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Iron in PDB 2e81: Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine

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

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

Protein crystallography data

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine, PDB code: 2e81 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) 25.00 / 2.00
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 119.891, 119.891, 186.224, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.3

Other elements in 2e81:

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine 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 Intermediate Hydroxylamine (pdb code 2e81). 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 Intermediate Hydroxylamine, PDB code: 2e81:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 2e81

Go back to Iron Binding Sites List in 2e81
Iron binding site 1 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine


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 Intermediate Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1508

b:29.1
occ:1.00
 FE A:HEM1508 0.0 29.1 1.0
N A:HOA704 1.7 32.3 1.0
NB A:HEM1508 2.0 27.6 1.0
ND A:HEM1508 2.0 27.8 1.0
NA A:HEM1508 2.0 27.1 1.0
NC A:HEM1508 2.0 26.5 1.0
NZ A:LYS134 2.1 26.1 1.0
O A:HOA704 2.8 34.6 1.0
C1B A:HEM1508 3.0 27.9 1.0
C4B A:HEM1508 3.0 29.3 1.0
C4A A:HEM1508 3.0 25.4 1.0
C1D A:HEM1508 3.0 31.0 1.0
C4C A:HEM1508 3.0 25.9 1.0
C4D A:HEM1508 3.0 29.9 1.0
C1C A:HEM1508 3.0 28.5 1.0
C1A A:HEM1508 3.0 29.8 1.0
CE A:LYS134 3.2 23.8 1.0
CHB A:HEM1508 3.4 26.4 1.0
CHD A:HEM1508 3.4 25.6 1.0
CHC A:HEM1508 3.4 27.0 1.0
CHA A:HEM1508 3.4 28.6 1.0
NE2 A:HIS277 4.1 28.6 1.0
O A:HOH1589 4.2 25.0 1.0
C2B A:HEM1508 4.2 29.6 1.0
C3B A:HEM1508 4.3 26.6 1.0
C2D A:HEM1508 4.3 26.0 1.0
C2C A:HEM1508 4.3 27.9 1.0
C3A A:HEM1508 4.3 26.3 1.0
C3D A:HEM1508 4.3 25.3 1.0
C3C A:HEM1508 4.3 27.6 1.0
C2A A:HEM1508 4.3 26.2 1.0
CD A:LYS134 4.5 27.5 1.0
O A:HOH1514 4.6 49.1 1.0
CD2 A:HIS277 4.7 26.8 1.0
O A:HOH1515 4.8 29.2 1.0

Iron binding site 2 out of 5 in 2e81

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


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 Intermediate Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1509

b:35.4
occ:1.00
 FE A:HEM1509 0.0 35.4 1.0
NE2 A:HIS172 2.0 30.7 1.0
ND A:HEM1509 2.0 39.0 1.0
NA A:HEM1509 2.0 38.9 1.0
NB A:HEM1509 2.0 33.7 1.0
NC A:HEM1509 2.0 35.6 1.0
NE2 A:HIS313 2.0 28.6 1.0
CE1 A:HIS172 2.9 32.9 1.0
CE1 A:HIS313 3.0 34.0 1.0
C4D A:HEM1509 3.0 37.2 1.0
C1D A:HEM1509 3.0 36.7 1.0
C1B A:HEM1509 3.0 36.2 1.0
CD2 A:HIS172 3.0 32.2 1.0
C4A A:HEM1509 3.0 34.2 1.0
C4C A:HEM1509 3.0 37.6 1.0
C1A A:HEM1509 3.0 40.1 1.0
C4B A:HEM1509 3.0 33.8 1.0
C1C A:HEM1509 3.0 34.0 1.0
CD2 A:HIS313 3.0 33.8 1.0
CHA A:HEM1509 3.4 34.7 1.0
CHB A:HEM1509 3.4 34.1 1.0
CHD A:HEM1509 3.4 39.1 1.0
CHC A:HEM1509 3.4 33.6 1.0
ND1 A:HIS172 4.1 31.8 1.0
CG A:HIS172 4.1 31.9 1.0
ND1 A:HIS313 4.1 28.7 1.0
CG A:HIS313 4.2 30.8 1.0
C3D A:HEM1509 4.2 39.4 1.0
C2D A:HEM1509 4.3 40.1 1.0
C2B A:HEM1509 4.3 34.5 1.0
C3A A:HEM1509 4.3 34.5 1.0
C2A A:HEM1509 4.3 35.6 1.0
C3B A:HEM1509 4.3 34.9 1.0
C3C A:HEM1509 4.3 39.0 1.0
C2C A:HEM1509 4.3 35.4 1.0
CE A:MET300 4.6 38.0 1.0

Iron binding site 3 out of 5 in 2e81

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


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 Intermediate Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1510

b:31.0
occ:1.00
 FE A:HEM1510 0.0 31.0 1.0
NA A:HEM1510 1.9 26.8 1.0
ND A:HEM1510 2.0 29.6 1.0
NC A:HEM1510 2.0 29.1 1.0
NB A:HEM1510 2.0 31.5 1.0
NE2 A:HIS102 2.0 32.0 1.0
NE2 A:HIS215 2.0 30.0 1.0
CE1 A:HIS102 2.9 31.0 1.0
CE1 A:HIS215 3.0 32.2 1.0
C4A A:HEM1510 3.0 29.8 1.0
C1D A:HEM1510 3.0 27.5 1.0
C4C A:HEM1510 3.0 27.3 1.0
C1B A:HEM1510 3.0 29.5 1.0
C1A A:HEM1510 3.0 29.1 1.0
C1C A:HEM1510 3.0 29.3 1.0
C4D A:HEM1510 3.0 25.6 1.0
C4B A:HEM1510 3.1 29.5 1.0
CD2 A:HIS102 3.1 24.5 1.0
CD2 A:HIS215 3.2 28.5 1.0
CHB A:HEM1510 3.3 25.8 1.0
CHD A:HEM1510 3.3 24.7 1.0
CHC A:HEM1510 3.4 31.0 1.0
CHA A:HEM1510 3.4 25.3 1.0
ND1 A:HIS102 4.1 32.0 1.0
ND1 A:HIS215 4.1 30.4 1.0
C3A A:HEM1510 4.2 26.7 1.0
C2D A:HEM1510 4.2 29.1 1.0
CG A:HIS102 4.2 35.2 1.0
C3C A:HEM1510 4.2 25.3 1.0
C2A A:HEM1510 4.2 29.1 1.0
C2C A:HEM1510 4.2 27.2 1.0
C3D A:HEM1510 4.2 27.0 1.0
C2B A:HEM1510 4.3 28.0 1.0
CG A:HIS215 4.3 28.8 1.0
C3B A:HEM1510 4.3 31.1 1.0
CMD A:HEM1508 4.9 23.6 1.0

Iron binding site 4 out of 5 in 2e81

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


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 Intermediate Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1511

b:33.9
occ:1.00
 FE A:HEM1511 0.0 33.9 1.0
NB A:HEM1511 1.9 27.5 1.0
ND A:HEM1511 1.9 33.0 1.0
NC A:HEM1511 2.0 31.8 1.0
NA A:HEM1511 2.0 29.1 1.0
NE2 A:HIS299 2.0 30.9 1.0
NE2 A:HIS405 2.1 32.1 1.0
CE1 A:HIS405 2.8 31.3 1.0
C1D A:HEM1511 3.0 31.9 1.0
C1B A:HEM1511 3.0 32.6 1.0
C4C A:HEM1511 3.0 24.0 1.0
C4B A:HEM1511 3.0 29.0 1.0
C4D A:HEM1511 3.0 32.9 1.0
C1C A:HEM1511 3.0 30.4 1.0
C1A A:HEM1511 3.0 26.0 1.0
C4A A:HEM1511 3.0 22.5 1.0
CE1 A:HIS299 3.0 28.7 1.0
CD2 A:HIS299 3.1 34.4 1.0
CD2 A:HIS405 3.3 29.8 1.0
CHD A:HEM1511 3.3 25.8 1.0
CHB A:HEM1511 3.4 28.5 1.0
CHC A:HEM1511 3.4 29.8 1.0
CHA A:HEM1511 3.4 24.6 1.0
ND1 A:HIS405 4.1 34.7 1.0
ND1 A:HIS299 4.2 29.6 1.0
C2D A:HEM1511 4.2 29.9 1.0
C3D A:HEM1511 4.2 31.1 1.0
C2B A:HEM1511 4.2 30.9 1.0
CG A:HIS299 4.2 28.6 1.0
C3B A:HEM1511 4.2 30.6 1.0
C2C A:HEM1511 4.2 29.5 1.0
C3C A:HEM1511 4.3 28.6 1.0
C2A A:HEM1511 4.3 24.6 1.0
C3A A:HEM1511 4.3 26.8 1.0
CG A:HIS405 4.3 35.5 1.0

Iron binding site 5 out of 5 in 2e81

Go back to Iron Binding Sites List in 2e81
Iron binding site 5 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes with Bound Intermediate Hydroxylamine


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 Intermediate Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1512

b:41.8
occ:1.00
 FE A:HEM1512 0.0 41.8 1.0
NC A:HEM1512 2.0 40.5 1.0
NB A:HEM1512 2.0 37.7 1.0
ND A:HEM1512 2.0 41.8 1.0
NA A:HEM1512 2.0 40.8 1.0
NE2 A:HIS330 2.0 50.7 1.0
NE2 A:HIS288 2.0 35.3 1.0
CE1 A:HIS330 2.9 52.1 1.0
C1C A:HEM1512 3.0 41.0 1.0
CE1 A:HIS288 3.0 32.6 1.0
C4B A:HEM1512 3.0 36.9 1.0
C4D A:HEM1512 3.0 44.4 1.0
C1A A:HEM1512 3.0 40.5 1.0
C4C A:HEM1512 3.0 43.1 1.0
C1D A:HEM1512 3.0 47.0 1.0
C1B A:HEM1512 3.0 39.4 1.0
C4A A:HEM1512 3.0 41.0 1.0
CD2 A:HIS288 3.1 30.6 1.0
CD2 A:HIS330 3.1 54.3 1.0
CHC A:HEM1512 3.3 37.7 1.0
CHA A:HEM1512 3.4 42.0 1.0
CHD A:HEM1512 3.4 45.7 1.0
CHB A:HEM1512 3.4 38.4 1.0
ND1 A:HIS330 4.1 57.0 1.0
ND1 A:HIS288 4.2 32.9 1.0
CG A:HIS288 4.2 29.3 1.0
CG A:HIS330 4.2 56.6 1.0
C2C A:HEM1512 4.2 44.8 1.0
C3B A:HEM1512 4.3 37.7 1.0
C3D A:HEM1512 4.3 45.2 1.0
C2B A:HEM1512 4.3 35.6 1.0
C2D A:HEM1512 4.3 46.2 1.0
C2A A:HEM1512 4.3 41.8 1.0
C3C A:HEM1512 4.3 43.0 1.0
C3A A:HEM1512 4.3 44.5 1.0
CBC A:HEM1511 4.7 33.0 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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