Iron in PDB 1nir: Oxydized Nitrite Reductase From Pseudomonas Aeruginosa
Enzymatic activity of Oxydized Nitrite Reductase From Pseudomonas Aeruginosa
All present enzymatic activity of Oxydized Nitrite Reductase From Pseudomonas Aeruginosa:
1.9.3.2;
Protein crystallography data
The structure of Oxydized Nitrite Reductase From Pseudomonas Aeruginosa, PDB code: 1nir
was solved by
D.Nurizzo,
M.Tegoni,
C.Cambillau,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.15
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
163.068,
90.072,
111.888,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.9 /
24.2
|
Other elements in 1nir:
The structure of Oxydized Nitrite Reductase From Pseudomonas Aeruginosa also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Oxydized Nitrite Reductase From Pseudomonas Aeruginosa
(pdb code 1nir). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Oxydized Nitrite Reductase From Pseudomonas Aeruginosa, PDB code: 1nir:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1nir
Go back to
Iron Binding Sites List in 1nir
Iron binding site 1 out
of 4 in the Oxydized Nitrite Reductase From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Oxydized Nitrite Reductase From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:29.9
occ:1.00
|
FE
|
A:HEC601
|
0.0
|
29.9
|
1.0
|
NA
|
A:HEC601
|
1.9
|
27.0
|
1.0
|
NB
|
A:HEC601
|
1.9
|
30.5
|
1.0
|
NC
|
A:HEC601
|
2.0
|
29.1
|
1.0
|
ND
|
A:HEC601
|
2.0
|
31.9
|
1.0
|
NE2
|
A:HIS51
|
2.1
|
32.1
|
1.0
|
SD
|
A:MET88
|
2.3
|
30.4
|
1.0
|
C1A
|
A:HEC601
|
3.0
|
26.4
|
1.0
|
C1B
|
A:HEC601
|
3.0
|
29.5
|
1.0
|
C4B
|
A:HEC601
|
3.0
|
30.4
|
1.0
|
C4A
|
A:HEC601
|
3.0
|
27.0
|
1.0
|
C4D
|
A:HEC601
|
3.0
|
28.4
|
1.0
|
CE1
|
A:HIS51
|
3.0
|
34.9
|
1.0
|
C1C
|
A:HEC601
|
3.0
|
28.8
|
1.0
|
C4C
|
A:HEC601
|
3.1
|
29.4
|
1.0
|
CD2
|
A:HIS51
|
3.1
|
31.5
|
1.0
|
C1D
|
A:HEC601
|
3.1
|
31.9
|
1.0
|
CHA
|
A:HEC601
|
3.4
|
26.1
|
1.0
|
CHB
|
A:HEC601
|
3.4
|
29.3
|
1.0
|
CHC
|
A:HEC601
|
3.4
|
24.2
|
1.0
|
CE
|
A:MET88
|
3.5
|
17.9
|
1.0
|
CHD
|
A:HEC601
|
3.5
|
30.0
|
1.0
|
CG
|
A:MET88
|
3.7
|
28.5
|
1.0
|
ND1
|
A:HIS51
|
4.2
|
32.5
|
1.0
|
C3B
|
A:HEC601
|
4.2
|
31.8
|
1.0
|
C2B
|
A:HEC601
|
4.2
|
27.4
|
1.0
|
CG
|
A:HIS51
|
4.2
|
32.1
|
1.0
|
C2A
|
A:HEC601
|
4.2
|
26.2
|
1.0
|
C3A
|
A:HEC601
|
4.2
|
24.1
|
1.0
|
CB
|
A:MET88
|
4.2
|
30.9
|
1.0
|
C3D
|
A:HEC601
|
4.3
|
30.7
|
1.0
|
C3C
|
A:HEC601
|
4.3
|
26.1
|
1.0
|
C2C
|
A:HEC601
|
4.3
|
27.9
|
1.0
|
C2D
|
A:HEC601
|
4.3
|
28.4
|
1.0
|
CA
|
A:MET88
|
4.7
|
34.1
|
1.0
|
CD1
|
A:LEU63
|
5.0
|
24.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 1nir
Go back to
Iron Binding Sites List in 1nir
Iron binding site 2 out
of 4 in the Oxydized Nitrite Reductase From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Oxydized Nitrite Reductase From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:29.6
occ:1.00
|
FE
|
A:DHE602
|
0.0
|
29.6
|
1.0
|
NE2
|
A:HIS182
|
2.0
|
28.9
|
1.0
|
O
|
A:OH603
|
2.1
|
36.4
|
1.0
|
NB
|
A:DHE602
|
2.1
|
27.7
|
1.0
|
NA
|
A:DHE602
|
2.1
|
27.1
|
1.0
|
ND
|
A:DHE602
|
2.1
|
27.8
|
1.0
|
NC
|
A:DHE602
|
2.1
|
31.5
|
1.0
|
CD2
|
A:HIS182
|
2.9
|
27.0
|
1.0
|
CE1
|
A:HIS182
|
3.0
|
28.4
|
1.0
|
C1B
|
A:DHE602
|
3.0
|
28.4
|
1.0
|
C1C
|
A:DHE602
|
3.0
|
29.6
|
1.0
|
C4B
|
A:DHE602
|
3.1
|
28.2
|
1.0
|
C4A
|
A:DHE602
|
3.1
|
26.6
|
1.0
|
C4C
|
A:DHE602
|
3.1
|
30.8
|
1.0
|
C1D
|
A:DHE602
|
3.1
|
28.0
|
1.0
|
C4D
|
A:DHE602
|
3.1
|
29.1
|
1.0
|
C1A
|
A:DHE602
|
3.1
|
26.0
|
1.0
|
CHC
|
A:DHE602
|
3.4
|
32.7
|
1.0
|
CHB
|
A:DHE602
|
3.4
|
22.1
|
1.0
|
CHD
|
A:DHE602
|
3.4
|
29.9
|
1.0
|
CHA
|
A:DHE602
|
3.4
|
23.2
|
1.0
|
CG
|
A:HIS182
|
4.1
|
26.8
|
1.0
|
ND1
|
A:HIS182
|
4.1
|
24.8
|
1.0
|
OH
|
B:TYR10
|
4.2
|
51.8
|
1.0
|
C2D
|
A:DHE602
|
4.3
|
29.7
|
1.0
|
C3D
|
A:DHE602
|
4.3
|
27.0
|
1.0
|
C3A
|
A:DHE602
|
4.3
|
30.9
|
1.0
|
C2A
|
A:DHE602
|
4.3
|
26.5
|
1.0
|
C2B
|
A:DHE602
|
4.3
|
30.9
|
1.0
|
C2C
|
A:DHE602
|
4.3
|
28.1
|
1.0
|
C3B
|
A:DHE602
|
4.4
|
30.4
|
1.0
|
C3C
|
A:DHE602
|
4.4
|
29.6
|
1.0
|
O2C
|
A:DHE602
|
4.8
|
33.7
|
1.0
|
O
|
A:HOH612
|
4.8
|
30.7
|
1.0
|
CE1
|
B:TYR10
|
4.9
|
47.2
|
1.0
|
O2B
|
A:DHE602
|
5.0
|
25.1
|
1.0
|
CE1
|
A:HIS327
|
5.0
|
25.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 1nir
Go back to
Iron Binding Sites List in 1nir
Iron binding site 3 out
of 4 in the Oxydized Nitrite Reductase From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Oxydized Nitrite Reductase From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe601
b:32.0
occ:1.00
|
FE
|
B:HEC601
|
0.0
|
32.0
|
1.0
|
NA
|
B:HEC601
|
2.0
|
31.8
|
1.0
|
NC
|
B:HEC601
|
2.0
|
29.3
|
1.0
|
NB
|
B:HEC601
|
2.0
|
29.7
|
1.0
|
ND
|
B:HEC601
|
2.0
|
31.3
|
1.0
|
NE2
|
B:HIS51
|
2.1
|
34.3
|
1.0
|
SD
|
B:MET88
|
2.3
|
33.1
|
1.0
|
C4C
|
B:HEC601
|
3.0
|
31.0
|
1.0
|
C4A
|
B:HEC601
|
3.0
|
31.8
|
1.0
|
CE1
|
B:HIS51
|
3.0
|
30.4
|
1.0
|
C1A
|
B:HEC601
|
3.0
|
32.3
|
1.0
|
C1C
|
B:HEC601
|
3.0
|
28.2
|
1.0
|
C1B
|
B:HEC601
|
3.0
|
29.1
|
1.0
|
C4D
|
B:HEC601
|
3.0
|
32.1
|
1.0
|
C1D
|
B:HEC601
|
3.0
|
30.0
|
1.0
|
C4B
|
B:HEC601
|
3.0
|
30.5
|
1.0
|
CD2
|
B:HIS51
|
3.1
|
31.1
|
1.0
|
CHB
|
B:HEC601
|
3.4
|
29.4
|
1.0
|
CHD
|
B:HEC601
|
3.4
|
30.7
|
1.0
|
CHA
|
B:HEC601
|
3.4
|
31.8
|
1.0
|
CHC
|
B:HEC601
|
3.4
|
24.6
|
1.0
|
CE
|
B:MET88
|
3.5
|
30.2
|
1.0
|
CG
|
B:MET88
|
3.6
|
31.0
|
1.0
|
ND1
|
B:HIS51
|
4.1
|
31.1
|
1.0
|
CB
|
B:MET88
|
4.2
|
32.4
|
1.0
|
CG
|
B:HIS51
|
4.2
|
32.0
|
1.0
|
C2A
|
B:HEC601
|
4.2
|
29.9
|
1.0
|
C3A
|
B:HEC601
|
4.3
|
29.3
|
1.0
|
C3C
|
B:HEC601
|
4.3
|
32.9
|
1.0
|
C2C
|
B:HEC601
|
4.3
|
31.8
|
1.0
|
C2B
|
B:HEC601
|
4.3
|
29.0
|
1.0
|
C2D
|
B:HEC601
|
4.3
|
29.9
|
1.0
|
C3B
|
B:HEC601
|
4.3
|
28.8
|
1.0
|
C3D
|
B:HEC601
|
4.3
|
31.7
|
1.0
|
CA
|
B:MET88
|
4.7
|
35.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 1nir
Go back to
Iron Binding Sites List in 1nir
Iron binding site 4 out
of 4 in the Oxydized Nitrite Reductase From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Oxydized Nitrite Reductase From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe602
b:30.2
occ:1.00
|
FE
|
B:DHE602
|
0.0
|
30.2
|
1.0
|
NE2
|
B:HIS182
|
2.0
|
27.5
|
1.0
|
O
|
B:OH603
|
2.0
|
39.9
|
1.0
|
NB
|
B:DHE602
|
2.1
|
28.9
|
1.0
|
NA
|
B:DHE602
|
2.1
|
30.1
|
1.0
|
ND
|
B:DHE602
|
2.1
|
29.3
|
1.0
|
NC
|
B:DHE602
|
2.1
|
32.2
|
1.0
|
CD2
|
B:HIS182
|
3.0
|
27.1
|
1.0
|
CE1
|
B:HIS182
|
3.0
|
28.9
|
1.0
|
C1B
|
B:DHE602
|
3.0
|
30.9
|
1.0
|
C1C
|
B:DHE602
|
3.0
|
29.5
|
1.0
|
C1D
|
B:DHE602
|
3.1
|
29.2
|
1.0
|
C4A
|
B:DHE602
|
3.1
|
29.3
|
1.0
|
C4B
|
B:DHE602
|
3.1
|
31.4
|
1.0
|
C4D
|
B:DHE602
|
3.1
|
32.2
|
1.0
|
C4C
|
B:DHE602
|
3.1
|
29.6
|
1.0
|
C1A
|
B:DHE602
|
3.1
|
31.2
|
1.0
|
CHC
|
B:DHE602
|
3.4
|
30.2
|
1.0
|
CHB
|
B:DHE602
|
3.4
|
27.8
|
1.0
|
CHD
|
B:DHE602
|
3.4
|
27.6
|
1.0
|
CHA
|
B:DHE602
|
3.4
|
29.2
|
1.0
|
OH
|
A:TYR10
|
4.1
|
49.2
|
1.0
|
ND1
|
B:HIS182
|
4.1
|
27.1
|
1.0
|
CG
|
B:HIS182
|
4.1
|
30.0
|
1.0
|
C3D
|
B:DHE602
|
4.3
|
29.4
|
1.0
|
C2D
|
B:DHE602
|
4.3
|
27.9
|
1.0
|
C2A
|
B:DHE602
|
4.3
|
30.7
|
1.0
|
C3A
|
B:DHE602
|
4.3
|
33.0
|
1.0
|
C2B
|
B:DHE602
|
4.3
|
28.2
|
1.0
|
C2C
|
B:DHE602
|
4.3
|
30.4
|
1.0
|
C3B
|
B:DHE602
|
4.4
|
29.1
|
1.0
|
C3C
|
B:DHE602
|
4.4
|
31.6
|
1.0
|
O
|
B:HOH659
|
4.8
|
29.2
|
1.0
|
O2C
|
B:DHE602
|
4.8
|
30.9
|
1.0
|
CE1
|
A:TYR10
|
4.8
|
45.9
|
1.0
|
O2B
|
B:DHE602
|
4.9
|
31.4
|
1.0
|
CZ
|
A:TYR10
|
4.9
|
45.9
|
1.0
|
|
Reference:
D.Nurizzo,
M.C.Silvestrini,
M.Mathieu,
F.Cutruzzola,
D.Bourgeois,
V.Fulop,
J.Hajdu,
M.Brunori,
M.Tegoni,
C.Cambillau.
N-Terminal Arm Exchange Is Observed in the 2.15 A Crystal Structure of Oxidized Nitrite Reductase From Pseudomonas Aeruginosa. Structure V. 5 1157 1997.
ISSN: ISSN 0969-2126
PubMed: 9331415
DOI: 10.1016/S0969-2126(97)00267-0
Page generated: Sat Aug 3 11:37:22 2024
|