Iron in PDB 6n1o: Oxidized Rat Cytochrome C Mutant (S47E)

Protein crystallography data

The structure of Oxidized Rat Cytochrome C Mutant (S47E), PDB code: 6n1o was solved by M.Huttemann, B.F.P.Edwards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.04 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 34.705, 52.357, 61.819, 109.89, 92.66, 91.15
R / Rfree (%) 16.6 / 19.2

Iron Binding Sites:

The binding sites of Iron atom in the Oxidized Rat Cytochrome C Mutant (S47E) (pdb code 6n1o). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Oxidized Rat Cytochrome C Mutant (S47E), PDB code: 6n1o:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6n1o

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Iron binding site 1 out of 8 in the Oxidized Rat Cytochrome C Mutant (S47E)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxidized Rat Cytochrome C Mutant (S47E) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:11.0
occ:1.00
FE A:HEC201 0.0 11.0 1.0
NE2 A:HIS18 2.0 9.9 1.0
NA A:HEC201 2.0 5.8 1.0
NC A:HEC201 2.0 5.8 1.0
ND A:HEC201 2.1 13.2 1.0
NB A:HEC201 2.1 12.8 1.0
SD A:MET80 2.2 11.7 1.0
CE1 A:HIS18 2.9 8.6 1.0
C4A A:HEC201 3.0 10.0 1.0
C4C A:HEC201 3.0 9.8 1.0
C1C A:HEC201 3.0 9.2 1.0
C1A A:HEC201 3.0 8.0 1.0
C4D A:HEC201 3.1 9.0 1.0
C1D A:HEC201 3.1 9.1 1.0
C1B A:HEC201 3.1 9.0 1.0
CD2 A:HIS18 3.1 12.7 1.0
C4B A:HEC201 3.1 9.5 1.0
CE A:MET80 3.3 18.3 1.0
CG A:MET80 3.3 12.2 1.0
CHD A:HEC201 3.4 10.2 1.0
CHB A:HEC201 3.4 9.9 1.0
CHA A:HEC201 3.4 10.3 1.0
CHC A:HEC201 3.4 8.6 1.0
ND1 A:HIS18 4.1 10.2 1.0
CG A:HIS18 4.1 9.8 1.0
CB A:MET80 4.2 11.6 1.0
C3C A:HEC201 4.3 14.6 1.0
C3A A:HEC201 4.3 11.2 1.0
C2A A:HEC201 4.3 11.0 1.0
C2C A:HEC201 4.3 10.6 1.0
C3D A:HEC201 4.3 10.2 1.0
C3B A:HEC201 4.3 9.1 1.0
C2D A:HEC201 4.3 13.7 1.0
C2B A:HEC201 4.4 9.1 1.0
OH A:TYR67 4.9 17.1 1.0

Iron binding site 2 out of 8 in 6n1o

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Iron binding site 2 out of 8 in the Oxidized Rat Cytochrome C Mutant (S47E)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxidized Rat Cytochrome C Mutant (S47E) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:33.8
occ:0.63
FE2 A:FC6204 0.0 33.8 0.6
C22 A:FC6204 1.8 30.8 0.6
C11 A:FC6204 1.8 37.6 0.6
C26 A:FC6204 1.8 40.1 0.6
C23 A:FC6204 1.8 37.9 0.6
C21 A:FC6204 1.8 58.4 0.6
C24 A:FC6204 1.8 49.1 0.6
N11 A:FC6204 3.0 21.9 0.6
N22 A:FC6204 3.0 29.6 0.6
N25 A:FC6204 3.0 39.2 0.6
N23 A:FC6204 3.0 49.5 0.6
N21 A:FC6204 3.0 38.1 0.6
N24 A:FC6204 3.0 33.4 0.6
NZ A:LYS25 4.9 45.5 1.0

Iron binding site 3 out of 8 in 6n1o

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Iron binding site 3 out of 8 in the Oxidized Rat Cytochrome C Mutant (S47E)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxidized Rat Cytochrome C Mutant (S47E) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:11.3
occ:1.00
FE B:HEC201 0.0 11.3 1.0
NE2 B:HIS18 1.9 10.7 1.0
NC B:HEC201 2.0 11.0 1.0
NA B:HEC201 2.0 13.3 1.0
ND B:HEC201 2.0 13.0 1.0
NB B:HEC201 2.0 13.3 1.0
SD B:MET80 2.3 11.9 1.0
CE1 B:HIS18 2.9 10.3 1.0
C1C B:HEC201 3.0 9.5 1.0
C4C B:HEC201 3.0 11.7 1.0
C1D B:HEC201 3.0 10.1 1.0
C1A B:HEC201 3.0 11.3 1.0
C1B B:HEC201 3.0 9.4 1.0
CD2 B:HIS18 3.1 13.1 1.0
C4D B:HEC201 3.1 11.6 1.0
C4B B:HEC201 3.1 8.7 1.0
C4A B:HEC201 3.1 13.9 1.0
CE B:MET80 3.3 14.6 1.0
CHD B:HEC201 3.4 8.5 1.0
CHC B:HEC201 3.4 11.2 1.0
CHA B:HEC201 3.4 9.8 1.0
CG B:MET80 3.4 10.8 1.0
CHB B:HEC201 3.4 13.5 1.0
ND1 B:HIS18 4.1 10.9 1.0
CB B:MET80 4.1 10.9 1.0
CG B:HIS18 4.1 10.4 1.0
C3C B:HEC201 4.3 15.0 1.0
C2C B:HEC201 4.3 11.7 1.0
C2D B:HEC201 4.3 12.7 1.0
C3B B:HEC201 4.3 11.4 1.0
C3D B:HEC201 4.3 9.6 1.0
C3A B:HEC201 4.3 13.5 1.0
C2A B:HEC201 4.3 13.3 1.0
C2B B:HEC201 4.4 9.6 1.0
OH B:TYR67 4.8 17.0 1.0

Iron binding site 4 out of 8 in 6n1o

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Iron binding site 4 out of 8 in the Oxidized Rat Cytochrome C Mutant (S47E)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxidized Rat Cytochrome C Mutant (S47E) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:19.9
occ:0.81
FE2 B:FC6202 0.0 19.9 0.8
C11 B:FC6202 1.8 17.5 0.8
C24 B:FC6202 1.8 19.0 0.8
C21 B:FC6202 1.8 32.5 0.8
C26 B:FC6202 1.8 12.6 0.8
C23 B:FC6202 1.8 22.2 0.8
C22 B:FC6202 1.8 23.0 0.8
N11 B:FC6202 3.0 24.6 0.8
N25 B:FC6202 3.0 18.4 0.8
N24 B:FC6202 3.0 22.6 0.8
N23 B:FC6202 3.0 24.4 0.8
N21 B:FC6202 3.0 22.3 0.8
N22 B:FC6202 3.0 27.7 0.8
N B:GLY89 4.6 25.2 1.0
CA B:GLY89 4.7 26.6 1.0
CB B:LYS87 4.9 24.5 1.0
CD B:LYS87 4.9 30.4 1.0

Iron binding site 5 out of 8 in 6n1o

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Iron binding site 5 out of 8 in the Oxidized Rat Cytochrome C Mutant (S47E)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Oxidized Rat Cytochrome C Mutant (S47E) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe203

b:30.3
occ:0.62
FE2 B:FC6203 0.0 30.3 0.6
C21 B:FC6203 1.8 21.1 0.6
C23 B:FC6203 1.8 26.7 0.6
C26 B:FC6203 1.8 40.9 0.6
C22 B:FC6203 1.8 35.3 0.6
C11 B:FC6203 1.8 31.4 0.6
C24 B:FC6203 1.8 27.5 0.6
N25 B:FC6203 3.0 39.3 0.6
N21 B:FC6203 3.0 41.7 0.6
N23 B:FC6203 3.0 44.9 0.6
N22 B:FC6203 3.0 43.6 0.6
N11 B:FC6203 3.0 37.8 0.6
N24 B:FC6203 3.0 48.6 0.6
CD B:LYS86 4.4 65.8 1.0
NZ C:LYS86 4.5 72.3 1.0
CE C:LYS87 4.6 36.4 1.0
NZ C:LYS87 4.7 58.5 1.0
NZ B:LYS87 4.7 49.6 1.0
CE C:LYS86 4.7 42.9 1.0
NZ B:LYS86 4.8 91.2 1.0
CE B:LYS87 4.9 37.2 1.0

Iron binding site 6 out of 8 in 6n1o

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Iron binding site 6 out of 8 in the Oxidized Rat Cytochrome C Mutant (S47E)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Oxidized Rat Cytochrome C Mutant (S47E) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:12.2
occ:1.00
FE C:HEC201 0.0 12.2 1.0
NE2 C:HIS18 2.0 9.3 1.0
NC C:HEC201 2.0 10.5 1.0
ND C:HEC201 2.0 11.7 1.0
NB C:HEC201 2.1 15.1 1.0
NA C:HEC201 2.1 12.2 1.0
SD C:MET80 2.3 11.7 1.0
CE1 C:HIS18 2.9 12.6 1.0
C1A C:HEC201 3.0 9.7 1.0
C1C C:HEC201 3.0 9.6 1.0
C1B C:HEC201 3.0 10.3 1.0
C4A C:HEC201 3.1 11.2 1.0
C4C C:HEC201 3.1 10.4 1.0
C1D C:HEC201 3.1 10.6 1.0
C4B C:HEC201 3.1 12.9 1.0
C4D C:HEC201 3.1 11.4 1.0
CD2 C:HIS18 3.1 13.0 1.0
CE C:MET80 3.3 13.1 1.0
CHC C:HEC201 3.4 11.4 1.0
CHD C:HEC201 3.4 10.5 1.0
CHA C:HEC201 3.4 12.2 1.0
CHB C:HEC201 3.4 12.3 1.0
CG C:MET80 3.4 12.6 1.0
ND1 C:HIS18 4.0 14.2 1.0
CG C:HIS18 4.1 13.1 1.0
CB C:MET80 4.2 11.0 1.0
C2A C:HEC201 4.3 11.9 1.0
C3C C:HEC201 4.3 15.6 1.0
C3A C:HEC201 4.3 14.4 1.0
C2C C:HEC201 4.3 12.7 1.0
C3B C:HEC201 4.3 13.7 1.0
C2B C:HEC201 4.4 12.2 1.0
C2D C:HEC201 4.4 10.9 1.0
C3D C:HEC201 4.4 10.5 1.0
OH C:TYR67 4.8 17.5 1.0

Iron binding site 7 out of 8 in 6n1o

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Iron binding site 7 out of 8 in the Oxidized Rat Cytochrome C Mutant (S47E)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Oxidized Rat Cytochrome C Mutant (S47E) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:17.9
occ:0.90
FE2 C:FC6202 0.0 17.9 0.9
C11 C:FC6202 1.8 16.9 0.9
C24 C:FC6202 1.8 17.0 0.9
C23 C:FC6202 1.8 22.5 0.9
C21 C:FC6202 1.8 24.4 0.9
C26 C:FC6202 1.8 18.0 0.9
C22 C:FC6202 1.8 20.2 0.9
N24 C:FC6202 3.0 17.3 0.9
N23 C:FC6202 3.0 16.8 0.9
N11 C:FC6202 3.0 19.1 0.9
N21 C:FC6202 3.0 23.9 0.9
N25 C:FC6202 3.0 18.4 0.9
N22 C:FC6202 3.0 22.4 0.9
N C:LYS88 4.6 19.7 1.0
CB C:LYS88 4.8 23.9 1.0

Iron binding site 8 out of 8 in 6n1o

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Iron binding site 8 out of 8 in the Oxidized Rat Cytochrome C Mutant (S47E)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Oxidized Rat Cytochrome C Mutant (S47E) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:13.4
occ:1.00
FE D:HEC201 0.0 13.4 1.0
NE2 D:HIS18 2.0 12.2 1.0
NA D:HEC201 2.0 6.7 1.0
NC D:HEC201 2.0 7.8 1.0
NB D:HEC201 2.0 17.1 1.0
ND D:HEC201 2.1 14.3 1.0
SD D:MET80 2.3 13.7 1.0
CE1 D:HIS18 2.9 13.7 1.0
C4A D:HEC201 3.0 12.3 1.0
C1A D:HEC201 3.0 10.5 1.0
C1C D:HEC201 3.0 10.4 1.0
C4C D:HEC201 3.0 12.4 1.0
C1B D:HEC201 3.0 12.6 1.0
C4B D:HEC201 3.1 10.3 1.0
C1D D:HEC201 3.1 12.4 1.0
C4D D:HEC201 3.1 11.2 1.0
CD2 D:HIS18 3.1 16.8 1.0
CE D:MET80 3.3 13.5 1.0
CG D:MET80 3.4 15.9 1.0
CHB D:HEC201 3.4 12.5 1.0
CHD D:HEC201 3.4 12.8 1.0
CHC D:HEC201 3.4 11.3 1.0
CHA D:HEC201 3.4 11.3 1.0
ND1 D:HIS18 4.1 13.7 1.0
CG D:HIS18 4.2 16.2 1.0
CB D:MET80 4.2 11.2 1.0
C3A D:HEC201 4.3 12.8 1.0
C2A D:HEC201 4.3 14.0 1.0
C3C D:HEC201 4.3 16.4 1.0
C2C D:HEC201 4.3 13.4 1.0
C3B D:HEC201 4.4 13.2 1.0
C2B D:HEC201 4.4 12.1 1.0
C2D D:HEC201 4.4 15.4 1.0
C3D D:HEC201 4.4 13.4 1.0
OH D:TYR67 4.9 19.0 1.0

Reference:

H.A.Kalpage, A.Vaishnav, J.Liu, A.Varughese, J.Wan, A.A.Turner, Q.Ji, M.P.Zurek, A.A.Kapralov, V.E.Kagan, J.S.Brunzelle, M.A.Recanati, L.I.Grossman, T.H.Sanderson, I.Lee, A.R.Salomon, B.F.P.Edwards, M.Huttemann. Serine-47 Phosphorylation of Cytochromecin the Mammalian Brain Regulates Cytochromecoxidase and Caspase-3 Activity. Faseb J. 1120R 2019.
ISSN: ESSN 1530-6860
PubMed: 31570002
DOI: 10.1096/FJ.201901120R
Page generated: Sun Dec 13 16:44:33 2020

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