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Iron in PDB 1wr5: Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F

Protein crystallography data

The structure of Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 1wr5 was solved by Y.Tomimoto, H.Ogata, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.118, 67.511, 34.142, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 28.2

Iron Binding Sites:

The binding sites of Iron atom in the Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F (pdb code 1wr5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 1wr5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1wr5

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Iron binding site 1 out of 4 in the Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1004

b:5.5
occ:1.00
FE A:HEC1004 0.0 5.5 1.0
NE2 A:HIS70 1.9 10.3 1.0
NE2 A:HIS106 1.9 10.9 1.0
NB A:HEC1004 2.1 11.9 1.0
ND A:HEC1004 2.1 9.9 1.0
NC A:HEC1004 2.1 10.3 1.0
NA A:HEC1004 2.1 11.6 1.0
CE1 A:HIS70 2.9 9.6 1.0
CE1 A:HIS106 2.9 11.2 1.0
CD2 A:HIS70 3.0 10.4 1.0
CD2 A:HIS106 3.0 12.5 1.0
C1D A:HEC1004 3.0 8.8 1.0
C1C A:HEC1004 3.0 9.5 1.0
C1B A:HEC1004 3.1 12.2 1.0
C4C A:HEC1004 3.1 9.0 1.0
C4A A:HEC1004 3.1 12.6 1.0
C4B A:HEC1004 3.1 10.8 1.0
C1A A:HEC1004 3.1 10.4 1.0
C4D A:HEC1004 3.1 10.1 1.0
CHD A:HEC1004 3.3 10.5 1.0
CHB A:HEC1004 3.4 14.6 1.0
CHC A:HEC1004 3.4 11.9 1.0
CHA A:HEC1004 3.5 10.8 1.0
ND1 A:HIS106 4.1 12.1 1.0
ND1 A:HIS70 4.1 10.5 1.0
CG A:HIS70 4.1 10.3 1.0
CG A:HIS106 4.2 12.2 1.0
C2A A:HEC1004 4.3 12.7 1.0
C3D A:HEC1004 4.3 10.6 1.0
C2C A:HEC1004 4.3 9.7 1.0
C2D A:HEC1004 4.3 9.5 1.0
C3C A:HEC1004 4.3 11.7 1.0
C3A A:HEC1004 4.3 14.9 1.0
C2B A:HEC1004 4.3 13.8 1.0
C3B A:HEC1004 4.3 12.1 1.0
CE2 A:TYR66 4.8 17.4 1.0

Iron binding site 2 out of 4 in 1wr5

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Iron binding site 2 out of 4 in the Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:5.8
occ:1.00
FE A:HEC1002 0.0 5.8 1.0
NE2 A:HIS52 2.0 9.9 1.0
NE2 A:HIS35 2.0 10.4 1.0
NB A:HEC1002 2.1 10.2 1.0
ND A:HEC1002 2.1 11.2 1.0
NC A:HEC1002 2.1 11.8 1.0
NA A:HEC1002 2.1 10.7 1.0
CE1 A:HIS52 2.9 9.9 1.0
CE1 A:HIS35 3.0 11.7 1.0
CD2 A:HIS52 3.0 9.0 1.0
CD2 A:HIS35 3.0 11.7 1.0
C1C A:HEC1002 3.1 12.3 1.0
C4B A:HEC1002 3.1 11.4 1.0
C1D A:HEC1002 3.1 12.1 1.0
C4C A:HEC1002 3.1 11.7 1.0
C1A A:HEC1002 3.1 10.7 1.0
C1B A:HEC1002 3.1 11.8 1.0
C4A A:HEC1002 3.1 9.7 1.0
C4D A:HEC1002 3.1 11.5 1.0
CHC A:HEC1002 3.3 12.3 1.0
CHD A:HEC1002 3.4 13.7 1.0
CHB A:HEC1002 3.4 11.8 1.0
CHA A:HEC1002 3.5 13.0 1.0
ND1 A:HIS52 4.1 11.1 1.0
ND1 A:HIS35 4.1 11.6 1.0
CG A:HIS52 4.1 10.7 1.0
CG A:HIS35 4.2 11.5 1.0
C2A A:HEC1002 4.3 11.0 1.0
C2C A:HEC1002 4.3 11.9 1.0
C3B A:HEC1002 4.3 11.5 1.0
C3A A:HEC1002 4.3 10.4 1.0
C2D A:HEC1002 4.3 13.7 1.0
C3D A:HEC1002 4.3 13.8 1.0
C2B A:HEC1002 4.3 12.1 1.0
C3C A:HEC1002 4.3 15.1 1.0

Iron binding site 3 out of 4 in 1wr5

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Iron binding site 3 out of 4 in the Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:7.3
occ:1.00
FE A:HEC1001 0.0 7.3 1.0
NE2 A:HIS34 1.9 11.2 1.0
NE2 A:HIS22 2.0 11.9 1.0
NA A:HEC1001 2.1 12.8 1.0
NB A:HEC1001 2.1 13.8 1.0
ND A:HEC1001 2.1 11.9 1.0
NC A:HEC1001 2.1 11.9 1.0
CE1 A:HIS34 2.9 10.5 1.0
CE1 A:HIS22 2.9 12.2 1.0
CD2 A:HIS34 3.0 13.7 1.0
CD2 A:HIS22 3.0 12.6 1.0
C1D A:HEC1001 3.1 11.5 1.0
C4B A:HEC1001 3.1 14.6 1.0
C1C A:HEC1001 3.1 12.4 1.0
C4A A:HEC1001 3.1 14.8 1.0
C4C A:HEC1001 3.1 11.4 1.0
C1A A:HEC1001 3.1 13.6 1.0
C4D A:HEC1001 3.1 11.9 1.0
C1B A:HEC1001 3.1 14.3 1.0
CHD A:HEC1001 3.4 12.1 1.0
CHC A:HEC1001 3.4 14.6 1.0
CHB A:HEC1001 3.4 15.6 1.0
CHA A:HEC1001 3.4 14.7 1.0
ND1 A:HIS34 4.0 13.2 1.0
ND1 A:HIS22 4.1 15.3 1.0
CG A:HIS34 4.1 13.4 1.0
CG A:HIS22 4.1 15.2 1.0
C2A A:HEC1001 4.3 16.1 1.0
C3A A:HEC1001 4.3 17.6 1.0
C3D A:HEC1001 4.3 13.1 1.0
C2C A:HEC1001 4.3 11.1 1.0
C3B A:HEC1001 4.3 15.4 1.0
C3C A:HEC1001 4.3 13.6 1.0
C2D A:HEC1001 4.3 11.3 1.0
C2B A:HEC1001 4.3 15.5 1.0
CE2 A:PHE20 4.6 12.9 1.0
CD A:PRO5 4.6 20.9 1.0

Iron binding site 4 out of 4 in 1wr5

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Iron binding site 4 out of 4 in the Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Three Dimensional Structure of the E41K Mutant of Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1003

b:5.0
occ:1.00
FE A:HEC1003 0.0 5.0 1.0
NE2 A:HIS83 1.9 9.6 1.0
NE2 A:HIS25 2.1 10.1 1.0
NA A:HEC1003 2.1 10.2 1.0
ND A:HEC1003 2.1 10.4 1.0
NB A:HEC1003 2.1 9.4 1.0
NC A:HEC1003 2.1 10.2 1.0
CE1 A:HIS83 2.9 9.3 1.0
CD2 A:HIS25 3.0 10.8 1.0
C1C A:HEC1003 3.1 9.1 1.0
CD2 A:HIS83 3.1 10.2 1.0
C4D A:HEC1003 3.1 10.3 1.0
C1D A:HEC1003 3.1 11.5 1.0
C1A A:HEC1003 3.1 11.3 1.0
CE1 A:HIS25 3.1 10.0 1.0
C4B A:HEC1003 3.1 8.8 1.0
C4A A:HEC1003 3.1 10.7 1.0
C4C A:HEC1003 3.1 9.2 1.0
C1B A:HEC1003 3.1 9.5 1.0
CHC A:HEC1003 3.3 10.6 1.0
CHD A:HEC1003 3.4 12.0 1.0
CHA A:HEC1003 3.4 12.5 1.0
CHB A:HEC1003 3.4 11.0 1.0
ND1 A:HIS83 4.0 10.5 1.0
ND1 A:HIS25 4.1 11.3 1.0
CG A:HIS25 4.1 10.5 1.0
CG A:HIS83 4.2 11.1 1.0
C3D A:HEC1003 4.3 13.2 1.0
C2A A:HEC1003 4.3 12.0 1.0
C3A A:HEC1003 4.3 11.9 1.0
C2D A:HEC1003 4.3 11.6 1.0
C2C A:HEC1003 4.3 9.7 1.0
C3B A:HEC1003 4.3 10.0 1.0
C3C A:HEC1003 4.3 9.4 1.0
C2B A:HEC1003 4.3 10.0 1.0

Reference:

K.Ozawa, Y.Takayama, F.Yasukawa, T.Ohmura, M.A.Cusanovich, Y.Tomimoto, H.Ogata, Y.Higuchi, H.Akutsu. Role of the Aromatic Ring of TYR43 in Tetraheme Cytochrome C(3) From Desulfovibrio Vulgaris Miyazaki F. Biophys.J. V. 85 3367 2003.
ISSN: ISSN 0006-3495
PubMed: 14581238
DOI: 10.1016/S0006-3495(03)74756-0
Page generated: Wed Jul 16 21:53:29 2025

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