Iron in PDB 7a9a: Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis
Protein crystallography data
The structure of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis, PDB code: 7a9a
was solved by
D.Vakhrameev,
A.Kavaleuski,
S.Bukhdruker,
E.Marin,
T.Sushko,
I.P.Grabovec,
A.Gilep,
N.Strushkevich,
V.Borshchevskiy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.95 /
1.17
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
21.035,
61.322,
76.91,
90.15,
90.32,
93.75
|
R / Rfree (%)
|
15.4 /
18.7
|
Other elements in 7a9a:
The structure of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis
(pdb code 7a9a). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis, PDB code: 7a9a:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 7a9a
Go back to
Iron Binding Sites List in 7a9a
Iron binding site 1 out
of 8 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis
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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:5.8
occ:1.00
|
SG
|
A:CYS45
|
2.3
|
9.0
|
1.0
|
SG
|
A:CYS12
|
2.3
|
8.4
|
1.0
|
SG
|
A:CYS9
|
2.3
|
8.7
|
1.0
|
SG
|
A:CYS42
|
2.3
|
7.0
|
1.0
|
HB3
|
A:CYS12
|
3.1
|
10.9
|
1.0
|
HB3
|
A:CYS45
|
3.2
|
10.4
|
1.0
|
HB3
|
A:CYS9
|
3.2
|
10.5
|
1.0
|
CB
|
A:CYS9
|
3.2
|
8.8
|
1.0
|
HB3
|
A:CYS42
|
3.2
|
8.2
|
1.0
|
CB
|
A:CYS42
|
3.2
|
6.9
|
1.0
|
H
|
A:CYS12
|
3.3
|
14.2
|
1.0
|
HB2
|
A:CYS9
|
3.3
|
10.5
|
1.0
|
CB
|
A:CYS12
|
3.3
|
9.1
|
1.0
|
CB
|
A:CYS45
|
3.3
|
8.7
|
1.0
|
HB2
|
A:CYS42
|
3.3
|
8.2
|
1.0
|
H
|
A:CYS45
|
3.4
|
9.9
|
1.0
|
HB3
|
A:GLN11
|
3.6
|
20.9
|
1.0
|
HB3
|
A:PHE14
|
3.6
|
9.8
|
1.0
|
N
|
A:CYS12
|
3.8
|
11.8
|
1.0
|
N
|
A:CYS45
|
3.8
|
8.3
|
1.0
|
HB3
|
A:ALA47
|
3.8
|
11.5
|
1.0
|
HB2
|
A:ASP44
|
4.0
|
10.7
|
1.0
|
H
|
A:ALA47
|
4.0
|
11.3
|
1.0
|
CA
|
A:CYS45
|
4.1
|
8.2
|
1.0
|
H
|
A:PHE14
|
4.1
|
10.6
|
1.0
|
CA
|
A:CYS12
|
4.1
|
10.0
|
1.0
|
HB2
|
A:CYS12
|
4.1
|
10.9
|
1.0
|
HB2
|
A:CYS45
|
4.1
|
10.4
|
1.0
|
HB2
|
A:ALA47
|
4.2
|
11.5
|
1.0
|
H
|
A:GLN11
|
4.4
|
16.9
|
1.0
|
H
|
A:ASP44
|
4.4
|
10.1
|
1.0
|
H
|
A:GLY13
|
4.4
|
11.5
|
1.0
|
HB2
|
A:PHE14
|
4.4
|
9.8
|
1.0
|
CB
|
A:PHE14
|
4.4
|
8.1
|
1.0
|
CB
|
A:ALA47
|
4.5
|
9.6
|
1.0
|
H
|
A:GLY46
|
4.5
|
10.0
|
1.0
|
CB
|
A:GLN11
|
4.5
|
17.4
|
1.0
|
C
|
A:ASP44
|
4.6
|
9.1
|
1.0
|
CA
|
A:CYS9
|
4.7
|
8.6
|
1.0
|
CA
|
A:CYS42
|
4.7
|
7.4
|
1.0
|
C
|
A:CYS45
|
4.7
|
8.5
|
1.0
|
C
|
A:CYS12
|
4.7
|
10.4
|
1.0
|
C
|
A:GLN11
|
4.7
|
13.1
|
1.0
|
N
|
A:GLY13
|
4.8
|
9.6
|
1.0
|
N
|
A:GLY46
|
4.8
|
8.4
|
1.0
|
N
|
A:ALA47
|
4.8
|
9.4
|
1.0
|
CB
|
A:ASP44
|
4.8
|
8.9
|
1.0
|
N
|
A:PHE14
|
4.9
|
8.8
|
1.0
|
HG2
|
A:GLN11
|
4.9
|
24.4
|
1.0
|
HA
|
A:CYS45
|
4.9
|
9.9
|
1.0
|
HA
|
A:CYS12
|
4.9
|
12.0
|
1.0
|
HD2
|
A:PHE14
|
4.9
|
9.3
|
1.0
|
N
|
A:ASP44
|
5.0
|
8.4
|
1.0
|
|
Iron binding site 2 out
of 8 in 7a9a
Go back to
Iron Binding Sites List in 7a9a
Iron binding site 2 out
of 8 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis
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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe101
b:8.4
occ:1.00
|
SG
|
B:CYS45
|
2.3
|
11.0
|
1.0
|
SG
|
B:CYS9
|
2.3
|
9.1
|
1.0
|
SG
|
B:CYS42
|
2.3
|
9.2
|
1.0
|
SG
|
B:CYS12
|
2.4
|
12.1
|
1.0
|
HB3
|
B:CYS9
|
3.1
|
10.6
|
1.0
|
HB3
|
B:CYS42
|
3.2
|
11.4
|
1.0
|
HB3
|
B:CYS12
|
3.2
|
15.6
|
1.0
|
CB
|
B:CYS42
|
3.2
|
9.5
|
1.0
|
HB3
|
B:CYS45
|
3.2
|
13.2
|
1.0
|
CB
|
B:CYS9
|
3.2
|
8.8
|
1.0
|
HB2
|
B:CYS42
|
3.3
|
11.4
|
1.0
|
HB2
|
B:CYS9
|
3.3
|
10.6
|
1.0
|
CB
|
B:CYS45
|
3.4
|
11.0
|
1.0
|
CB
|
B:CYS12
|
3.4
|
13.0
|
1.0
|
H
|
B:CYS45
|
3.4
|
13.2
|
1.0
|
H
|
B:CYS12
|
3.4
|
15.8
|
1.0
|
HB3
|
B:PHE14
|
3.5
|
11.3
|
1.0
|
HB3
|
B:ALA47
|
3.6
|
13.2
|
1.0
|
HB2
|
B:GLN11
|
3.8
|
16.2
|
0.6
|
HB2
|
B:ASP44
|
3.8
|
15.1
|
1.0
|
N
|
B:CYS45
|
3.8
|
11.0
|
1.0
|
HB3
|
B:GLN11
|
3.8
|
16.7
|
0.4
|
N
|
B:CYS12
|
3.9
|
13.1
|
1.0
|
H
|
B:ALA47
|
3.9
|
12.4
|
1.0
|
H
|
B:PHE14
|
4.0
|
12.4
|
1.0
|
CA
|
B:CYS45
|
4.1
|
10.4
|
1.0
|
HB2
|
B:ALA47
|
4.1
|
13.2
|
1.0
|
HB2
|
B:CYS45
|
4.1
|
13.2
|
1.0
|
HB2
|
B:CYS12
|
4.2
|
15.6
|
1.0
|
CA
|
B:CYS12
|
4.2
|
13.2
|
1.0
|
HG2
|
B:GLN11
|
4.3
|
17.3
|
0.4
|
CB
|
B:ALA47
|
4.3
|
11.0
|
1.0
|
HB2
|
B:PHE14
|
4.4
|
11.3
|
1.0
|
CB
|
B:PHE14
|
4.4
|
9.4
|
1.0
|
H
|
B:ASP44
|
4.4
|
14.2
|
1.0
|
H
|
B:GLY13
|
4.5
|
14.6
|
1.0
|
H
|
B:GLY46
|
4.6
|
12.4
|
1.0
|
CA
|
B:CYS9
|
4.7
|
8.7
|
1.0
|
CA
|
B:CYS42
|
4.7
|
9.6
|
1.0
|
CB
|
B:GLN11
|
4.7
|
13.9
|
0.4
|
H
|
B:GLN11
|
4.7
|
15.9
|
0.6
|
H
|
B:GLN11
|
4.7
|
15.9
|
0.4
|
C
|
B:ASP44
|
4.7
|
11.8
|
1.0
|
CB
|
B:ASP44
|
4.7
|
12.6
|
1.0
|
CB
|
B:GLN11
|
4.7
|
13.5
|
0.6
|
C
|
B:CYS45
|
4.7
|
10.5
|
1.0
|
N
|
B:ALA47
|
4.8
|
10.3
|
1.0
|
C
|
B:CYS12
|
4.8
|
13.1
|
1.0
|
C
|
B:GLN11
|
4.8
|
13.6
|
1.0
|
N
|
B:PHE14
|
4.8
|
10.4
|
1.0
|
N
|
B:GLY13
|
4.8
|
12.2
|
1.0
|
N
|
B:GLY46
|
4.9
|
10.3
|
1.0
|
HZ
|
B:PHE52
|
4.9
|
10.6
|
1.0
|
CG
|
B:GLN11
|
4.9
|
14.4
|
0.4
|
HD2
|
B:PHE14
|
4.9
|
11.6
|
1.0
|
HB3
|
B:GLN11
|
5.0
|
16.2
|
0.6
|
HB3
|
B:ASP44
|
5.0
|
15.1
|
1.0
|
HA
|
B:CYS45
|
5.0
|
12.5
|
1.0
|
N
|
B:ASP44
|
5.0
|
11.8
|
1.0
|
HA
|
B:CYS12
|
5.0
|
15.9
|
1.0
|
|
Iron binding site 3 out
of 8 in 7a9a
Go back to
Iron Binding Sites List in 7a9a
Iron binding site 3 out
of 8 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis
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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:7.1
occ:1.00
|
SG
|
C:CYS12
|
2.3
|
8.4
|
1.0
|
SG
|
C:CYS45
|
2.3
|
8.7
|
1.0
|
SG
|
C:CYS9
|
2.3
|
7.5
|
1.0
|
SG
|
C:CYS42
|
2.3
|
7.4
|
1.0
|
HB3
|
C:CYS12
|
3.1
|
10.1
|
1.0
|
HB3
|
C:CYS9
|
3.1
|
8.9
|
1.0
|
HB3
|
C:CYS42
|
3.2
|
7.8
|
1.0
|
CB
|
C:CYS42
|
3.2
|
6.5
|
1.0
|
CB
|
C:CYS9
|
3.2
|
7.4
|
1.0
|
HB3
|
C:CYS45
|
3.2
|
11.0
|
1.0
|
HB2
|
C:CYS42
|
3.3
|
7.8
|
1.0
|
CB
|
C:CYS12
|
3.3
|
8.4
|
1.0
|
H
|
C:CYS12
|
3.3
|
11.2
|
1.0
|
CB
|
C:CYS45
|
3.4
|
9.1
|
1.0
|
HB2
|
C:CYS9
|
3.4
|
8.9
|
1.0
|
H
|
C:CYS45
|
3.4
|
10.7
|
1.0
|
HB3
|
C:PHE14
|
3.5
|
9.9
|
1.0
|
HB2
|
C:GLN11
|
3.7
|
15.3
|
1.0
|
HB3
|
C:ALA47
|
3.8
|
11.2
|
1.0
|
N
|
C:CYS45
|
3.8
|
8.9
|
1.0
|
N
|
C:CYS12
|
3.8
|
9.3
|
1.0
|
H
|
C:ALA47
|
3.9
|
10.6
|
1.0
|
HB2
|
C:ASP44
|
4.0
|
12.0
|
1.0
|
H
|
C:PHE14
|
4.0
|
10.3
|
1.0
|
CA
|
C:CYS12
|
4.1
|
8.2
|
1.0
|
HB2
|
C:CYS12
|
4.1
|
10.1
|
1.0
|
CA
|
C:CYS45
|
4.1
|
9.1
|
1.0
|
HB2
|
C:CYS45
|
4.2
|
11.0
|
1.0
|
HB2
|
C:ALA47
|
4.3
|
11.2
|
1.0
|
H
|
C:ASP44
|
4.4
|
10.2
|
1.0
|
CB
|
C:PHE14
|
4.4
|
8.2
|
1.0
|
HB2
|
C:PHE14
|
4.4
|
9.9
|
1.0
|
CB
|
C:ALA47
|
4.5
|
9.4
|
1.0
|
H
|
C:GLY13
|
4.5
|
10.7
|
1.0
|
H
|
C:GLY46
|
4.5
|
11.2
|
1.0
|
H
|
C:GLN11
|
4.5
|
12.7
|
1.0
|
C
|
C:ASP44
|
4.6
|
10.0
|
1.0
|
CB
|
C:GLN11
|
4.6
|
12.8
|
1.0
|
CA
|
C:CYS42
|
4.6
|
7.6
|
1.0
|
CA
|
C:CYS9
|
4.7
|
7.7
|
1.0
|
C
|
C:CYS45
|
4.7
|
9.4
|
1.0
|
C
|
C:CYS12
|
4.7
|
8.4
|
1.0
|
C
|
C:GLN11
|
4.7
|
10.6
|
1.0
|
N
|
C:ALA47
|
4.8
|
8.8
|
1.0
|
N
|
C:GLY46
|
4.8
|
9.3
|
1.0
|
N
|
C:GLY13
|
4.8
|
8.9
|
1.0
|
N
|
C:PHE14
|
4.8
|
8.6
|
1.0
|
CB
|
C:ASP44
|
4.8
|
10.0
|
1.0
|
HD2
|
C:PHE14
|
4.9
|
9.7
|
1.0
|
HA
|
C:CYS12
|
4.9
|
9.8
|
1.0
|
HA
|
C:CYS45
|
4.9
|
10.9
|
1.0
|
HB3
|
C:GLN11
|
5.0
|
15.3
|
1.0
|
N
|
C:ASP44
|
5.0
|
8.5
|
1.0
|
HA
|
C:CYS42
|
5.0
|
9.1
|
1.0
|
|
Iron binding site 4 out
of 8 in 7a9a
Go back to
Iron Binding Sites List in 7a9a
Iron binding site 4 out
of 8 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis
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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe101
b:8.1
occ:1.00
|
SG
|
D:CYS45
|
2.3
|
9.7
|
1.0
|
SG
|
D:CYS42
|
2.3
|
8.3
|
1.0
|
SG
|
D:CYS12
|
2.3
|
8.7
|
1.0
|
SG
|
D:CYS9
|
2.3
|
8.9
|
1.0
|
HB3
|
D:CYS45
|
3.2
|
12.2
|
1.0
|
HB3
|
D:CYS9
|
3.2
|
10.6
|
1.0
|
HB3
|
D:CYS42
|
3.2
|
9.8
|
1.0
|
HB3
|
D:CYS12
|
3.2
|
10.9
|
1.0
|
CB
|
D:CYS42
|
3.2
|
8.2
|
1.0
|
CB
|
D:CYS9
|
3.3
|
8.8
|
1.0
|
CB
|
D:CYS45
|
3.3
|
10.2
|
1.0
|
HB2
|
D:CYS42
|
3.3
|
9.8
|
1.0
|
CB
|
D:CYS12
|
3.4
|
9.1
|
1.0
|
H
|
D:CYS12
|
3.4
|
12.4
|
1.0
|
H
|
D:CYS45
|
3.4
|
11.5
|
1.0
|
HB2
|
D:CYS9
|
3.4
|
10.6
|
1.0
|
HB3
|
D:PHE14
|
3.5
|
10.3
|
1.0
|
HB3
|
D:GLN11
|
3.7
|
15.0
|
0.6
|
HB3
|
D:ALA47
|
3.7
|
13.2
|
1.0
|
HB2
|
D:GLN11
|
3.7
|
14.3
|
0.4
|
N
|
D:CYS45
|
3.8
|
9.6
|
1.0
|
N
|
D:CYS12
|
3.8
|
10.4
|
1.0
|
H
|
D:ALA47
|
3.9
|
13.4
|
1.0
|
HB2
|
D:ASP44
|
4.0
|
10.9
|
1.0
|
CA
|
D:CYS45
|
4.1
|
9.7
|
1.0
|
H
|
D:PHE14
|
4.1
|
10.8
|
1.0
|
HB2
|
D:ALA47
|
4.1
|
13.2
|
1.0
|
HB2
|
D:CYS45
|
4.1
|
12.2
|
1.0
|
CA
|
D:CYS12
|
4.1
|
9.6
|
1.0
|
HB2
|
D:CYS12
|
4.1
|
10.9
|
1.0
|
H
|
D:ASP44
|
4.3
|
11.2
|
1.0
|
HB2
|
D:PHE14
|
4.4
|
10.3
|
1.0
|
CB
|
D:ALA47
|
4.4
|
11.0
|
1.0
|
CB
|
D:PHE14
|
4.4
|
8.6
|
1.0
|
H
|
D:GLY46
|
4.5
|
12.5
|
1.0
|
H
|
D:GLN11
|
4.5
|
14.7
|
0.4
|
H
|
D:GLN11
|
4.5
|
14.7
|
0.6
|
C
|
D:ASP44
|
4.6
|
9.8
|
1.0
|
CB
|
D:GLN11
|
4.6
|
12.5
|
0.6
|
H
|
D:GLY13
|
4.6
|
11.2
|
1.0
|
C
|
D:CYS45
|
4.7
|
10.7
|
1.0
|
CB
|
D:GLN11
|
4.7
|
11.9
|
0.4
|
CA
|
D:CYS42
|
4.7
|
8.0
|
1.0
|
CA
|
D:CYS9
|
4.7
|
8.8
|
1.0
|
C
|
D:GLN11
|
4.7
|
11.2
|
1.0
|
C
|
D:CYS12
|
4.7
|
9.7
|
1.0
|
N
|
D:ALA47
|
4.7
|
11.2
|
1.0
|
N
|
D:GLY46
|
4.8
|
10.4
|
1.0
|
CB
|
D:ASP44
|
4.8
|
9.1
|
1.0
|
N
|
D:PHE14
|
4.9
|
9.0
|
1.0
|
N
|
D:GLY13
|
4.9
|
9.4
|
1.0
|
HD2
|
D:PHE14
|
4.9
|
10.9
|
1.0
|
HA
|
D:CYS45
|
4.9
|
11.6
|
1.0
|
HA
|
D:CYS12
|
5.0
|
11.4
|
1.0
|
N
|
D:ASP44
|
5.0
|
9.3
|
1.0
|
|
Iron binding site 5 out
of 8 in 7a9a
Go back to
Iron Binding Sites List in 7a9a
Iron binding site 5 out
of 8 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis
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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe101
b:9.7
occ:1.00
|
SG
|
E:CYS45
|
2.3
|
12.2
|
1.0
|
SG
|
E:CYS42
|
2.3
|
9.8
|
1.0
|
SG
|
E:CYS12
|
2.3
|
12.1
|
1.0
|
SG
|
E:CYS9
|
2.4
|
9.8
|
1.0
|
HB3
|
E:CYS45
|
3.1
|
14.6
|
1.0
|
HB3
|
E:CYS9
|
3.1
|
11.6
|
1.0
|
HB3
|
E:CYS42
|
3.2
|
11.6
|
1.0
|
HB3
|
E:CYS12
|
3.2
|
15.2
|
1.0
|
CB
|
E:CYS42
|
3.2
|
9.6
|
1.0
|
CB
|
E:CYS9
|
3.2
|
9.7
|
1.0
|
HB2
|
E:CYS42
|
3.3
|
11.6
|
1.0
|
CB
|
E:CYS45
|
3.3
|
12.2
|
1.0
|
HB2
|
E:CYS9
|
3.4
|
11.6
|
1.0
|
CB
|
E:CYS12
|
3.4
|
12.7
|
1.0
|
HB3
|
E:PHE14
|
3.5
|
13.4
|
1.0
|
H
|
E:CYS45
|
3.5
|
14.9
|
1.0
|
H
|
E:CYS12
|
3.5
|
17.5
|
1.0
|
HB2
|
E:GLN11
|
3.7
|
19.9
|
1.0
|
HB3
|
E:ALA47
|
3.7
|
13.1
|
1.0
|
N
|
E:CYS45
|
3.8
|
12.4
|
1.0
|
N
|
E:CYS12
|
3.9
|
14.6
|
1.0
|
H
|
E:ALA47
|
3.9
|
12.5
|
1.0
|
HB2
|
E:ASP44
|
4.0
|
16.0
|
1.0
|
H
|
E:PHE14
|
4.0
|
14.4
|
1.0
|
HB2
|
E:CYS45
|
4.1
|
14.6
|
1.0
|
HB2
|
E:ALA47
|
4.1
|
13.1
|
1.0
|
CA
|
E:CYS45
|
4.1
|
12.0
|
1.0
|
HB2
|
E:CYS12
|
4.1
|
15.2
|
1.0
|
CA
|
E:CYS12
|
4.2
|
13.8
|
1.0
|
HB2
|
E:PHE14
|
4.3
|
13.4
|
1.0
|
CB
|
E:PHE14
|
4.3
|
11.2
|
1.0
|
CB
|
E:ALA47
|
4.4
|
10.9
|
1.0
|
H
|
E:ASP44
|
4.4
|
13.9
|
1.0
|
H
|
E:GLY46
|
4.5
|
13.8
|
1.0
|
H
|
E:GLN11
|
4.5
|
18.9
|
1.0
|
CB
|
E:GLN11
|
4.5
|
16.6
|
1.0
|
H
|
E:GLY13
|
4.6
|
16.9
|
1.0
|
CA
|
E:CYS42
|
4.6
|
9.9
|
1.0
|
C
|
E:ASP44
|
4.6
|
12.9
|
1.0
|
HB3
|
E:GLN11
|
4.7
|
19.9
|
1.0
|
CA
|
E:CYS9
|
4.7
|
9.5
|
1.0
|
C
|
E:CYS45
|
4.7
|
11.8
|
1.0
|
C
|
E:GLN11
|
4.7
|
15.6
|
1.0
|
N
|
E:ALA47
|
4.8
|
10.4
|
1.0
|
C
|
E:CYS12
|
4.8
|
14.6
|
1.0
|
N
|
E:GLY46
|
4.8
|
11.5
|
1.0
|
N
|
E:PHE14
|
4.8
|
12.0
|
1.0
|
HZ
|
E:PHE52
|
4.8
|
8.6
|
1.0
|
CB
|
E:ASP44
|
4.9
|
13.3
|
1.0
|
N
|
E:GLY13
|
4.9
|
14.1
|
1.0
|
HD2
|
E:PHE14
|
4.9
|
12.7
|
1.0
|
HA
|
E:CYS45
|
4.9
|
14.4
|
1.0
|
HA
|
E:CYS42
|
5.0
|
11.9
|
1.0
|
|
Iron binding site 6 out
of 8 in 7a9a
Go back to
Iron Binding Sites List in 7a9a
Iron binding site 6 out
of 8 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe101
b:8.0
occ:1.00
|
SG
|
F:CYS45
|
2.3
|
10.3
|
1.0
|
SG
|
F:CYS9
|
2.3
|
8.9
|
1.0
|
SG
|
F:CYS12
|
2.3
|
9.8
|
1.0
|
SG
|
F:CYS42
|
2.3
|
8.7
|
1.0
|
HB3
|
F:CYS12
|
3.2
|
12.7
|
1.0
|
HB3
|
F:CYS42
|
3.2
|
10.4
|
1.0
|
HB3
|
F:CYS9
|
3.2
|
10.2
|
1.0
|
HB3
|
F:CYS45
|
3.2
|
13.2
|
1.0
|
CB
|
F:CYS42
|
3.2
|
8.7
|
1.0
|
CB
|
F:CYS9
|
3.2
|
8.5
|
1.0
|
HB2
|
F:CYS42
|
3.3
|
10.4
|
1.0
|
H
|
F:CYS12
|
3.3
|
13.5
|
1.0
|
CB
|
F:CYS12
|
3.3
|
10.6
|
1.0
|
HB2
|
F:CYS9
|
3.3
|
10.2
|
1.0
|
CB
|
F:CYS45
|
3.3
|
11.0
|
1.0
|
H
|
F:CYS45
|
3.4
|
13.2
|
1.0
|
HB3
|
F:PHE14
|
3.5
|
11.2
|
1.0
|
HB3
|
F:ALA47
|
3.6
|
12.6
|
1.0
|
N
|
F:CYS45
|
3.8
|
11.0
|
1.0
|
HB3
|
F:GLN11
|
3.8
|
15.9
|
1.0
|
N
|
F:CYS12
|
3.8
|
11.3
|
1.0
|
H
|
F:ALA47
|
3.8
|
12.5
|
1.0
|
HB2
|
F:ALA47
|
3.9
|
12.6
|
1.0
|
H
|
F:PHE14
|
3.9
|
12.8
|
1.0
|
HB2
|
F:ASP44
|
4.0
|
13.9
|
1.0
|
CA
|
F:CYS45
|
4.1
|
10.6
|
1.0
|
CA
|
F:CYS12
|
4.1
|
11.0
|
1.0
|
HB2
|
F:CYS12
|
4.1
|
12.7
|
1.0
|
HB2
|
F:CYS45
|
4.1
|
13.2
|
1.0
|
CB
|
F:ALA47
|
4.2
|
10.5
|
1.0
|
HB2
|
F:PHE14
|
4.3
|
11.2
|
1.0
|
CB
|
F:PHE14
|
4.3
|
9.3
|
1.0
|
H
|
F:ASP44
|
4.3
|
12.8
|
1.0
|
H
|
F:GLY13
|
4.5
|
12.4
|
1.0
|
H
|
F:GLY46
|
4.5
|
12.2
|
1.0
|
H
|
F:GLN11
|
4.6
|
14.0
|
1.0
|
C
|
F:ASP44
|
4.6
|
11.1
|
1.0
|
CA
|
F:CYS42
|
4.6
|
8.8
|
1.0
|
N
|
F:ALA47
|
4.6
|
10.4
|
1.0
|
C
|
F:CYS45
|
4.6
|
10.4
|
1.0
|
C
|
F:CYS12
|
4.7
|
11.1
|
1.0
|
CA
|
F:CYS9
|
4.7
|
7.7
|
1.0
|
N
|
F:PHE14
|
4.7
|
10.7
|
1.0
|
CB
|
F:GLN11
|
4.7
|
13.2
|
1.0
|
C
|
F:GLN11
|
4.7
|
12.6
|
1.0
|
N
|
F:GLY13
|
4.8
|
10.3
|
1.0
|
N
|
F:GLY46
|
4.8
|
10.2
|
1.0
|
CB
|
F:ASP44
|
4.8
|
11.6
|
1.0
|
HZ
|
F:PHE52
|
4.9
|
11.0
|
1.0
|
HA
|
F:CYS45
|
4.9
|
12.7
|
1.0
|
HA
|
F:CYS12
|
4.9
|
13.2
|
1.0
|
HD2
|
F:PHE14
|
4.9
|
11.1
|
1.0
|
HB1
|
F:ALA47
|
4.9
|
12.6
|
1.0
|
N
|
F:ASP44
|
4.9
|
10.7
|
1.0
|
HA
|
F:CYS42
|
5.0
|
10.6
|
1.0
|
CA
|
F:ASP44
|
5.0
|
10.7
|
1.0
|
|
Iron binding site 7 out
of 8 in 7a9a
Go back to
Iron Binding Sites List in 7a9a
Iron binding site 7 out
of 8 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe101
b:6.8
occ:1.00
|
SG
|
G:CYS45
|
2.3
|
9.3
|
1.0
|
SG
|
G:CYS12
|
2.3
|
8.0
|
1.0
|
SG
|
G:CYS9
|
2.3
|
8.5
|
1.0
|
SG
|
G:CYS42
|
2.3
|
8.1
|
1.0
|
HB3
|
G:CYS9
|
3.1
|
9.3
|
1.0
|
HB3
|
G:CYS42
|
3.2
|
10.2
|
1.0
|
HB3
|
G:CYS12
|
3.2
|
9.9
|
1.0
|
HB3
|
G:CYS45
|
3.2
|
11.6
|
1.0
|
CB
|
G:CYS42
|
3.2
|
8.5
|
1.0
|
CB
|
G:CYS9
|
3.2
|
7.8
|
1.0
|
HB2
|
G:CYS42
|
3.3
|
10.2
|
1.0
|
H
|
G:CYS45
|
3.3
|
11.7
|
1.0
|
CB
|
G:CYS45
|
3.3
|
9.7
|
1.0
|
H
|
G:CYS12
|
3.3
|
12.1
|
1.0
|
CB
|
G:CYS12
|
3.4
|
8.3
|
1.0
|
HB2
|
G:CYS9
|
3.4
|
9.3
|
1.0
|
HB3
|
G:PHE14
|
3.6
|
9.1
|
1.0
|
HB3
|
G:ALA47
|
3.7
|
13.4
|
1.0
|
HB3
|
G:GLN11
|
3.8
|
16.4
|
0.6
|
N
|
G:CYS45
|
3.8
|
9.8
|
1.0
|
HB2
|
G:GLN11
|
3.8
|
15.4
|
0.4
|
N
|
G:CYS12
|
3.8
|
10.1
|
1.0
|
HB2
|
G:ASP44
|
3.9
|
11.8
|
1.0
|
H
|
G:ALA47
|
3.9
|
13.0
|
1.0
|
H
|
G:PHE14
|
4.0
|
9.0
|
1.0
|
CA
|
G:CYS45
|
4.1
|
9.6
|
1.0
|
CA
|
G:CYS12
|
4.1
|
8.8
|
1.0
|
HB2
|
G:CYS45
|
4.1
|
11.6
|
1.0
|
HB2
|
G:ALA47
|
4.1
|
13.4
|
1.0
|
HB2
|
G:CYS12
|
4.1
|
9.9
|
1.0
|
HB2
|
G:PHE14
|
4.3
|
9.1
|
1.0
|
CB
|
G:PHE14
|
4.4
|
7.5
|
1.0
|
H
|
G:ASP44
|
4.4
|
10.7
|
1.0
|
CB
|
G:ALA47
|
4.4
|
11.1
|
1.0
|
H
|
G:GLY13
|
4.4
|
9.4
|
1.0
|
H
|
G:GLY46
|
4.5
|
13.2
|
1.0
|
H
|
G:GLN11
|
4.5
|
15.0
|
0.4
|
H
|
G:GLN11
|
4.5
|
15.0
|
0.6
|
C
|
G:ASP44
|
4.6
|
10.1
|
1.0
|
CA
|
G:CYS42
|
4.7
|
8.6
|
1.0
|
C
|
G:CYS45
|
4.7
|
10.2
|
1.0
|
CA
|
G:CYS9
|
4.7
|
7.6
|
1.0
|
CB
|
G:GLN11
|
4.7
|
13.7
|
0.6
|
C
|
G:GLN11
|
4.7
|
12.0
|
1.0
|
CB
|
G:GLN11
|
4.7
|
12.8
|
0.4
|
CB
|
G:ASP44
|
4.7
|
9.8
|
1.0
|
N
|
G:ALA47
|
4.7
|
10.8
|
1.0
|
C
|
G:CYS12
|
4.8
|
8.2
|
1.0
|
N
|
G:GLY46
|
4.8
|
11.0
|
1.0
|
HG2
|
G:GLN11
|
4.8
|
17.6
|
0.6
|
N
|
G:PHE14
|
4.8
|
7.5
|
1.0
|
N
|
G:GLY13
|
4.8
|
7.9
|
1.0
|
HA
|
G:CYS45
|
4.9
|
11.5
|
1.0
|
HA
|
G:CYS12
|
5.0
|
10.5
|
1.0
|
HB3
|
G:ASP44
|
5.0
|
11.8
|
1.0
|
N
|
G:ASP44
|
5.0
|
8.9
|
1.0
|
|
Iron binding site 8 out
of 8 in 7a9a
Go back to
Iron Binding Sites List in 7a9a
Iron binding site 8 out
of 8 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe102
b:6.5
occ:1.00
|
SG
|
H:CYS12
|
2.3
|
10.4
|
1.0
|
SG
|
H:CYS9
|
2.3
|
7.4
|
1.0
|
SG
|
H:CYS42
|
2.3
|
8.3
|
1.0
|
SG
|
H:CYS45
|
2.3
|
10.3
|
1.0
|
HB3
|
H:CYS12
|
3.1
|
12.8
|
1.0
|
HB3
|
H:CYS9
|
3.2
|
8.5
|
1.0
|
HB3
|
H:CYS42
|
3.2
|
10.4
|
1.0
|
HB3
|
H:CYS45
|
3.2
|
11.9
|
1.0
|
CB
|
H:CYS42
|
3.2
|
8.6
|
1.0
|
CB
|
H:CYS9
|
3.2
|
7.1
|
1.0
|
HB2
|
H:CYS42
|
3.3
|
10.4
|
1.0
|
CB
|
H:CYS12
|
3.3
|
10.6
|
1.0
|
H
|
H:CYS12
|
3.4
|
13.1
|
1.0
|
CB
|
H:CYS45
|
3.4
|
9.9
|
1.0
|
HB2
|
H:CYS9
|
3.4
|
8.5
|
1.0
|
H
|
H:CYS45
|
3.4
|
12.3
|
1.0
|
HB3
|
H:PHE14
|
3.5
|
9.3
|
1.0
|
HB3
|
H:ALA47
|
3.7
|
12.2
|
1.0
|
HB3
|
H:GLN11
|
3.8
|
14.3
|
0.7
|
HB2
|
H:GLN11
|
3.8
|
13.3
|
0.3
|
N
|
H:CYS45
|
3.8
|
10.2
|
1.0
|
N
|
H:CYS12
|
3.9
|
10.9
|
1.0
|
H
|
H:ALA47
|
3.9
|
12.9
|
1.0
|
HB2
|
H:ASP44
|
3.9
|
14.5
|
1.0
|
H
|
H:PHE14
|
4.0
|
10.5
|
1.0
|
HB2
|
H:ALA47
|
4.0
|
12.2
|
1.0
|
HB2
|
H:CYS12
|
4.1
|
12.8
|
1.0
|
CA
|
H:CYS45
|
4.1
|
10.3
|
1.0
|
CA
|
H:CYS12
|
4.1
|
10.8
|
1.0
|
HB2
|
H:CYS45
|
4.2
|
11.9
|
1.0
|
CB
|
H:ALA47
|
4.3
|
10.2
|
1.0
|
CB
|
H:PHE14
|
4.3
|
7.8
|
1.0
|
HB2
|
H:PHE14
|
4.3
|
9.3
|
1.0
|
H
|
H:ASP44
|
4.3
|
12.1
|
1.0
|
H
|
H:GLY13
|
4.5
|
12.1
|
1.0
|
C
|
H:ASP44
|
4.6
|
10.7
|
1.0
|
H
|
H:GLY46
|
4.6
|
13.0
|
1.0
|
CB
|
H:GLN11
|
4.6
|
11.1
|
0.3
|
CA
|
H:CYS42
|
4.7
|
8.9
|
1.0
|
CA
|
H:CYS9
|
4.7
|
7.5
|
1.0
|
C
|
H:CYS45
|
4.7
|
11.1
|
1.0
|
CB
|
H:GLN11
|
4.7
|
12.0
|
0.7
|
N
|
H:ALA47
|
4.7
|
10.7
|
1.0
|
H
|
H:GLN11
|
4.7
|
13.4
|
0.7
|
C
|
H:CYS12
|
4.7
|
11.1
|
1.0
|
H
|
H:GLN11
|
4.7
|
13.4
|
0.3
|
CB
|
H:ASP44
|
4.8
|
12.1
|
1.0
|
HB3
|
H:GLN11
|
4.8
|
13.3
|
0.3
|
N
|
H:PHE14
|
4.8
|
8.8
|
1.0
|
C
|
H:GLN11
|
4.8
|
11.5
|
1.0
|
N
|
H:GLY13
|
4.8
|
10.1
|
1.0
|
N
|
H:GLY46
|
4.8
|
10.8
|
1.0
|
HG2
|
H:GLN11
|
4.9
|
14.8
|
0.7
|
HD2
|
H:PHE14
|
4.9
|
10.2
|
1.0
|
HA
|
H:CYS45
|
4.9
|
12.3
|
1.0
|
HA
|
H:CYS12
|
5.0
|
12.9
|
1.0
|
N
|
H:ASP44
|
5.0
|
10.1
|
1.0
|
HA
|
H:CYS42
|
5.0
|
10.7
|
1.0
|
HZ
|
H:PHE52
|
5.0
|
11.2
|
1.0
|
|
Reference:
T.Sushko,
A.Kavaleuski,
I.Grabovec,
A.Kavaleuskaya,
D.Vakhrameev,
S.Bukhdruker,
E.Marin,
A.Kuzikov,
R.Masamrekh,
V.Shumyantseva,
K.Tsumoto,
V.Borshchevskiy,
A.Gilep,
N.Strushkevich.
A New Twist of Rubredoxin Function in M. Tuberculosis. Bioorg.Chem. V. 109 04721 2021.
ISSN: ISSN 0045-2068
PubMed: 33618255
DOI: 10.1016/J.BIOORG.2021.104721
Page generated: Wed Aug 7 21:55:00 2024
|