Iron in PDB 5gyr: Tetrameric Allochromatium Vinosum Cytochrome C'

Protein crystallography data

The structure of Tetrameric Allochromatium Vinosum Cytochrome C', PDB code: 5gyr was solved by M.Yamanaka, M.Hoshizumi, S.Nagao, R.Nakayama, N.Shibata, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.40 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.949, 48.620, 130.550, 90.00, 92.28, 90.00
R / Rfree (%) 20.4 / 23.2

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 5gyr

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Iron binding site 1 out of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'


Mono view


Stereo pair view

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

b:19.9
occ:1.00
FE A:HEC201 0.0 19.9 1.0
ND A:HEC201 1.9 17.8 1.0
NA A:HEC201 2.0 20.6 1.0
NB A:HEC201 2.1 18.2 1.0
NC A:HEC201 2.1 15.7 1.0
NE2 A:HIS125 2.3 21.6 1.0
C4D A:HEC201 2.9 22.3 1.0
C1D A:HEC201 2.9 21.0 1.0
C4B A:HEC201 3.0 17.0 1.0
C1A A:HEC201 3.0 19.0 1.0
C1C A:HEC201 3.1 16.3 1.0
C4A A:HEC201 3.1 20.4 1.0
C1B A:HEC201 3.1 19.7 1.0
C4C A:HEC201 3.1 19.3 1.0
CE1 A:HIS125 3.2 18.9 1.0
CD2 A:HIS125 3.2 21.7 1.0
CD1 N:TYR16 3.4 20.1 1.0
CHC A:HEC201 3.4 12.6 1.0
CHA A:HEC201 3.4 14.9 1.0
CHD A:HEC201 3.4 19.5 1.0
CHB A:HEC201 3.5 17.5 1.0
CG N:TYR16 3.7 18.7 1.0
CE1 N:TYR16 3.7 17.7 1.0
C3D A:HEC201 4.2 22.3 1.0
CB N:TYR16 4.2 20.0 1.0
C2D A:HEC201 4.2 21.6 1.0
CD2 N:TYR16 4.2 16.2 1.0
CZ N:TYR16 4.2 18.7 1.0
C3A A:HEC201 4.3 21.4 1.0
C2A A:HEC201 4.3 21.8 1.0
C3B A:HEC201 4.3 18.8 1.0
C2B A:HEC201 4.3 19.4 1.0
C2C A:HEC201 4.3 19.7 1.0
C3C A:HEC201 4.3 18.1 1.0
ND1 A:HIS125 4.3 20.6 1.0
CG A:HIS125 4.4 20.4 1.0
CE2 N:TYR16 4.5 20.8 1.0
NH1 A:ARG129 4.7 29.4 1.0

Iron binding site 2 out of 8 in 5gyr

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Iron binding site 2 out of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:12.3
occ:1.00
FE B:HEC201 0.0 12.3 1.0
ND B:HEC201 1.9 11.0 1.0
NA B:HEC201 2.0 12.3 1.0
NB B:HEC201 2.1 12.7 1.0
NC B:HEC201 2.1 14.0 1.0
NE2 B:HIS125 2.2 14.0 1.0
C4D B:HEC201 3.0 12.2 1.0
C1D B:HEC201 3.0 11.7 1.0
C4B B:HEC201 3.0 13.4 1.0
C1A B:HEC201 3.0 11.4 1.0
C1B B:HEC201 3.1 13.0 1.0
C4A B:HEC201 3.1 11.3 1.0
C4C B:HEC201 3.1 12.9 1.0
C1C B:HEC201 3.1 13.9 1.0
CD2 B:HIS125 3.1 15.6 1.0
CE1 B:HIS125 3.2 17.2 1.0
CD1 B:TYR16 3.2 11.3 1.0
CHD B:HEC201 3.4 13.0 1.0
CHA B:HEC201 3.4 11.5 1.0
CHC B:HEC201 3.4 13.4 1.0
CHB B:HEC201 3.4 12.2 1.0
CE1 B:TYR16 3.5 12.8 1.0
CG B:TYR16 3.6 11.6 1.0
CZ B:TYR16 4.1 12.9 1.0
CB B:TYR16 4.2 12.8 1.0
CD2 B:TYR16 4.2 11.0 1.0
C3D B:HEC201 4.2 11.6 1.0
C2D B:HEC201 4.2 11.7 1.0
C3A B:HEC201 4.3 12.9 1.0
ND1 B:HIS125 4.3 19.0 1.0
C2A B:HEC201 4.3 13.6 1.0
C2B B:HEC201 4.3 12.8 1.0
CG B:HIS125 4.3 17.3 1.0
C3C B:HEC201 4.3 14.9 1.0
C2C B:HEC201 4.3 15.4 1.0
C3B B:HEC201 4.3 13.5 1.0
CE2 B:TYR16 4.4 12.6 1.0
NH1 B:ARG129 4.5 18.1 1.0
OH B:TYR16 5.0 13.4 1.0
CD B:ARG129 5.0 16.7 1.0

Iron binding site 3 out of 8 in 5gyr

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Iron binding site 3 out of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:19.9
occ:1.00
FE E:HEC201 0.0 19.9 1.0
ND E:HEC201 1.9 21.1 1.0
NA E:HEC201 2.0 20.5 1.0
NB E:HEC201 2.1 17.2 1.0
NC E:HEC201 2.1 18.0 1.0
NE2 E:HIS125 2.3 21.9 1.0
C4D E:HEC201 2.9 21.6 1.0
C1D E:HEC201 2.9 19.5 1.0
C4B E:HEC201 3.0 17.7 1.0
C1A E:HEC201 3.0 20.5 1.0
C4A E:HEC201 3.1 18.9 1.0
C1B E:HEC201 3.1 18.5 1.0
C4C E:HEC201 3.1 19.3 1.0
C1C E:HEC201 3.1 17.9 1.0
CD2 E:HIS125 3.2 20.8 1.0
CE1 E:HIS125 3.2 18.6 1.0
CD1 J:TYR16 3.3 18.5 1.0
CHA E:HEC201 3.4 17.5 1.0
CHD E:HEC201 3.4 19.3 1.0
CHC E:HEC201 3.4 16.1 1.0
CHB E:HEC201 3.5 16.6 1.0
CE1 J:TYR16 3.7 17.6 1.0
CG J:TYR16 3.7 17.8 1.0
CB J:TYR16 4.2 20.2 1.0
C3D E:HEC201 4.2 20.1 1.0
C2D E:HEC201 4.2 19.2 1.0
CZ J:TYR16 4.3 18.1 1.0
CD2 J:TYR16 4.3 16.6 1.0
C3A E:HEC201 4.3 20.9 1.0
C2A E:HEC201 4.3 24.2 1.0
C2C E:HEC201 4.3 19.7 1.0
C2B E:HEC201 4.3 19.0 1.0
C3B E:HEC201 4.3 19.2 1.0
C3C E:HEC201 4.3 19.8 1.0
ND1 E:HIS125 4.4 20.5 1.0
CG E:HIS125 4.4 20.5 1.0
CE2 J:TYR16 4.5 16.2 1.0
NH1 E:ARG129 4.6 27.1 1.0

Iron binding site 4 out of 8 in 5gyr

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Iron binding site 4 out of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:12.6
occ:1.00
FE F:HEC201 0.0 12.6 1.0
ND F:HEC201 1.9 12.0 1.0
NA F:HEC201 2.0 12.9 1.0
NB F:HEC201 2.1 12.3 1.0
NC F:HEC201 2.1 13.7 1.0
NE2 F:HIS125 2.2 16.3 1.0
C4D F:HEC201 3.0 14.2 1.0
C1D F:HEC201 3.0 11.8 1.0
C4B F:HEC201 3.0 12.2 1.0
C1B F:HEC201 3.0 13.2 1.0
C4A F:HEC201 3.0 11.4 1.0
C1A F:HEC201 3.1 12.4 1.0
C4C F:HEC201 3.1 12.0 1.0
C1C F:HEC201 3.1 12.9 1.0
CD2 F:HIS125 3.1 16.1 1.0
CE1 F:HIS125 3.2 16.6 1.0
CD1 F:TYR16 3.2 13.1 1.0
CHA F:HEC201 3.4 12.8 1.0
CHB F:HEC201 3.4 12.0 1.0
CHD F:HEC201 3.4 12.2 1.0
CHC F:HEC201 3.4 12.5 1.0
CE1 F:TYR16 3.5 12.9 1.0
CG F:TYR16 3.6 11.4 1.0
CZ F:TYR16 4.1 13.2 1.0
CD2 F:TYR16 4.2 11.6 1.0
CB F:TYR16 4.2 12.2 1.0
C3D F:HEC201 4.2 13.0 1.0
C2D F:HEC201 4.2 12.9 1.0
ND1 F:HIS125 4.3 15.4 1.0
C3A F:HEC201 4.3 13.1 1.0
C2B F:HEC201 4.3 12.7 1.0
CG F:HIS125 4.3 16.8 1.0
C2C F:HEC201 4.3 14.5 1.0
C3C F:HEC201 4.3 13.5 1.0
C2A F:HEC201 4.3 14.1 1.0
C3B F:HEC201 4.3 13.4 1.0
CE2 F:TYR16 4.4 13.4 1.0
NH1 F:ARG129 4.5 17.2 1.0
CD F:ARG129 4.9 16.5 1.0
OH F:TYR16 4.9 14.7 1.0

Iron binding site 5 out of 8 in 5gyr

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Iron binding site 5 out of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:20.4
occ:1.00
FE I:HEC201 0.0 20.4 1.0
ND I:HEC201 1.9 20.3 1.0
NA I:HEC201 2.0 20.1 1.0
NC I:HEC201 2.1 22.9 1.0
NB I:HEC201 2.1 23.2 1.0
NE2 I:HIS125 2.3 24.6 1.0
C1D I:HEC201 2.9 21.2 1.0
C4D I:HEC201 2.9 20.3 1.0
C1A I:HEC201 3.0 20.0 1.0
C4A I:HEC201 3.0 20.6 1.0
C4C I:HEC201 3.1 23.0 1.0
C4B I:HEC201 3.1 20.4 1.0
C1B I:HEC201 3.1 20.5 1.0
C1C I:HEC201 3.1 22.4 1.0
CD2 I:HIS125 3.2 22.8 1.0
CD1 I:TYR16 3.2 21.8 1.0
CE1 I:HIS125 3.3 22.9 1.0
CHD I:HEC201 3.4 19.4 1.0
CHA I:HEC201 3.4 19.8 1.0
CHB I:HEC201 3.4 20.1 1.0
CHC I:HEC201 3.5 20.4 1.0
CE1 I:TYR16 3.5 20.7 1.0
CG I:TYR16 3.6 18.9 1.0
CZ I:TYR16 4.1 20.2 1.0
CB I:TYR16 4.1 19.2 1.0
CD2 I:TYR16 4.1 19.2 1.0
C2D I:HEC201 4.2 21.4 1.0
C3D I:HEC201 4.2 22.1 1.0
C2A I:HEC201 4.2 21.5 1.0
C3A I:HEC201 4.2 20.9 1.0
C3C I:HEC201 4.3 22.6 1.0
C2C I:HEC201 4.3 22.6 1.0
C2B I:HEC201 4.3 22.2 1.0
C3B I:HEC201 4.3 22.6 1.0
ND1 I:HIS125 4.4 25.0 1.0
CG I:HIS125 4.4 21.0 1.0
CE2 I:TYR16 4.4 19.3 1.0
NH1 I:ARG129 4.6 25.4 1.0
OH I:TYR16 4.9 24.5 1.0

Iron binding site 6 out of 8 in 5gyr

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Iron binding site 6 out of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe201

b:16.0
occ:1.00
FE J:HEC201 0.0 16.0 1.0
ND J:HEC201 1.9 15.7 1.0
NA J:HEC201 2.0 16.2 1.0
NC J:HEC201 2.1 14.4 1.0
NB J:HEC201 2.1 16.3 1.0
NE2 J:HIS125 2.2 17.1 1.0
C1D J:HEC201 2.9 15.6 1.0
C4D J:HEC201 2.9 16.5 1.0
C1A J:HEC201 3.0 16.7 1.0
C4A J:HEC201 3.0 14.9 1.0
C4B J:HEC201 3.1 13.7 1.0
C4C J:HEC201 3.1 15.8 1.0
C1B J:HEC201 3.1 14.6 1.0
C1C J:HEC201 3.1 16.2 1.0
CD2 J:HIS125 3.2 17.9 1.0
CE1 J:HIS125 3.2 15.6 1.0
CD1 E:TYR16 3.3 14.0 1.0
CHD J:HEC201 3.4 15.2 1.0
CHA J:HEC201 3.4 16.4 1.0
CHB J:HEC201 3.4 14.9 1.0
CHC J:HEC201 3.5 14.5 1.0
CE1 E:TYR16 3.6 13.9 1.0
CG E:TYR16 3.6 13.7 1.0
CB E:TYR16 4.2 13.9 1.0
C2D J:HEC201 4.2 16.6 1.0
CZ E:TYR16 4.2 14.0 1.0
CD2 E:TYR16 4.2 15.0 1.0
C3D J:HEC201 4.2 16.1 1.0
C3A J:HEC201 4.2 15.3 1.0
C2A J:HEC201 4.2 17.2 1.0
C2C J:HEC201 4.3 15.7 1.0
C3C J:HEC201 4.3 16.4 1.0
C2B J:HEC201 4.3 16.1 1.0
ND1 J:HIS125 4.3 17.4 1.0
C3B J:HEC201 4.3 14.7 1.0
CG J:HIS125 4.4 19.9 1.0
CE2 E:TYR16 4.5 14.0 1.0
NH1 J:ARG129 4.6 21.5 1.0

Iron binding site 7 out of 8 in 5gyr

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Iron binding site 7 out of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe201

b:21.2
occ:1.00
FE M:HEC201 0.0 21.2 1.0
ND M:HEC201 1.9 23.1 1.0
NA M:HEC201 2.0 19.6 1.0
NC M:HEC201 2.1 24.6 1.0
NB M:HEC201 2.1 22.4 1.0
NE2 M:HIS125 2.2 24.7 1.0
C4D M:HEC201 2.9 21.0 1.0
C1D M:HEC201 3.0 22.1 1.0
C1A M:HEC201 3.0 21.2 1.0
C4A M:HEC201 3.0 19.9 1.0
C4B M:HEC201 3.1 22.7 1.0
C4C M:HEC201 3.1 24.1 1.0
C1C M:HEC201 3.1 24.3 1.0
C1B M:HEC201 3.1 20.6 1.0
CD2 M:HIS125 3.2 22.5 1.0
CE1 M:HIS125 3.2 22.0 1.0
CD1 M:TYR16 3.2 22.9 1.0
CHA M:HEC201 3.4 20.5 1.0
CHD M:HEC201 3.4 21.5 1.0
CHC M:HEC201 3.5 23.7 1.0
CHB M:HEC201 3.5 19.0 1.0
CE1 M:TYR16 3.5 24.4 1.0
CG M:TYR16 3.6 21.0 1.0
CZ M:TYR16 4.1 21.7 1.0
CD2 M:TYR16 4.2 20.6 1.0
C2D M:HEC201 4.2 23.1 1.0
C3D M:HEC201 4.2 23.7 1.0
CB M:TYR16 4.2 19.6 1.0
C3A M:HEC201 4.2 20.8 1.0
C2A M:HEC201 4.2 22.5 1.0
C2C M:HEC201 4.3 25.1 1.0
C3C M:HEC201 4.3 25.9 1.0
C2B M:HEC201 4.3 22.0 1.0
ND1 M:HIS125 4.3 24.1 1.0
CG M:HIS125 4.3 22.1 1.0
C3B M:HEC201 4.3 23.7 1.0
CE2 M:TYR16 4.4 22.1 1.0
NH1 M:ARG129 4.6 27.5 1.0
OH M:TYR16 4.9 26.9 1.0

Iron binding site 8 out of 8 in 5gyr

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Iron binding site 8 out of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe201

b:14.4
occ:1.00
FE N:HEC201 0.0 14.4 1.0
ND N:HEC201 1.9 15.2 1.0
NA N:HEC201 2.0 12.3 1.0
NB N:HEC201 2.1 13.0 1.0
NC N:HEC201 2.1 13.4 1.0
NE2 N:HIS125 2.2 14.4 1.0
C1D N:HEC201 3.0 14.1 1.0
C4D N:HEC201 3.0 15.0 1.0
C4A N:HEC201 3.0 13.0 1.0
C1A N:HEC201 3.0 13.4 1.0
C4B N:HEC201 3.0 12.7 1.0
C1B N:HEC201 3.1 11.9 1.0
C4C N:HEC201 3.1 12.5 1.0
C1C N:HEC201 3.1 13.4 1.0
CD2 N:HIS125 3.2 15.2 1.0
CE1 N:HIS125 3.2 12.8 1.0
CD1 A:TYR16 3.3 14.2 1.0
CHD N:HEC201 3.4 14.1 1.0
CHA N:HEC201 3.4 13.4 1.0
CHB N:HEC201 3.4 11.7 1.0
CHC N:HEC201 3.4 13.8 1.0
CE1 A:TYR16 3.6 12.2 1.0
CG A:TYR16 3.7 13.3 1.0
CB A:TYR16 4.2 13.6 1.0
CZ A:TYR16 4.2 13.3 1.0
CD2 A:TYR16 4.2 14.9 1.0
C2D N:HEC201 4.2 14.5 1.0
C3D N:HEC201 4.2 13.7 1.0
C3A N:HEC201 4.2 13.2 1.0
C2A N:HEC201 4.2 14.8 1.0
C2C N:HEC201 4.3 13.3 1.0
ND1 N:HIS125 4.3 16.3 1.0
C3C N:HEC201 4.3 14.8 1.0
C2B N:HEC201 4.3 14.5 1.0
C3B N:HEC201 4.3 14.0 1.0
CG N:HIS125 4.3 16.7 1.0
CE2 A:TYR16 4.5 11.9 1.0
NH1 N:ARG129 4.6 18.2 1.0

Reference:

M.Yamanaka, M.Hoshizumi, S.Nagao, R.Nakayama, N.Shibata, Y.Higuchi, S.Hirota. Formation and Carbon Monoxide-Dependent Dissociation of Allochromatium Vinosum Cytochrome C' Oligomers Using Domain-Swapped Dimers Protein Sci. V. 26 464 2017.
ISSN: ESSN 1469-896X
PubMed: 27883268
DOI: 10.1002/PRO.3090
Page generated: Sun Dec 13 16:02:52 2020

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