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Iron in PDB 2e80: Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite

Enzymatic activity of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite

All present enzymatic activity of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite:
1.7.2.2;

Protein crystallography data

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite, PDB code: 2e80 was solved by O.Einsle, P.M.H.Kroneck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.60
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 118.984, 118.984, 186.731, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21

Other elements in 2e80:

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite 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 with Bound Substrate Nitrite (pdb code 2e80). 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 with Bound Substrate Nitrite, PDB code: 2e80:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 2e80

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Iron binding site 1 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite


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 with Bound Substrate Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1508

b:19.0
occ:1.00
FE A:HEM1508 0.0 19.0 1.0
N A:NO2704 1.9 23.5 1.0
NB A:HEM1508 2.0 21.8 1.0
NA A:HEM1508 2.0 17.9 1.0
ND A:HEM1508 2.0 21.0 1.0
NC A:HEM1508 2.0 18.8 1.0
NZ A:LYS134 2.1 19.4 1.0
C4A A:HEM1508 3.0 18.1 1.0
C1B A:HEM1508 3.0 19.3 1.0
O2 A:NO2704 3.0 29.5 1.0
C4C A:HEM1508 3.0 19.3 1.0
C1D A:HEM1508 3.0 20.0 1.0
C4D A:HEM1508 3.0 18.2 1.0
C1A A:HEM1508 3.0 18.5 1.0
C1C A:HEM1508 3.0 16.8 1.0
C4B A:HEM1508 3.0 19.1 1.0
CE A:LYS134 3.2 21.0 1.0
O1 A:NO2704 3.3 35.2 1.0
CHB A:HEM1508 3.4 19.8 1.0
CHD A:HEM1508 3.4 18.7 1.0
CHC A:HEM1508 3.4 17.4 1.0
CHA A:HEM1508 3.4 19.0 1.0
O A:HOH1615 4.2 18.8 1.0
C3A A:HEM1508 4.3 16.9 1.0
C2B A:HEM1508 4.3 21.3 1.0
C2C A:HEM1508 4.3 19.2 1.0
C2A A:HEM1508 4.3 18.0 1.0
C3D A:HEM1508 4.3 17.9 1.0
C2D A:HEM1508 4.3 18.9 1.0
C3C A:HEM1508 4.3 19.0 1.0
C3B A:HEM1508 4.3 18.9 1.0
NE2 A:HIS277 4.3 20.0 1.0
CD A:LYS134 4.5 19.0 1.0
O A:HOH1513 4.9 31.3 1.0
CMD A:HEM1510 5.0 15.5 1.0
CD2 A:HIS277 5.0 20.2 1.0

Iron binding site 2 out of 5 in 2e80

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Iron binding site 2 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite


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 with Bound Substrate Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1509

b:22.4
occ:1.00
FE A:HEM1509 0.0 22.4 1.0
NE2 A:HIS172 1.9 23.3 1.0
ND A:HEM1509 2.0 22.3 1.0
NB A:HEM1509 2.0 20.0 1.0
NA A:HEM1509 2.0 21.0 1.0
NC A:HEM1509 2.0 21.1 1.0
NE2 A:HIS313 2.0 25.0 1.0
CE1 A:HIS172 2.8 24.6 1.0
C4D A:HEM1509 3.0 24.2 1.0
C1B A:HEM1509 3.0 22.6 1.0
C4A A:HEM1509 3.0 24.1 1.0
C4B A:HEM1509 3.0 21.0 1.0
C1D A:HEM1509 3.0 23.2 1.0
C1A A:HEM1509 3.0 25.0 1.0
CD2 A:HIS313 3.0 20.6 1.0
CD2 A:HIS172 3.0 21.6 1.0
C1C A:HEM1509 3.0 22.3 1.0
C4C A:HEM1509 3.0 24.3 1.0
CE1 A:HIS313 3.1 23.6 1.0
CHB A:HEM1509 3.4 22.3 1.0
CHA A:HEM1509 3.4 24.7 1.0
CHC A:HEM1509 3.4 21.5 1.0
CHD A:HEM1509 3.4 22.7 1.0
ND1 A:HIS172 4.0 23.1 1.0
CG A:HIS172 4.1 22.9 1.0
ND1 A:HIS313 4.2 24.1 1.0
CG A:HIS313 4.2 22.7 1.0
C3D A:HEM1509 4.2 21.3 1.0
C2B A:HEM1509 4.3 22.8 1.0
C3A A:HEM1509 4.3 24.3 1.0
C2A A:HEM1509 4.3 25.8 1.0
C2D A:HEM1509 4.3 20.7 1.0
C3B A:HEM1509 4.3 22.5 1.0
C2C A:HEM1509 4.3 21.2 1.0
C3C A:HEM1509 4.3 22.5 1.0
CE A:MET300 4.5 23.5 1.0

Iron binding site 3 out of 5 in 2e80

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Iron binding site 3 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite


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 with Bound Substrate Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1510

b:19.2
occ:1.00
FE A:HEM1510 0.0 19.2 1.0
NC A:HEM1510 1.9 19.3 1.0
NA A:HEM1510 1.9 17.7 1.0
ND A:HEM1510 2.0 18.7 1.0
NB A:HEM1510 2.0 20.1 1.0
NE2 A:HIS215 2.0 18.1 1.0
NE2 A:HIS102 2.1 18.7 1.0
C4A A:HEM1510 3.0 21.0 1.0
C4C A:HEM1510 3.0 17.8 1.0
CE1 A:HIS102 3.0 22.0 1.0
C1D A:HEM1510 3.0 17.8 1.0
C1C A:HEM1510 3.0 20.5 1.0
CE1 A:HIS215 3.0 17.1 1.0
C1A A:HEM1510 3.0 20.1 1.0
C1B A:HEM1510 3.0 19.1 1.0
C4B A:HEM1510 3.0 18.9 1.0
C4D A:HEM1510 3.1 17.9 1.0
CD2 A:HIS215 3.1 20.9 1.0
CD2 A:HIS102 3.2 22.8 1.0
CHD A:HEM1510 3.3 18.5 1.0
CHB A:HEM1510 3.3 20.6 1.0
CHC A:HEM1510 3.4 20.4 1.0
CHA A:HEM1510 3.4 19.0 1.0
ND1 A:HIS215 4.2 17.2 1.0
ND1 A:HIS102 4.2 21.0 1.0
C3A A:HEM1510 4.2 19.8 1.0
CG A:HIS215 4.2 20.1 1.0
C2A A:HEM1510 4.2 19.9 1.0
C2C A:HEM1510 4.2 20.7 1.0
C3C A:HEM1510 4.2 18.9 1.0
C2D A:HEM1510 4.3 16.2 1.0
C2B A:HEM1510 4.3 20.2 1.0
C3D A:HEM1510 4.3 17.9 1.0
CG A:HIS102 4.3 19.3 1.0
C3B A:HEM1510 4.3 17.8 1.0
CD1 A:ILE166 4.9 30.3 1.0

Iron binding site 4 out of 5 in 2e80

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Iron binding site 4 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite


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 with Bound Substrate Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1511

b:21.9
occ:1.00
FE A:HEM1511 0.0 21.9 1.0
NB A:HEM1511 1.9 19.8 1.0
ND A:HEM1511 1.9 21.9 1.0
NA A:HEM1511 2.0 19.9 1.0
NC A:HEM1511 2.0 19.5 1.0
NE2 A:HIS299 2.1 20.1 1.0
NE2 A:HIS405 2.1 19.2 1.0
CE1 A:HIS405 2.9 22.2 1.0
C1B A:HEM1511 3.0 21.8 1.0
C1D A:HEM1511 3.0 23.1 1.0
C4D A:HEM1511 3.0 21.3 1.0
C4B A:HEM1511 3.0 20.4 1.0
C4A A:HEM1511 3.0 21.1 1.0
C1C A:HEM1511 3.0 20.8 1.0
C1A A:HEM1511 3.0 22.7 1.0
C4C A:HEM1511 3.0 22.3 1.0
CE1 A:HIS299 3.1 21.7 1.0
CD2 A:HIS299 3.1 25.0 1.0
CD2 A:HIS405 3.3 22.5 1.0
CHB A:HEM1511 3.4 21.2 1.0
CHD A:HEM1511 3.4 20.6 1.0
CHC A:HEM1511 3.4 20.5 1.0
CHA A:HEM1511 3.4 20.5 1.0
ND1 A:HIS405 4.1 23.1 1.0
C3D A:HEM1511 4.2 22.9 1.0
C2D A:HEM1511 4.2 22.4 1.0
C2B A:HEM1511 4.2 21.1 1.0
C3B A:HEM1511 4.2 19.9 1.0
ND1 A:HIS299 4.2 19.9 1.0
C3A A:HEM1511 4.3 18.9 1.0
C2A A:HEM1511 4.3 21.0 1.0
C2C A:HEM1511 4.3 21.3 1.0
CG A:HIS299 4.3 23.9 1.0
C3C A:HEM1511 4.3 21.0 1.0
CG A:HIS405 4.3 23.3 1.0

Iron binding site 5 out of 5 in 2e80

Go back to Iron Binding Sites List in 2e80
Iron binding site 5 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Substrate Nitrite


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 with Bound Substrate Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1512

b:26.2
occ:1.00
FE A:HEM1512 0.0 26.2 1.0
ND A:HEM1512 2.0 27.2 1.0
NC A:HEM1512 2.0 29.3 1.0
NA A:HEM1512 2.0 25.7 1.0
NB A:HEM1512 2.0 26.4 1.0
NE2 A:HIS288 2.1 24.1 1.0
NE2 A:HIS330 2.1 33.1 1.0
CE1 A:HIS330 2.9 33.0 1.0
CE1 A:HIS288 3.0 23.0 1.0
C4D A:HEM1512 3.0 29.4 1.0
C1A A:HEM1512 3.0 28.8 1.0
C1C A:HEM1512 3.0 28.9 1.0
C4B A:HEM1512 3.0 29.3 1.0
C4C A:HEM1512 3.0 28.6 1.0
C1D A:HEM1512 3.0 28.6 1.0
C4A A:HEM1512 3.0 27.1 1.0
C1B A:HEM1512 3.0 25.8 1.0
CD2 A:HIS288 3.1 19.1 1.0
CD2 A:HIS330 3.3 34.1 1.0
CHA A:HEM1512 3.4 26.5 1.0
CHC A:HEM1512 3.4 30.5 1.0
CHD A:HEM1512 3.4 27.5 1.0
CHB A:HEM1512 3.4 25.5 1.0
ND1 A:HIS330 4.1 35.5 1.0
ND1 A:HIS288 4.2 20.5 1.0
CG A:HIS288 4.3 21.0 1.0
C3D A:HEM1512 4.3 30.2 1.0
C2A A:HEM1512 4.3 25.6 1.0
C2C A:HEM1512 4.3 29.9 1.0
C3B A:HEM1512 4.3 29.4 1.0
C2D A:HEM1512 4.3 28.9 1.0
C2B A:HEM1512 4.3 25.5 1.0
C3C A:HEM1512 4.3 30.8 1.0
C3A A:HEM1512 4.3 27.8 1.0
CG A:HIS330 4.3 36.5 1.0
CBC A:HEM1511 4.8 21.6 1.0

Reference:

O.Einsle, A.Messerschmidt, R.Huber, P.M.H.Kroneck, F.Neese. Mechanism of the Six-Electron Reduction of Nitrite to Ammonia By Cytochrome C Nitrite Reductase J.Am.Chem.Soc. V. 124 11737 2002.
ISSN: ISSN 0002-7863
PubMed: 12296741
DOI: 10.1021/JA0206487
Page generated: Sun Dec 13 14:43:22 2020

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