Iron in PDB 5nhk: Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron
Protein crystallography data
The structure of Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron, PDB code: 5nhk
was solved by
J.Perard,
L.Arnaud,
P.Carpentier,
I.Michaud-Soret,
C.Cavazza,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.21 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.350,
90.040,
64.050,
90.00,
93.53,
90.00
|
R / Rfree (%)
|
20.4 /
24.3
|
Other elements in 5nhk:
The structure of Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron
(pdb code 5nhk). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron, PDB code: 5nhk:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 5nhk
Go back to
Iron Binding Sites List in 5nhk
Iron binding site 1 out
of 4 in the Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:14.6
occ:1.00
|
OE2
|
A:GLU101
|
2.1
|
21.2
|
1.0
|
NE2
|
A:HIS90
|
2.2
|
11.3
|
1.0
|
OE2
|
A:GLU81
|
2.2
|
13.7
|
1.0
|
NE2
|
A:HIS33
|
2.2
|
14.8
|
1.0
|
NE2
|
A:HIS88
|
2.3
|
23.2
|
1.0
|
OE1
|
A:GLU81
|
2.4
|
15.3
|
1.0
|
CD
|
A:GLU81
|
2.6
|
12.2
|
1.0
|
CD
|
A:GLU101
|
3.1
|
22.1
|
1.0
|
CD2
|
A:HIS90
|
3.1
|
10.7
|
1.0
|
CE1
|
A:HIS90
|
3.2
|
12.2
|
1.0
|
CE1
|
A:HIS33
|
3.2
|
18.9
|
1.0
|
CD2
|
A:HIS88
|
3.2
|
15.1
|
1.0
|
CD2
|
A:HIS33
|
3.2
|
18.2
|
1.0
|
CE1
|
A:HIS88
|
3.3
|
20.4
|
1.0
|
CG
|
A:GLU101
|
3.5
|
15.9
|
1.0
|
CG
|
A:GLU81
|
4.1
|
12.2
|
1.0
|
OE1
|
A:GLU101
|
4.2
|
24.4
|
1.0
|
ND1
|
A:HIS90
|
4.3
|
7.2
|
1.0
|
CG
|
A:HIS90
|
4.3
|
11.7
|
1.0
|
ND1
|
A:HIS33
|
4.3
|
17.1
|
1.0
|
CG
|
A:HIS33
|
4.3
|
15.5
|
1.0
|
CG
|
A:HIS88
|
4.4
|
16.0
|
1.0
|
ND1
|
A:HIS88
|
4.4
|
20.3
|
1.0
|
O
|
A:HOH332
|
4.6
|
36.1
|
1.0
|
CB
|
A:GLU81
|
4.7
|
12.7
|
1.0
|
O
|
A:HOH378
|
4.9
|
37.7
|
1.0
|
CB
|
A:GLU101
|
4.9
|
15.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 5nhk
Go back to
Iron Binding Sites List in 5nhk
Iron binding site 2 out
of 4 in the Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:16.6
occ:1.00
|
OE2
|
B:GLU81
|
2.1
|
15.5
|
1.0
|
OE2
|
B:GLU101
|
2.2
|
20.0
|
1.0
|
NE2
|
B:HIS90
|
2.2
|
14.8
|
1.0
|
OE1
|
B:GLU81
|
2.2
|
17.9
|
1.0
|
NE2
|
B:HIS88
|
2.2
|
18.7
|
1.0
|
NE2
|
B:HIS33
|
2.3
|
15.4
|
1.0
|
CD
|
B:GLU81
|
2.4
|
14.9
|
1.0
|
CE1
|
B:HIS90
|
3.1
|
10.8
|
1.0
|
CD2
|
B:HIS88
|
3.1
|
18.8
|
1.0
|
CD
|
B:GLU101
|
3.2
|
22.2
|
1.0
|
CD2
|
B:HIS33
|
3.2
|
21.9
|
1.0
|
CD2
|
B:HIS90
|
3.2
|
13.9
|
1.0
|
CE1
|
B:HIS33
|
3.2
|
16.1
|
1.0
|
CE1
|
B:HIS88
|
3.3
|
18.4
|
1.0
|
CG
|
B:GLU101
|
3.6
|
17.4
|
1.0
|
CG
|
B:GLU81
|
3.9
|
16.5
|
1.0
|
OE1
|
B:GLU101
|
4.2
|
20.7
|
1.0
|
ND1
|
B:HIS90
|
4.2
|
9.7
|
1.0
|
CG
|
B:HIS88
|
4.3
|
14.4
|
1.0
|
CG
|
B:HIS90
|
4.3
|
10.5
|
1.0
|
ND1
|
B:HIS33
|
4.4
|
17.0
|
1.0
|
ND1
|
B:HIS88
|
4.4
|
20.3
|
1.0
|
CG
|
B:HIS33
|
4.4
|
14.9
|
1.0
|
CB
|
B:GLU81
|
4.6
|
18.1
|
1.0
|
O
|
B:HOH322
|
4.6
|
36.3
|
1.0
|
O
|
B:HOH319
|
4.9
|
32.1
|
1.0
|
CB
|
B:GLU101
|
4.9
|
19.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 5nhk
Go back to
Iron Binding Sites List in 5nhk
Iron binding site 3 out
of 4 in the Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:14.0
occ:1.00
|
OE2
|
C:GLU101
|
2.0
|
18.4
|
1.0
|
NE2
|
C:HIS90
|
2.1
|
10.5
|
1.0
|
NE2
|
C:HIS33
|
2.2
|
13.4
|
1.0
|
OE2
|
C:GLU81
|
2.2
|
15.1
|
1.0
|
NE2
|
C:HIS88
|
2.3
|
15.6
|
1.0
|
OE1
|
C:GLU81
|
2.3
|
14.6
|
1.0
|
CD
|
C:GLU81
|
2.5
|
18.1
|
1.0
|
CD
|
C:GLU101
|
3.0
|
20.5
|
1.0
|
CE1
|
C:HIS90
|
3.0
|
9.9
|
1.0
|
CE1
|
C:HIS33
|
3.1
|
18.8
|
1.0
|
CD2
|
C:HIS88
|
3.2
|
14.1
|
1.0
|
CD2
|
C:HIS90
|
3.2
|
9.5
|
1.0
|
CD2
|
C:HIS33
|
3.2
|
13.3
|
1.0
|
CE1
|
C:HIS88
|
3.2
|
20.9
|
1.0
|
CG
|
C:GLU101
|
3.5
|
18.0
|
1.0
|
OE1
|
C:GLU101
|
4.0
|
18.9
|
1.0
|
CG
|
C:GLU81
|
4.0
|
12.0
|
1.0
|
ND1
|
C:HIS90
|
4.2
|
9.0
|
1.0
|
ND1
|
C:HIS33
|
4.2
|
22.7
|
1.0
|
CG
|
C:HIS90
|
4.3
|
9.5
|
1.0
|
CG
|
C:HIS33
|
4.3
|
19.2
|
1.0
|
ND1
|
C:HIS88
|
4.3
|
16.5
|
1.0
|
CG
|
C:HIS88
|
4.3
|
14.7
|
1.0
|
O
|
C:HOH319
|
4.5
|
25.5
|
1.0
|
O
|
C:HOH397
|
4.6
|
34.1
|
1.0
|
CB
|
C:GLU81
|
4.7
|
15.6
|
1.0
|
CB
|
C:GLU101
|
4.8
|
15.4
|
1.0
|
CD2
|
C:LEU71
|
4.9
|
27.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 5nhk
Go back to
Iron Binding Sites List in 5nhk
Iron binding site 4 out
of 4 in the Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Ferric Uptake Regulator From Francisella Tularensis with Iron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:12.4
occ:1.00
|
OE2
|
D:GLU101
|
2.1
|
16.5
|
1.0
|
NE2
|
D:HIS90
|
2.1
|
12.5
|
1.0
|
NE2
|
D:HIS88
|
2.2
|
12.5
|
1.0
|
OE2
|
D:GLU81
|
2.2
|
12.2
|
1.0
|
NE2
|
D:HIS33
|
2.2
|
13.2
|
1.0
|
OE1
|
D:GLU81
|
2.3
|
16.6
|
1.0
|
CD
|
D:GLU81
|
2.5
|
12.6
|
1.0
|
CE1
|
D:HIS33
|
3.0
|
17.7
|
1.0
|
CD
|
D:GLU101
|
3.0
|
18.4
|
1.0
|
CE1
|
D:HIS90
|
3.1
|
10.6
|
1.0
|
CE1
|
D:HIS88
|
3.1
|
20.1
|
1.0
|
CD2
|
D:HIS90
|
3.2
|
13.2
|
1.0
|
CD2
|
D:HIS88
|
3.2
|
10.3
|
1.0
|
CD2
|
D:HIS33
|
3.4
|
13.3
|
1.0
|
CG
|
D:GLU101
|
3.4
|
10.8
|
1.0
|
CG
|
D:GLU81
|
4.0
|
11.8
|
1.0
|
OE1
|
D:GLU101
|
4.1
|
17.6
|
1.0
|
ND1
|
D:HIS33
|
4.2
|
22.1
|
1.0
|
ND1
|
D:HIS90
|
4.2
|
12.0
|
1.0
|
ND1
|
D:HIS88
|
4.3
|
16.7
|
1.0
|
CG
|
D:HIS90
|
4.3
|
9.8
|
1.0
|
CG
|
D:HIS88
|
4.3
|
13.6
|
1.0
|
CG
|
D:HIS33
|
4.4
|
17.6
|
1.0
|
CE
|
D:LYS32
|
4.4
|
16.5
|
1.0
|
O
|
D:HOH345
|
4.5
|
19.6
|
1.0
|
CB
|
D:GLU81
|
4.7
|
12.2
|
1.0
|
CD
|
D:LYS32
|
4.7
|
24.6
|
1.0
|
CB
|
D:GLU101
|
4.8
|
10.9
|
1.0
|
NZ
|
D:LYS32
|
4.9
|
19.8
|
1.0
|
|
Reference:
J.Perard,
S.Nader,
M.Levert,
L.Arnaud,
P.Carpentier,
C.Siebert,
F.Blanquet,
C.Cavazza,
P.Renesto,
D.Schneider,
M.Maurin,
J.Coves,
S.Crouzy,
I.Michaud-Soret.
Structural and Functional Studies of the Metalloregulator Fur Identify A Promoter-Binding Mechanism and Its Role Infrancisella Tularensisvirulence. Commun Biol V. 1 93 2018.
ISSN: ESSN 2399-3642
PubMed: 30271974
DOI: 10.1038/S42003-018-0095-6
Page generated: Tue Aug 6 06:12:32 2024
|