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Iron in PDB 1fs7: Cytochrome C Nitrite Reductase From Wolinella Succinogenes

Protein crystallography data

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes, PDB code: 1fs7 was solved by O.Einsle, P.Stach, A.Messerschmidt, J.Simon, A.Kroeger, R.Huber, P.M.H.Kroneck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.60
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 119.822, 119.822, 186.025, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.7

Other elements in 1fs7:

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes also contains other interesting chemical elements:

Yttrium (Y) 3 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes (pdb code 1fs7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes, PDB code: 1fs7:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 1fs7

Go back to Iron Binding Sites List in 1fs7
Iron binding site 1 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe508

b:17.1
occ:1.00
FE A:HEM508 0.0 17.1 1.0
ND A:HEM508 2.0 18.0 1.0
NC A:HEM508 2.0 20.0 1.0
NA A:HEM508 2.0 18.0 1.0
NB A:HEM508 2.0 17.6 1.0
O A:HOH658 2.0 17.0 1.0
NZ A:LYS134 2.1 15.1 1.0
C4C A:HEM508 3.0 13.1 1.0
C4D A:HEM508 3.0 16.6 1.0
C1A A:HEM508 3.0 15.6 1.0
C1D A:HEM508 3.0 17.1 1.0
C1C A:HEM508 3.0 17.5 1.0
C4A A:HEM508 3.0 16.4 1.0
C4B A:HEM508 3.0 17.9 1.0
CE A:LYS134 3.0 14.3 1.0
C1B A:HEM508 3.0 18.5 1.0
CHD A:HEM508 3.4 14.3 1.0
CHA A:HEM508 3.4 16.9 1.0
CHC A:HEM508 3.4 17.0 1.0
CHB A:HEM508 3.4 18.2 1.0
NE2 A:HIS277 4.0 17.6 1.0
O A:HOH660 4.2 22.3 1.0
O A:HOH724 4.3 17.5 1.0
C2A A:HEM508 4.3 17.5 1.0
C3D A:HEM508 4.3 17.0 1.0
C2D A:HEM508 4.3 16.4 1.0
C2C A:HEM508 4.3 17.0 1.0
C3A A:HEM508 4.3 19.7 1.0
C3C A:HEM508 4.3 16.3 1.0
C2B A:HEM508 4.3 19.6 1.0
C3B A:HEM508 4.3 16.9 1.0
CD A:LYS134 4.4 13.4 1.0
O A:HOH712 4.5 19.8 1.0
CD2 A:HIS277 4.7 14.6 1.0
CMD A:HEM510 4.9 18.2 1.0
CE1 A:HIS277 5.0 19.0 1.0

Iron binding site 2 out of 5 in 1fs7

Go back to Iron Binding Sites List in 1fs7
Iron binding site 2 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe509

b:20.3
occ:1.00
FE A:HEM509 0.0 20.3 1.0
NE2 A:HIS172 2.0 21.4 1.0
ND A:HEM509 2.0 23.4 1.0
NA A:HEM509 2.0 18.0 1.0
NC A:HEM509 2.0 18.9 1.0
NB A:HEM509 2.0 18.9 1.0
NE2 A:HIS313 2.0 20.4 1.0
CE1 A:HIS172 2.9 22.1 1.0
C4D A:HEM509 3.0 23.2 1.0
C4C A:HEM509 3.0 21.6 1.0
C1D A:HEM509 3.0 23.4 1.0
C4A A:HEM509 3.0 24.1 1.0
C1A A:HEM509 3.0 25.8 1.0
CD2 A:HIS313 3.0 21.5 1.0
C1C A:HEM509 3.0 22.3 1.0
CD2 A:HIS172 3.0 18.4 1.0
C1B A:HEM509 3.0 21.9 1.0
C4B A:HEM509 3.1 19.3 1.0
CE1 A:HIS313 3.1 21.4 1.0
CHD A:HEM509 3.4 23.2 1.0
CHA A:HEM509 3.4 24.9 1.0
CHB A:HEM509 3.4 21.7 1.0
CHC A:HEM509 3.4 20.9 1.0
ND1 A:HIS172 4.1 21.0 1.0
CG A:HIS172 4.1 20.9 1.0
CG A:HIS313 4.2 21.1 1.0
ND1 A:HIS313 4.2 21.5 1.0
C3D A:HEM509 4.2 23.2 1.0
C3A A:HEM509 4.3 22.7 1.0
C2D A:HEM509 4.3 23.9 1.0
C3C A:HEM509 4.3 20.1 1.0
C2C A:HEM509 4.3 21.2 1.0
C2A A:HEM509 4.3 23.8 1.0
C2B A:HEM509 4.3 23.5 1.0
C3B A:HEM509 4.3 20.9 1.0
CE A:MET300 4.6 22.8 1.0

Iron binding site 3 out of 5 in 1fs7

Go back to Iron Binding Sites List in 1fs7
Iron binding site 3 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe510

b:16.8
occ:1.00
FE A:HEM510 0.0 16.8 1.0
NC A:HEM510 2.0 12.4 1.0
NA A:HEM510 2.0 13.0 1.0
ND A:HEM510 2.0 16.4 1.0
NB A:HEM510 2.0 16.1 1.0
NE2 A:HIS215 2.0 15.6 1.0
NE2 A:HIS102 2.0 15.9 1.0
CE1 A:HIS102 2.9 16.8 1.0
CE1 A:HIS215 3.0 15.7 1.0
C4A A:HEM510 3.0 16.8 1.0
C1B A:HEM510 3.0 16.8 1.0
C1D A:HEM510 3.0 15.4 1.0
C1C A:HEM510 3.0 16.2 1.0
C4C A:HEM510 3.0 14.6 1.0
C1A A:HEM510 3.0 16.5 1.0
C4B A:HEM510 3.0 16.6 1.0
C4D A:HEM510 3.1 16.5 1.0
CD2 A:HIS215 3.1 18.9 1.0
CD2 A:HIS102 3.2 17.9 1.0
CHB A:HEM510 3.3 15.1 1.0
CHD A:HEM510 3.4 15.3 1.0
CHC A:HEM510 3.4 15.8 1.0
CHA A:HEM510 3.4 17.9 1.0
ND1 A:HIS102 4.1 16.4 1.0
ND1 A:HIS215 4.2 16.5 1.0
C2C A:HEM510 4.2 16.6 1.0
C2D A:HEM510 4.2 15.2 1.0
C3A A:HEM510 4.2 15.2 1.0
CG A:HIS215 4.2 14.9 1.0
C3C A:HEM510 4.2 14.7 1.0
C2B A:HEM510 4.3 17.2 1.0
C2A A:HEM510 4.3 16.2 1.0
CG A:HIS102 4.3 17.7 1.0
C3D A:HEM510 4.3 16.2 1.0
C3B A:HEM510 4.3 15.5 1.0

Iron binding site 4 out of 5 in 1fs7

Go back to Iron Binding Sites List in 1fs7
Iron binding site 4 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe511

b:19.4
occ:1.00
FE A:HEM511 0.0 19.4 1.0
ND A:HEM511 1.9 16.8 1.0
NB A:HEM511 1.9 13.3 1.0
NC A:HEM511 2.0 18.1 1.0
NA A:HEM511 2.0 16.0 1.0
NE2 A:HIS299 2.0 17.8 1.0
NE2 A:HIS405 2.1 18.9 1.0
CE1 A:HIS405 2.9 20.7 1.0
C4D A:HEM511 3.0 18.5 1.0
C1D A:HEM511 3.0 19.1 1.0
C1B A:HEM511 3.0 18.1 1.0
C4A A:HEM511 3.0 17.3 1.0
C4C A:HEM511 3.0 18.4 1.0
C1A A:HEM511 3.0 17.8 1.0
C1C A:HEM511 3.0 17.8 1.0
C4B A:HEM511 3.0 17.6 1.0
CE1 A:HIS299 3.0 19.9 1.0
CD2 A:HIS299 3.1 21.4 1.0
CD2 A:HIS405 3.3 21.1 1.0
CHD A:HEM511 3.4 16.1 1.0
CHA A:HEM511 3.4 16.4 1.0
CHB A:HEM511 3.4 15.2 1.0
CHC A:HEM511 3.4 18.6 1.0
ND1 A:HIS405 4.1 20.3 1.0
ND1 A:HIS299 4.2 19.5 1.0
C3D A:HEM511 4.2 20.1 1.0
CG A:HIS299 4.2 22.3 1.0
C2D A:HEM511 4.2 20.5 1.0
C3A A:HEM511 4.2 14.2 1.0
C2B A:HEM511 4.2 17.5 1.0
C2A A:HEM511 4.3 17.6 1.0
C2C A:HEM511 4.3 18.6 1.0
C3C A:HEM511 4.3 19.1 1.0
C3B A:HEM511 4.3 17.6 1.0
CG A:HIS405 4.3 19.4 1.0

Iron binding site 5 out of 5 in 1fs7

Go back to Iron Binding Sites List in 1fs7
Iron binding site 5 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe512

b:25.7
occ:1.00
FE A:HEM512 0.0 25.7 1.0
NC A:HEM512 2.0 27.7 1.0
NB A:HEM512 2.0 22.2 1.0
ND A:HEM512 2.0 25.7 1.0
NA A:HEM512 2.0 24.3 1.0
NE2 A:HIS330 2.0 36.1 1.0
NE2 A:HIS288 2.0 21.6 1.0
CE1 A:HIS330 2.8 35.5 1.0
CE1 A:HIS288 3.0 18.1 1.0
C1C A:HEM512 3.0 26.3 1.0
C4B A:HEM512 3.0 23.2 1.0
C4D A:HEM512 3.0 28.4 1.0
C1A A:HEM512 3.0 26.0 1.0
C1B A:HEM512 3.0 19.2 1.0
C4C A:HEM512 3.0 30.6 1.0
C1D A:HEM512 3.0 29.6 1.0
C4A A:HEM512 3.0 24.7 1.0
CD2 A:HIS288 3.1 19.0 1.0
CD2 A:HIS330 3.2 36.2 1.0
CHC A:HEM512 3.3 25.5 1.0
CHA A:HEM512 3.4 26.0 1.0
CHD A:HEM512 3.4 29.4 1.0
CHB A:HEM512 3.4 22.3 1.0
ND1 A:HIS330 4.1 36.6 1.0
ND1 A:HIS288 4.1 19.7 1.0
CG A:HIS288 4.2 19.9 1.0
C2C A:HEM512 4.2 30.6 1.0
C3B A:HEM512 4.3 25.6 1.0
CG A:HIS330 4.3 39.0 1.0
C2B A:HEM512 4.3 21.4 1.0
C3D A:HEM512 4.3 30.2 1.0
C2A A:HEM512 4.3 25.3 1.0
C2D A:HEM512 4.3 29.6 1.0
C3C A:HEM512 4.3 29.2 1.0
C3A A:HEM512 4.3 26.9 1.0
CBC A:HEM511 4.8 21.5 1.0

Reference:

O.Einsle, P.Stach, A.Messerschmidt, J.Simon, A.Kroger, R.Huber, P.M.Kroneck. Cytochrome C Nitrite Reductase From Wolinella Succinogenes. Structure at 1.6 A Resolution, Inhibitor Binding, and Heme-Packing Motifs. J.Biol.Chem. V. 275 39608 2000.
ISSN: ISSN 0021-9258
PubMed: 10984487
DOI: 10.1074/JBC.M006188200
Page generated: Sun Dec 13 14:14:24 2020

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