Iron in PDB 2ozy: Crystal Structure of E.Coli Nrfb
Protein crystallography data
The structure of Crystal Structure of E.Coli Nrfb, PDB code: 2ozy
was solved by
T.A.Clarke,
D.J.Richardson,
A.M.Hemmings,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
44.02 /
1.74
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.683,
59.668,
65.207,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.9 /
20.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of E.Coli Nrfb
(pdb code 2ozy). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Crystal Structure of E.Coli Nrfb, PDB code: 2ozy:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 2ozy
Go back to
Iron Binding Sites List in 2ozy
Iron binding site 1 out
of 5 in the Crystal Structure of E.Coli Nrfb
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of E.Coli Nrfb within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:10.1
occ:1.00
|
FE
|
A:HEC201
|
0.0
|
10.1
|
1.0
|
|
ND
|
A:HEC201
|
2.0
|
8.8
|
1.0
|
|
NC
|
A:HEC201
|
2.0
|
9.7
|
1.0
|
|
NA
|
A:HEC201
|
2.0
|
10.3
|
1.0
|
|
NB
|
A:HEC201
|
2.0
|
10.6
|
1.0
|
|
NE2
|
A:HIS64
|
2.1
|
8.5
|
1.0
|
|
NE2
|
A:HIS28
|
2.1
|
7.7
|
1.0
|
|
CD2
|
A:HIS64
|
3.0
|
9.3
|
1.0
|
|
C4C
|
A:HEC201
|
3.0
|
11.3
|
1.0
|
|
C1D
|
A:HEC201
|
3.0
|
11.2
|
1.0
|
|
C1B
|
A:HEC201
|
3.1
|
10.3
|
1.0
|
|
C4B
|
A:HEC201
|
3.1
|
11.0
|
1.0
|
|
C4A
|
A:HEC201
|
3.1
|
9.2
|
1.0
|
|
CE1
|
A:HIS28
|
3.1
|
7.7
|
1.0
|
|
C1A
|
A:HEC201
|
3.1
|
9.1
|
1.0
|
|
C4D
|
A:HEC201
|
3.1
|
11.3
|
1.0
|
|
C1C
|
A:HEC201
|
3.1
|
9.2
|
1.0
|
|
CD2
|
A:HIS28
|
3.1
|
8.8
|
1.0
|
|
CE1
|
A:HIS64
|
3.2
|
10.8
|
1.0
|
|
CHD
|
A:HEC201
|
3.4
|
10.7
|
1.0
|
|
CHB
|
A:HEC201
|
3.4
|
10.3
|
1.0
|
|
CHA
|
A:HEC201
|
3.4
|
10.5
|
1.0
|
|
CHC
|
A:HEC201
|
3.4
|
10.8
|
1.0
|
|
CG
|
A:HIS64
|
4.2
|
12.4
|
1.0
|
|
ND1
|
A:HIS28
|
4.2
|
8.6
|
1.0
|
|
ND1
|
A:HIS64
|
4.2
|
10.7
|
1.0
|
|
CG
|
A:HIS28
|
4.3
|
7.4
|
1.0
|
|
C3C
|
A:HEC201
|
4.3
|
11.0
|
1.0
|
|
C3B
|
A:HEC201
|
4.3
|
11.1
|
1.0
|
|
C2B
|
A:HEC201
|
4.3
|
11.5
|
1.0
|
|
C2D
|
A:HEC201
|
4.3
|
11.6
|
1.0
|
|
C2C
|
A:HEC201
|
4.3
|
10.2
|
1.0
|
|
C3A
|
A:HEC201
|
4.3
|
9.6
|
1.0
|
|
C2A
|
A:HEC201
|
4.3
|
11.7
|
1.0
|
|
C3D
|
A:HEC201
|
4.3
|
11.8
|
1.0
|
|
Iron binding site 2 out
of 5 in 2ozy
Go back to
Iron Binding Sites List in 2ozy
Iron binding site 2 out
of 5 in the Crystal Structure of E.Coli Nrfb
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of E.Coli Nrfb within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe202
b:6.2
occ:1.00
|
FE
|
A:HEC202
|
0.0
|
6.2
|
1.0
|
|
NC
|
A:HEC202
|
2.0
|
5.8
|
1.0
|
|
NA
|
A:HEC202
|
2.0
|
4.8
|
1.0
|
|
ND
|
A:HEC202
|
2.1
|
4.9
|
1.0
|
|
NB
|
A:HEC202
|
2.1
|
4.8
|
1.0
|
|
NE2
|
A:HIS57
|
2.1
|
4.2
|
1.0
|
|
NE2
|
A:HIS120
|
2.1
|
9.9
|
1.0
|
|
C4C
|
A:HEC202
|
3.0
|
6.9
|
1.0
|
|
C1A
|
A:HEC202
|
3.0
|
6.0
|
1.0
|
|
C4D
|
A:HEC202
|
3.0
|
3.4
|
1.0
|
|
C1C
|
A:HEC202
|
3.1
|
7.2
|
1.0
|
|
C1D
|
A:HEC202
|
3.1
|
6.0
|
1.0
|
|
CD2
|
A:HIS57
|
3.1
|
5.0
|
1.0
|
|
C4B
|
A:HEC202
|
3.1
|
5.4
|
1.0
|
|
CD2
|
A:HIS120
|
3.1
|
6.7
|
1.0
|
|
C4A
|
A:HEC202
|
3.1
|
5.2
|
1.0
|
|
CE1
|
A:HIS57
|
3.1
|
6.6
|
1.0
|
|
CE1
|
A:HIS120
|
3.1
|
8.7
|
1.0
|
|
C1B
|
A:HEC202
|
3.1
|
5.7
|
1.0
|
|
CHA
|
A:HEC202
|
3.4
|
5.6
|
1.0
|
|
CHD
|
A:HEC202
|
3.4
|
6.0
|
1.0
|
|
CHC
|
A:HEC202
|
3.4
|
5.3
|
1.0
|
|
CHB
|
A:HEC202
|
3.5
|
6.7
|
1.0
|
|
ND1
|
A:HIS57
|
4.2
|
5.5
|
1.0
|
|
ND1
|
A:HIS120
|
4.2
|
7.9
|
1.0
|
|
CG
|
A:HIS57
|
4.2
|
5.3
|
1.0
|
|
CG
|
A:HIS120
|
4.2
|
6.5
|
1.0
|
|
C3C
|
A:HEC202
|
4.2
|
6.2
|
1.0
|
|
C2A
|
A:HEC202
|
4.3
|
9.0
|
1.0
|
|
C2C
|
A:HEC202
|
4.3
|
5.7
|
1.0
|
|
C3D
|
A:HEC202
|
4.3
|
5.7
|
1.0
|
|
C2D
|
A:HEC202
|
4.3
|
5.5
|
1.0
|
|
C3A
|
A:HEC202
|
4.3
|
7.7
|
1.0
|
|
C3B
|
A:HEC202
|
4.3
|
8.0
|
1.0
|
|
C2B
|
A:HEC202
|
4.3
|
6.9
|
1.0
|
|
CE
|
A:MET35
|
5.0
|
10.7
|
1.0
|
|
Iron binding site 3 out
of 5 in 2ozy
Go back to
Iron Binding Sites List in 2ozy
Iron binding site 3 out
of 5 in the Crystal Structure of E.Coli Nrfb
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of E.Coli Nrfb within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe203
b:6.5
occ:1.00
|
FE
|
A:HEC203
|
0.0
|
6.5
|
1.0
|
|
NC
|
A:HEC203
|
2.0
|
5.7
|
1.0
|
|
NB
|
A:HEC203
|
2.0
|
4.3
|
1.0
|
|
NE2
|
A:HIS39
|
2.0
|
6.4
|
1.0
|
|
NA
|
A:HEC203
|
2.1
|
6.0
|
1.0
|
|
ND
|
A:HEC203
|
2.1
|
5.7
|
1.0
|
|
NE2
|
A:HIS92
|
2.1
|
4.9
|
1.0
|
|
CE1
|
A:HIS92
|
3.0
|
4.2
|
1.0
|
|
CE1
|
A:HIS39
|
3.0
|
5.9
|
1.0
|
|
CD2
|
A:HIS39
|
3.0
|
7.1
|
1.0
|
|
C4C
|
A:HEC203
|
3.0
|
5.7
|
1.0
|
|
C1B
|
A:HEC203
|
3.0
|
5.9
|
1.0
|
|
C1D
|
A:HEC203
|
3.1
|
6.0
|
1.0
|
|
C4A
|
A:HEC203
|
3.1
|
6.8
|
1.0
|
|
C4D
|
A:HEC203
|
3.1
|
6.7
|
1.0
|
|
C1A
|
A:HEC203
|
3.1
|
8.3
|
1.0
|
|
C1C
|
A:HEC203
|
3.1
|
4.3
|
1.0
|
|
C4B
|
A:HEC203
|
3.1
|
4.4
|
1.0
|
|
CD2
|
A:HIS92
|
3.2
|
5.6
|
1.0
|
|
CHD
|
A:HEC203
|
3.4
|
4.4
|
1.0
|
|
CHB
|
A:HEC203
|
3.4
|
5.8
|
1.0
|
|
CHA
|
A:HEC203
|
3.4
|
6.5
|
1.0
|
|
CHC
|
A:HEC203
|
3.5
|
5.4
|
1.0
|
|
ND1
|
A:HIS39
|
4.1
|
7.2
|
1.0
|
|
ND1
|
A:HIS92
|
4.1
|
4.5
|
1.0
|
|
CG
|
A:HIS39
|
4.2
|
8.2
|
1.0
|
|
CG
|
A:HIS92
|
4.3
|
4.2
|
1.0
|
|
C3C
|
A:HEC203
|
4.3
|
4.8
|
1.0
|
|
C2B
|
A:HEC203
|
4.3
|
5.2
|
1.0
|
|
C2D
|
A:HEC203
|
4.3
|
7.5
|
1.0
|
|
C2A
|
A:HEC203
|
4.3
|
9.2
|
1.0
|
|
C3A
|
A:HEC203
|
4.3
|
7.4
|
1.0
|
|
C3D
|
A:HEC203
|
4.3
|
9.6
|
1.0
|
|
C3B
|
A:HEC203
|
4.3
|
3.6
|
1.0
|
|
C2C
|
A:HEC203
|
4.3
|
4.2
|
1.0
|
|
CMA
|
A:HEC204
|
5.0
|
5.8
|
1.0
|
|
Iron binding site 4 out
of 5 in 2ozy
Go back to
Iron Binding Sites List in 2ozy
Iron binding site 4 out
of 5 in the Crystal Structure of E.Coli Nrfb
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of E.Coli Nrfb within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe204
b:6.4
occ:1.00
|
FE
|
A:HEC204
|
0.0
|
6.4
|
1.0
|
|
NB
|
A:HEC204
|
2.0
|
6.4
|
1.0
|
|
NE2
|
A:HIS104
|
2.0
|
4.1
|
1.0
|
|
NC
|
A:HEC204
|
2.0
|
4.7
|
1.0
|
|
NA
|
A:HEC204
|
2.1
|
7.0
|
1.0
|
|
ND
|
A:HEC204
|
2.1
|
5.9
|
1.0
|
|
NE2
|
A:HIS117
|
2.1
|
5.3
|
1.0
|
|
CE1
|
A:HIS104
|
3.0
|
7.7
|
1.0
|
|
C4B
|
A:HEC204
|
3.0
|
4.5
|
1.0
|
|
C1B
|
A:HEC204
|
3.0
|
5.7
|
1.0
|
|
C1C
|
A:HEC204
|
3.0
|
6.2
|
1.0
|
|
CE1
|
A:HIS117
|
3.1
|
7.3
|
1.0
|
|
CD2
|
A:HIS104
|
3.1
|
5.3
|
1.0
|
|
CD2
|
A:HIS117
|
3.1
|
6.5
|
1.0
|
|
C1A
|
A:HEC204
|
3.1
|
7.5
|
1.0
|
|
C4A
|
A:HEC204
|
3.1
|
6.3
|
1.0
|
|
C4D
|
A:HEC204
|
3.1
|
6.2
|
1.0
|
|
C4C
|
A:HEC204
|
3.1
|
6.2
|
1.0
|
|
C1D
|
A:HEC204
|
3.1
|
5.2
|
1.0
|
|
CHC
|
A:HEC204
|
3.4
|
5.5
|
1.0
|
|
CHA
|
A:HEC204
|
3.4
|
7.3
|
1.0
|
|
CHB
|
A:HEC204
|
3.4
|
6.1
|
1.0
|
|
CHD
|
A:HEC204
|
3.4
|
7.0
|
1.0
|
|
ND1
|
A:HIS104
|
4.1
|
9.2
|
1.0
|
|
ND1
|
A:HIS117
|
4.2
|
5.8
|
1.0
|
|
CG
|
A:HIS104
|
4.2
|
5.5
|
1.0
|
|
CG
|
A:HIS117
|
4.2
|
5.6
|
1.0
|
|
C3B
|
A:HEC204
|
4.2
|
5.8
|
1.0
|
|
C2B
|
A:HEC204
|
4.2
|
6.5
|
1.0
|
|
C2A
|
A:HEC204
|
4.3
|
8.0
|
1.0
|
|
C3A
|
A:HEC204
|
4.3
|
7.0
|
1.0
|
|
C2C
|
A:HEC204
|
4.3
|
6.0
|
1.0
|
|
C3C
|
A:HEC204
|
4.3
|
6.5
|
1.0
|
|
C3D
|
A:HEC204
|
4.3
|
7.0
|
1.0
|
|
C2D
|
A:HEC204
|
4.3
|
7.7
|
1.0
|
|
Iron binding site 5 out
of 5 in 2ozy
Go back to
Iron Binding Sites List in 2ozy
Iron binding site 5 out
of 5 in the Crystal Structure of E.Coli Nrfb
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of E.Coli Nrfb within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe205
b:7.3
occ:1.00
|
FE
|
A:HEC205
|
0.0
|
7.3
|
1.0
|
|
NA
|
A:HEC205
|
2.0
|
6.0
|
1.0
|
|
NB
|
A:HEC205
|
2.0
|
5.8
|
1.0
|
|
NC
|
A:HEC205
|
2.0
|
5.6
|
1.0
|
|
NE2
|
A:HIS142
|
2.0
|
10.2
|
1.0
|
|
NE2
|
A:HIS107
|
2.1
|
6.9
|
1.0
|
|
ND
|
A:HEC205
|
2.1
|
5.9
|
1.0
|
|
CE1
|
A:HIS142
|
3.0
|
10.7
|
1.0
|
|
C1B
|
A:HEC205
|
3.0
|
6.0
|
1.0
|
|
C1A
|
A:HEC205
|
3.0
|
7.1
|
1.0
|
|
CE1
|
A:HIS107
|
3.0
|
8.9
|
1.0
|
|
CD2
|
A:HIS107
|
3.0
|
6.0
|
1.0
|
|
C4A
|
A:HEC205
|
3.1
|
6.6
|
1.0
|
|
C4B
|
A:HEC205
|
3.1
|
5.4
|
1.0
|
|
C4C
|
A:HEC205
|
3.1
|
6.7
|
1.0
|
|
C1D
|
A:HEC205
|
3.1
|
8.0
|
1.0
|
|
C4D
|
A:HEC205
|
3.1
|
6.8
|
1.0
|
|
C1C
|
A:HEC205
|
3.1
|
6.3
|
1.0
|
|
CD2
|
A:HIS142
|
3.1
|
8.3
|
1.0
|
|
CHB
|
A:HEC205
|
3.4
|
6.6
|
1.0
|
|
CHA
|
A:HEC205
|
3.4
|
6.7
|
1.0
|
|
CHD
|
A:HEC205
|
3.4
|
7.1
|
1.0
|
|
CHC
|
A:HEC205
|
3.5
|
6.7
|
1.0
|
|
ND1
|
A:HIS142
|
4.1
|
9.1
|
1.0
|
|
ND1
|
A:HIS107
|
4.1
|
9.2
|
1.0
|
|
CG
|
A:HIS107
|
4.2
|
6.1
|
1.0
|
|
CG
|
A:HIS142
|
4.2
|
7.7
|
1.0
|
|
C2B
|
A:HEC205
|
4.2
|
6.0
|
1.0
|
|
C2A
|
A:HEC205
|
4.3
|
9.4
|
1.0
|
|
C3B
|
A:HEC205
|
4.3
|
5.9
|
1.0
|
|
C3A
|
A:HEC205
|
4.3
|
6.6
|
1.0
|
|
C3C
|
A:HEC205
|
4.3
|
4.2
|
1.0
|
|
C2C
|
A:HEC205
|
4.3
|
5.2
|
1.0
|
|
C2D
|
A:HEC205
|
4.3
|
9.8
|
1.0
|
|
C3D
|
A:HEC205
|
4.3
|
8.7
|
1.0
|
|
Reference:
T.A.Clarke,
J.A.Cole,
D.J.Richardson,
A.M.Hemmings.
The Crystal Structure of the Pentahaem C-Type Cytochrome Nrfb and Characterization of Its Solution-State Interaction with the Pentahaem Nitrite Reductase Nrfa. Biochem.J. V. 406 19 2007.
ISSN: ISSN 0264-6021
PubMed: 17521287
DOI: 10.1042/BJ20070321
Page generated: Sun Aug 4 01:08:42 2024
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