Atomistry » Iron » PDB 1iro-1j3y » 1j0o
Atomistry »
  Iron »
    PDB 1iro-1j3y »
      1j0o »

Iron in PDB 1j0o: High Resolution Crystal Structure of the Wild Type Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F

Protein crystallography data

The structure of High Resolution Crystal Structure of the Wild Type Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 1j0o was solved by K.Ozawa, F.Yasukawa, J.Kumagai, T.Ohmura, M.A.Cusanvich, Y.Tomimoto, H.Ogata, Y.Higuchi, H.Akutsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.336, 67.347, 34.094, 90.00, 90.00, 90.00
R / Rfree (%) 10.8 / 16.7

Iron Binding Sites:

The binding sites of Iron atom in the High Resolution Crystal Structure of the Wild Type Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F (pdb code 1j0o). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the High Resolution Crystal Structure of the Wild Type Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F, PDB code: 1j0o:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1j0o

Go back to Iron Binding Sites List in 1j0o
Iron binding site 1 out of 4 in the High Resolution Crystal Structure of the Wild Type 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 High Resolution Crystal Structure of the Wild Type Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1004

b:9.1
occ:1.00
FE A:HEM1004 0.0 9.1 1.0
NE2 A:HIS106 1.9 9.9 1.0
NE2 A:HIS70 1.9 8.8 1.0
NC A:HEM1004 2.0 9.1 1.0
NB A:HEM1004 2.0 9.5 1.0
ND A:HEM1004 2.1 8.7 1.0
NA A:HEM1004 2.1 9.8 1.0
CE1 A:HIS70 2.9 9.4 1.0
CE1 A:HIS106 2.9 9.5 1.0
C1C A:HEM1004 3.0 9.1 1.0
CD2 A:HIS106 3.0 10.1 1.0
C4C A:HEM1004 3.0 8.9 1.0
CD2 A:HIS70 3.0 9.5 1.0
C1D A:HEM1004 3.0 8.5 1.0
C1B A:HEM1004 3.1 9.9 1.0
C4D A:HEM1004 3.1 8.9 1.0
C4A A:HEM1004 3.1 9.7 1.0
C1A A:HEM1004 3.1 9.6 1.0
C4B A:HEM1004 3.1 9.9 1.0
CHD A:HEM1004 3.4 8.3 1.0
CHC A:HEM1004 3.4 9.4 1.0
CHA A:HEM1004 3.4 9.3 1.0
CHB A:HEM1004 3.4 10.8 1.0
ND1 A:HIS70 4.1 9.5 1.0
ND1 A:HIS106 4.1 10.3 1.0
CG A:HIS106 4.2 10.2 1.0
CG A:HIS70 4.2 9.5 1.0
C2C A:HEM1004 4.2 10.1 1.0
C2D A:HEM1004 4.3 9.0 1.0
C3C A:HEM1004 4.3 9.4 1.0
C2A A:HEM1004 4.3 10.6 1.0
C3D A:HEM1004 4.3 8.6 1.0
C3A A:HEM1004 4.3 11.1 1.0
C2B A:HEM1004 4.3 11.3 1.0
C3B A:HEM1004 4.3 10.9 1.0
CE2 A:TYR66 4.7 13.8 1.0
C2 A:EOH2001 4.9 28.3 1.0

Iron binding site 2 out of 4 in 1j0o

Go back to Iron Binding Sites List in 1j0o
Iron binding site 2 out of 4 in the High Resolution Crystal Structure of the Wild Type 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 High Resolution Crystal Structure of the Wild Type Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:9.2
occ:1.00
FE A:HEM1002 0.0 9.2 1.0
NE2 A:HIS52 2.0 9.0 1.0
NE2 A:HIS35 2.0 9.1 1.0
NA A:HEM1002 2.0 8.8 1.0
ND A:HEM1002 2.0 9.7 1.0
NB A:HEM1002 2.1 9.4 1.0
NC A:HEM1002 2.1 9.2 1.0
CE1 A:HIS52 2.9 9.5 1.0
CE1 A:HIS35 3.0 10.1 1.0
CD2 A:HIS35 3.0 9.8 1.0
C1A A:HEM1002 3.0 9.5 1.0
CD2 A:HIS52 3.0 8.7 1.0
C4D A:HEM1002 3.0 9.4 1.0
C1D A:HEM1002 3.0 10.5 1.0
C4A A:HEM1002 3.0 9.3 1.0
C1C A:HEM1002 3.1 8.9 1.0
C1B A:HEM1002 3.1 9.9 1.0
C4B A:HEM1002 3.1 8.9 1.0
C4C A:HEM1002 3.1 9.9 1.0
CHA A:HEM1002 3.4 9.8 1.0
CHD A:HEM1002 3.4 10.2 1.0
CHC A:HEM1002 3.4 9.7 1.0
CHB A:HEM1002 3.4 10.4 1.0
ND1 A:HIS52 4.1 9.7 1.0
ND1 A:HIS35 4.1 10.3 1.0
CG A:HIS52 4.2 9.0 1.0
CG A:HIS35 4.2 9.8 1.0
C2A A:HEM1002 4.2 9.9 1.0
C3D A:HEM1002 4.3 11.4 1.0
C3A A:HEM1002 4.3 9.5 1.0
C2C A:HEM1002 4.3 9.8 1.0
C2D A:HEM1002 4.3 11.4 1.0
C2B A:HEM1002 4.3 10.6 1.0
C3B A:HEM1002 4.3 9.8 1.0
C3C A:HEM1002 4.3 10.1 1.0

Iron binding site 3 out of 4 in 1j0o

Go back to Iron Binding Sites List in 1j0o
Iron binding site 3 out of 4 in the High Resolution Crystal Structure of the Wild Type 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 High Resolution Crystal Structure of the Wild Type Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:11.2
occ:1.00
FE A:HEM1001 0.0 11.2 1.0
NE2 A:HIS34 1.9 10.2 1.0
NE2 A:HIS22 2.0 12.1 1.0
NA A:HEM1001 2.1 12.5 1.0
ND A:HEM1001 2.1 10.6 1.0
NB A:HEM1001 2.1 12.0 1.0
NC A:HEM1001 2.1 11.0 1.0
CE1 A:HIS34 2.9 10.7 1.0
CE1 A:HIS22 3.0 12.3 1.0
CD2 A:HIS34 3.0 11.3 1.0
C1D A:HEM1001 3.0 10.4 1.0
CD2 A:HIS22 3.0 13.8 1.0
C4D A:HEM1001 3.0 10.8 1.0
C1C A:HEM1001 3.1 11.3 1.0
C4A A:HEM1001 3.1 13.1 1.0
C1A A:HEM1001 3.1 12.7 1.0
C4B A:HEM1001 3.1 13.2 1.0
C1B A:HEM1001 3.1 13.2 1.0
C4C A:HEM1001 3.1 10.3 1.0
CHC A:HEM1001 3.4 13.4 1.0
CHD A:HEM1001 3.4 10.1 1.0
CHB A:HEM1001 3.4 14.0 1.0
CHA A:HEM1001 3.4 11.8 1.0
ND1 A:HIS34 4.1 10.4 1.0
ND1 A:HIS22 4.1 13.5 1.0
CG A:HIS34 4.1 10.5 1.0
CG A:HIS22 4.2 13.2 1.0
C2D A:HEM1001 4.3 10.3 1.0
C3D A:HEM1001 4.3 10.0 1.0
C2A A:HEM1001 4.3 14.0 1.0
C3A A:HEM1001 4.3 14.7 1.0
C2C A:HEM1001 4.3 12.5 1.0
C2B A:HEM1001 4.3 14.8 1.0
C3B A:HEM1001 4.3 15.0 1.0
C3C A:HEM1001 4.3 11.0 1.0
CD A:PRO5 4.6 18.0 1.0
CE2 A:PHE20 4.7 12.4 1.0

Iron binding site 4 out of 4 in 1j0o

Go back to Iron Binding Sites List in 1j0o
Iron binding site 4 out of 4 in the High Resolution Crystal Structure of the Wild Type 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 High Resolution Crystal Structure of the Wild Type Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1003

b:11.5
occ:1.00
FE A:HEM1003 0.0 11.5 1.0
NE2 A:HIS83 2.0 11.0 1.0
ND A:HEM1003 2.0 12.6 1.0
NA A:HEM1003 2.1 12.5 1.0
NB A:HEM1003 2.1 10.3 1.0
NE2 A:HIS25 2.1 11.9 1.0
NC A:HEM1003 2.1 11.4 1.0
CE1 A:HIS83 2.9 11.8 1.0
CD2 A:HIS25 3.0 12.8 1.0
C1C A:HEM1003 3.0 10.0 1.0
C1D A:HEM1003 3.0 14.3 1.0
C4D A:HEM1003 3.1 14.7 1.0
C4B A:HEM1003 3.1 10.6 1.0
C4A A:HEM1003 3.1 11.5 1.0
CE1 A:HIS25 3.1 15.5 1.0
C1B A:HEM1003 3.1 10.6 1.0
CD2 A:HIS83 3.1 11.3 1.0
C1A A:HEM1003 3.1 13.4 1.0
C4C A:HEM1003 3.1 12.3 1.0
CHC A:HEM1003 3.4 10.9 1.0
CHA A:HEM1003 3.4 14.7 1.0
CHB A:HEM1003 3.4 11.6 1.0
CHD A:HEM1003 3.4 13.8 1.0
ND1 A:HIS83 4.1 12.4 1.0
ND1 A:HIS25 4.2 14.4 1.0
CG A:HIS25 4.2 13.4 1.0
CG A:HIS83 4.2 11.4 1.0
C3D A:HEM1003 4.3 16.4 1.0
C2A A:HEM1003 4.3 13.9 1.0
C3A A:HEM1003 4.3 13.2 1.0
C2D A:HEM1003 4.3 15.9 1.0
C2B A:HEM1003 4.3 9.7 1.0
C3B A:HEM1003 4.3 10.3 1.0
C2C A:HEM1003 4.3 12.2 1.0
C3C A:HEM1003 4.3 12.4 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: Sat Aug 3 08:19:15 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy