS421 3.4 63.4 1.0
CE1 C:HIS102 3.5 66.0 1.0
C3A C:HEA605 4.1 63.6 1.0
C2A C:HEA605 4.2 63.3 1.0
C3C C:HEA605 4.3 62.7 1.0
C3B C:HEA605 4.4 64.3 1.0
C2D C:HEA605 4.4 57.9 1.0
C2B C:HEA605 4.4 58.4 1.0
C2C C:HEA605 4.4 70.8 1.0
C3D C:HEA605 4.4 62.5 1.0
CG C:HIS102 4.4 74.2 1.0
ND1 C:HIS102 4.5 75.4 1.0
ND1 C:HIS421 4.6 67.4 1.0
CG C:HIS421 4.6 70.8 1.0
CG2 C:THR48 4.9 63.2 1.0
CE1 C:PHE420 5.0 58.2 1.0

Iron binding site 4 out of 4 in 6ci0

Go back to Iron Binding Sites List in 6ci0
Iron binding site 4 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe606

b:57.5
occ:1.00
 FE C:HEA606 0.0 57.5 1.0
NA C:HEA606 2.0 71.3 1.0
ND C:HEA606 2.1 66.4 1.0
NC C:HEA606 2.1 71.7 1.0
NB C:HEA606 2.1 71.9 1.0
NE2 C:HIS419 2.4 51.5 1.0
O C:HOH730 2.6 51.4 1.0
C1A C:HEA606 3.0 57.3 1.0
C4A C:HEA606 3.0 56.9 1.0
C1D C:HEA606 3.1 67.2 1.0
C1C C:HEA606 3.1 59.9 1.0
C4D C:HEA606 3.1 54.3 1.0
C4B C:HEA606 3.1 67.5 1.0
C4C C:HEA606 3.1 65.7 1.0
C1B C:HEA606 3.2 64.5 1.0
CE1 C:HIS419 3.4 62.6 1.0
CD2 C:HIS419 3.4 65.1 1.0
CHA C:HEA606 3.5 59.7 1.0
CHD C:HEA606 3.5 65.3 1.0
CHC C:HEA606 3.5 61.7 1.0
CHB C:HEA606 3.5 67.2 1.0
C3A C:HEA606 4.3 57.9 1.0
C2A C:HEA606 4.3 63.1 1.0
C3C C:HEA606 4.5 75.3 1.0
C3D C:HEA606 4.5 60.5 1.0
C2D C:HEA606 4.5 66.1 1.0
C3B C:HEA606 4.5 68.3 1.0
C2B C:HEA606 4.5 66.4 1.0
C2C C:HEA606 4.5 73.9 1.0
ND1 C:HIS419 4.5 61.1 1.0
CG C:HIS419 4.5 58.8 1.0
CU C:CU604 4.7 62.1 1.0

Reference:

C.Hiser, J.Liu, S.Ferguson-Miller. The K-Path Entrance in Cytochrome C Oxidase Is Defined By Mutation of E101 and Controlled By An Adjacent Ligand Binding Domain. Biochim. Biophys. Acta V.1859 725 2018.
ISSN: ISSN 0006-3002
PubMed: 29626419
DOI: 10.1016/J.BBABIO.2018.03.017
Page generated: Sun Dec 13 16:22:33 2020

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