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Iron in PDB 5cib: Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C

Enzymatic activity of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C

All present enzymatic activity of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C:
1.11.1.5;

Protein crystallography data

The structure of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C, PDB code: 5cib was solved by B.R.Crane, T.M.Payne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.30 / 3.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.371, 107.461, 87.217, 90.00, 104.49, 90.00
R / Rfree (%) 23.6 / 30.4

Iron Binding Sites:

The binding sites of Iron atom in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C (pdb code 5cib). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C, PDB code: 5cib:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5cib

Go back to Iron Binding Sites List in 5cib
Iron binding site 1 out of 4 in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:40.8
occ:1.00
 FE A:HEM301 0.0 40.8 1.0
NE2 A:HIS175 2.0 44.4 1.0
NA A:HEM301 2.1 55.3 1.0
NC A:HEM301 2.1 47.9 1.0
ND A:HEM301 2.1 49.0 1.0
NB A:HEM301 2.1 52.8 1.0
CD2 A:HIS175 3.0 44.1 1.0
CE1 A:HIS175 3.0 44.9 1.0
C1D A:HEM301 3.1 43.1 1.0
C1B A:HEM301 3.1 47.9 1.0
C4D A:HEM301 3.1 40.8 1.0
C4B A:HEM301 3.1 49.8 1.0
C4C A:HEM301 3.1 52.5 1.0
C1A A:HEM301 3.1 52.8 1.0
C4A A:HEM301 3.1 48.1 1.0
C1C A:HEM301 3.1 46.5 1.0
CHD A:HEM301 3.4 43.1 1.0
CHA A:HEM301 3.4 40.8 1.0
CHB A:HEM301 3.4 46.4 1.0
CHC A:HEM301 3.4 53.9 1.0
NE1 A:TRP51 4.0 40.4 1.0
CD1 A:TRP51 4.0 40.0 1.0
ND1 A:HIS175 4.1 45.0 1.0
CG A:HIS175 4.2 45.1 1.0
C2B A:HEM301 4.2 43.7 1.0
C3B A:HEM301 4.3 40.8 1.0
C2D A:HEM301 4.3 40.8 1.0
C3D A:HEM301 4.3 40.8 1.0
C3C A:HEM301 4.3 41.7 1.0
C2A A:HEM301 4.3 49.4 1.0
C3A A:HEM301 4.3 46.6 1.0
C2C A:HEM301 4.3 40.8 1.0
CG A:ARG48 4.5 42.7 1.0

Iron binding site 2 out of 4 in 5cib

Go back to Iron Binding Sites List in 5cib
Iron binding site 2 out of 4 in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:82.6
occ:1.00
 FE B:HEM201 0.0 82.6 1.0
NE2 B:HIS18 2.0 53.6 1.0
NC B:HEM201 2.0 56.9 1.0
NA B:HEM201 2.1 55.6 1.0
NB B:HEM201 2.1 53.5 1.0
ND B:HEM201 2.1 55.1 1.0
SD B:MET80 2.2 66.6 1.0
CE1 B:HIS18 2.9 55.5 1.0
CD2 B:HIS18 3.0 53.4 1.0
C4C B:HEM201 3.0 56.8 1.0
C1D B:HEM201 3.1 57.6 1.0
C4A B:HEM201 3.1 55.7 1.0
C1A B:HEM201 3.1 63.5 1.0
C1B B:HEM201 3.1 60.2 1.0
C4D B:HEM201 3.1 60.5 1.0
C1C B:HEM201 3.1 58.9 1.0
C4B B:HEM201 3.1 56.8 1.0
CE B:MET80 3.3 58.6 1.0
CHD B:HEM201 3.4 61.1 1.0
CHB B:HEM201 3.4 59.5 1.0
CHA B:HEM201 3.4 66.8 1.0
CHC B:HEM201 3.5 53.2 1.0
CG B:MET80 3.6 58.8 1.0
ND1 B:HIS18 4.0 56.9 1.0
CG B:HIS18 4.1 56.4 1.0
C3A B:HEM201 4.2 57.4 1.0
C2A B:HEM201 4.2 61.0 1.0
C2D B:HEM201 4.3 62.3 1.0
C3C B:HEM201 4.3 56.8 1.0
C3D B:HEM201 4.3 66.7 1.0
C2C B:HEM201 4.3 58.0 1.0
C2B B:HEM201 4.3 66.7 1.0
C3B B:HEM201 4.3 66.5 1.0
CB B:MET80 4.4 57.9 1.0

Iron binding site 3 out of 4 in 5cib

Go back to Iron Binding Sites List in 5cib
Iron binding site 3 out of 4 in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:42.6
occ:1.00
 FE C:HEM301 0.0 42.6 1.0
NE2 C:HIS175 2.0 43.5 1.0
NA C:HEM301 2.0 46.8 1.0
NC C:HEM301 2.1 49.9 1.0
ND C:HEM301 2.1 53.2 1.0
NB C:HEM301 2.1 53.8 1.0
CE1 C:HIS175 2.8 48.1 1.0
C1B C:HEM301 3.1 52.1 1.0
C1D C:HEM301 3.1 42.6 1.0
C4A C:HEM301 3.1 42.6 1.0
C4B C:HEM301 3.1 49.3 1.0
C1A C:HEM301 3.1 57.0 1.0
C4D C:HEM301 3.1 50.2 1.0
C4C C:HEM301 3.1 46.4 1.0
C1C C:HEM301 3.1 46.6 1.0
CD2 C:HIS175 3.2 43.8 1.0
CHD C:HEM301 3.4 43.6 1.0
CHA C:HEM301 3.4 53.6 1.0
CHB C:HEM301 3.4 45.2 1.0
CHC C:HEM301 3.5 50.4 1.0
ND1 C:HIS175 3.9 47.3 1.0
NE1 C:TRP51 4.0 41.6 1.0
CG C:HIS175 4.1 46.0 1.0
CD1 C:TRP51 4.2 42.2 1.0
C2B C:HEM301 4.3 46.2 1.0
C3B C:HEM301 4.3 47.4 1.0
C3A C:HEM301 4.3 49.8 1.0
C2A C:HEM301 4.3 51.5 1.0
C2D C:HEM301 4.3 44.1 1.0
C3D C:HEM301 4.3 46.3 1.0
C3C C:HEM301 4.3 42.6 1.0
C2C C:HEM301 4.3 47.3 1.0
CD C:ARG48 4.8 39.4 1.0
NH1 C:ARG48 4.8 59.4 1.0
CE2 C:TRP51 4.9 40.8 1.0

Iron binding site 4 out of 4 in 5cib

Go back to Iron Binding Sites List in 5cib
Iron binding site 4 out of 4 in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 2,4- Dimethylaniline with Iso-1 Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:0.4
occ:1.00
 FE D:HEM201 0.0 0.4 1.0
NE2 D:HIS18 2.0 0.4 1.0
NC D:HEM201 2.1 0.8 1.0
NA D:HEM201 2.1 0.1 1.0
ND D:HEM201 2.1 0.6 1.0
NB D:HEM201 2.1 0.4 1.0
SD D:MET80 2.3 0.0 0.8
CE1 D:HIS18 2.6 0.2 1.0
CE D:MET80 3.0 0.9 0.6
C1D D:HEM201 3.0 0.3 1.0
C4C D:HEM201 3.1 0.3 1.0
C4D D:HEM201 3.1 0.8 1.0
C1A D:HEM201 3.1 0.8 1.0
C4A D:HEM201 3.1 0.1 1.0
C1C D:HEM201 3.1 0.4 1.0
C1B D:HEM201 3.1 0.8 1.0
C4B D:HEM201 3.1 0.8 1.0
CD2 D:HIS18 3.2 0.5 0.0
CHD D:HEM201 3.4 0.1 1.0
CHA D:HEM201 3.4 0.0 1.0
CHB D:HEM201 3.5 0.9 1.0
CHC D:HEM201 3.5 0.0 1.0
ND1 D:HIS18 3.9 97.8 0.0
CG D:MET80 4.0 0.8 1.0
CG D:HIS18 4.2 97.2 0.0
C2D D:HEM201 4.3 0.4 1.0
C3D D:HEM201 4.3 0.7 1.0
C3A D:HEM201 4.3 0.9 1.0
C2A D:HEM201 4.3 0.4 1.0
C3C D:HEM201 4.3 0.7 1.0
C2C D:HEM201 4.3 0.7 1.0
C2B D:HEM201 4.3 0.2 1.0
C3B D:HEM201 4.3 1.0 1.0
CD2 D:PHE82 4.8 0.7 1.0
CE2 D:PHE82 4.8 0.4 0.2

Reference:

T.M.Payne, E.F.Yee, B.Dzikovski, B.R.Crane. Constraints on the Radical Cation Center of Cytochrome C Peroxidase For Electron Transfer From Cytochrome C. Biochemistry V. 55 4807 2016.
ISSN: ISSN 0006-2960
PubMed: 27499202
DOI: 10.1021/ACS.BIOCHEM.6B00262
Page generated: Sun Dec 13 15:58:00 2020

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