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:
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
Go back to
Iron Binding Sites List in 2e80
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
Go back to
Iron Binding Sites List in 2e80
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
Go back to
Iron Binding Sites List in 2e80
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
Go back to
Iron Binding Sites List in 2e80
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: Sat Aug 3 21:01:08 2024
|