Iron in PDB 6xtf: Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor
Protein crystallography data
The structure of Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor, PDB code: 6xtf
was solved by
R.M.Buey,
G.Gonzalez-Holgado,
D.Fernandez-Justel,
M.Balsera,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
83.37 /
2.23
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
166.741,
181.312,
80.369,
90,
90,
90
|
|
R / Rfree (%)
|
20.1 /
23.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor
(pdb code 6xtf). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor, PDB code: 6xtf:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6xtf
Go back to
Iron Binding Sites List in 6xtf
Iron binding site 1 out
of 4 in the Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:32.2
occ:1.00
|
FE1
|
C:FES101
|
0.0
|
32.2
|
1.0
|
|
SG
|
C:CYS40
|
2.0
|
36.6
|
1.0
|
|
S1
|
C:FES101
|
2.2
|
26.1
|
1.0
|
|
S2
|
C:FES101
|
2.2
|
24.1
|
1.0
|
|
SG
|
C:CYS45
|
2.5
|
23.3
|
1.0
|
|
FE2
|
C:FES101
|
2.7
|
38.5
|
1.0
|
|
H
|
C:CYS40
|
2.7
|
40.6
|
1.0
|
|
H
|
C:ARG41
|
2.9
|
19.2
|
1.0
|
|
H
|
C:CYS45
|
3.4
|
31.4
|
1.0
|
|
CB
|
C:CYS40
|
3.4
|
16.9
|
1.0
|
|
N
|
C:CYS40
|
3.5
|
33.2
|
1.0
|
|
H
|
C:SER39
|
3.5
|
55.3
|
1.0
|
|
HB3
|
C:CYS40
|
3.6
|
21.1
|
1.0
|
|
N
|
C:ARG41
|
3.6
|
15.7
|
1.0
|
|
H
|
C:ALA42
|
3.6
|
36.0
|
1.0
|
|
CB
|
C:CYS45
|
3.7
|
15.7
|
1.0
|
|
HB3
|
C:CYS45
|
3.8
|
18.3
|
1.0
|
|
H
|
C:GLY43
|
3.9
|
24.5
|
1.0
|
|
HB3
|
C:SER39
|
3.9
|
36.4
|
1.0
|
|
H
|
C:ALA44
|
3.9
|
24.9
|
1.0
|
|
CA
|
C:CYS40
|
3.9
|
23.0
|
1.0
|
|
N
|
C:CYS45
|
3.9
|
25.5
|
1.0
|
|
HB
|
C:THR47
|
3.9
|
18.6
|
1.0
|
|
HA
|
C:ARG41
|
4.1
|
30.0
|
1.0
|
|
H
|
C:THR47
|
4.1
|
29.7
|
1.0
|
|
CA
|
C:CYS45
|
4.1
|
15.5
|
1.0
|
|
HB2
|
C:CYS40
|
4.2
|
21.1
|
1.0
|
|
H
|
C:CYS48
|
4.2
|
23.6
|
1.0
|
|
SG
|
C:CYS78
|
4.2
|
28.7
|
1.0
|
|
C
|
C:CYS45
|
4.2
|
19.0
|
1.0
|
|
C
|
C:CYS40
|
4.2
|
35.1
|
1.0
|
|
HG
|
C:CYS78
|
4.2
|
35.2
|
1.0
|
|
N
|
C:SER39
|
4.3
|
45.4
|
1.0
|
|
CA
|
C:ARG41
|
4.4
|
24.3
|
1.0
|
|
SG
|
C:CYS48
|
4.4
|
26.8
|
1.0
|
|
N
|
C:ALA42
|
4.4
|
29.3
|
1.0
|
|
HB2
|
C:CYS45
|
4.5
|
18.3
|
1.0
|
|
O
|
C:CYS45
|
4.5
|
44.9
|
1.0
|
|
HB3
|
C:CYS48
|
4.5
|
18.2
|
1.0
|
|
C
|
C:SER39
|
4.6
|
35.2
|
1.0
|
|
N
|
C:GLY43
|
4.6
|
19.8
|
1.0
|
|
N
|
C:ALA44
|
4.6
|
20.1
|
1.0
|
|
N
|
C:SER46
|
4.6
|
24.9
|
1.0
|
|
N
|
C:THR47
|
4.7
|
24.1
|
1.0
|
|
CB
|
C:SER39
|
4.7
|
29.6
|
1.0
|
|
CA
|
C:SER39
|
4.7
|
32.5
|
1.0
|
|
HG1
|
C:THR47
|
4.8
|
44.9
|
1.0
|
|
HD13
|
C:LEU76
|
4.8
|
26.5
|
1.0
|
|
HA2
|
C:GLY43
|
4.8
|
34.4
|
1.0
|
|
HA
|
C:PHE38
|
4.8
|
35.4
|
1.0
|
|
HA
|
C:CYS40
|
4.8
|
28.4
|
1.0
|
|
CB
|
C:THR47
|
4.8
|
17.4
|
1.0
|
|
C
|
C:ALA44
|
4.9
|
27.9
|
1.0
|
|
HA
|
C:SER46
|
4.9
|
26.7
|
1.0
|
|
N
|
C:CYS48
|
4.9
|
19.0
|
1.0
|
|
H
|
C:SER46
|
4.9
|
30.6
|
1.0
|
|
C
|
C:ARG41
|
4.9
|
24.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 6xtf
Go back to
Iron Binding Sites List in 6xtf
Iron binding site 2 out
of 4 in the Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:38.5
occ:1.00
|
FE2
|
C:FES101
|
0.0
|
38.5
|
1.0
|
|
HG
|
C:CYS78
|
1.7
|
35.2
|
1.0
|
|
SG
|
C:CYS78
|
2.0
|
28.7
|
1.0
|
|
SG
|
C:CYS48
|
2.2
|
26.8
|
1.0
|
|
S2
|
C:FES101
|
2.2
|
24.1
|
1.0
|
|
S1
|
C:FES101
|
2.2
|
26.1
|
1.0
|
|
FE1
|
C:FES101
|
2.7
|
32.2
|
1.0
|
|
HB3
|
C:CYS78
|
3.0
|
29.2
|
1.0
|
|
HB3
|
C:CYS48
|
3.1
|
18.2
|
1.0
|
|
CB
|
C:CYS78
|
3.1
|
23.6
|
1.0
|
|
CB
|
C:CYS48
|
3.3
|
17.7
|
1.0
|
|
HB3
|
C:LEU76
|
3.4
|
13.3
|
1.0
|
|
H
|
C:CYS78
|
3.4
|
19.4
|
1.0
|
|
H
|
C:CYS48
|
3.6
|
23.6
|
1.0
|
|
H
|
C:GLY43
|
3.7
|
24.5
|
1.0
|
|
HA
|
C:ARG41
|
3.7
|
30.0
|
1.0
|
|
HB2
|
C:CYS78
|
3.7
|
29.2
|
1.0
|
|
HB2
|
C:CYS48
|
3.8
|
18.2
|
1.0
|
|
H
|
C:ARG41
|
4.0
|
19.2
|
1.0
|
|
SG
|
C:CYS40
|
4.1
|
36.6
|
1.0
|
|
N
|
C:CYS78
|
4.1
|
15.5
|
1.0
|
|
HD13
|
C:LEU76
|
4.2
|
26.5
|
1.0
|
|
HA2
|
C:GLY43
|
4.2
|
34.4
|
1.0
|
|
CA
|
C:CYS78
|
4.2
|
21.4
|
1.0
|
|
N
|
C:CYS48
|
4.3
|
19.0
|
1.0
|
|
H
|
C:ALA42
|
4.3
|
36.0
|
1.0
|
|
CB
|
C:LEU76
|
4.3
|
11.8
|
1.0
|
|
CA
|
C:CYS48
|
4.4
|
18.1
|
1.0
|
|
HD22
|
C:LEU76
|
4.4
|
25.6
|
1.0
|
|
N
|
C:GLY43
|
4.5
|
19.8
|
1.0
|
|
CA
|
C:ARG41
|
4.5
|
24.3
|
1.0
|
|
N
|
C:ARG41
|
4.6
|
15.7
|
1.0
|
|
HG22
|
C:VAL79
|
4.6
|
91.2
|
1.0
|
|
HA
|
C:LEU76
|
4.6
|
31.8
|
1.0
|
|
H
|
C:SER39
|
4.6
|
55.3
|
1.0
|
|
HA
|
C:PHE38
|
4.7
|
35.4
|
1.0
|
|
SG
|
C:CYS45
|
4.7
|
23.3
|
1.0
|
|
HD12
|
C:LEU76
|
4.8
|
26.5
|
1.0
|
|
H
|
C:CYS45
|
4.8
|
31.4
|
1.0
|
|
N
|
C:ALA42
|
4.8
|
29.3
|
1.0
|
|
H
|
C:THR77
|
4.8
|
27.9
|
1.0
|
|
CD1
|
C:LEU76
|
4.8
|
21.4
|
1.0
|
|
HB2
|
C:LEU76
|
4.8
|
13.3
|
1.0
|
|
HA
|
C:SER46
|
4.8
|
26.7
|
1.0
|
|
CA
|
C:GLY43
|
4.8
|
28.0
|
1.0
|
|
CA
|
C:LEU76
|
4.9
|
25.8
|
1.0
|
|
HD22
|
C:LEU26
|
4.9
|
30.1
|
1.0
|
|
C
|
C:LEU76
|
4.9
|
18.7
|
1.0
|
|
HA
|
C:CYS78
|
5.0
|
26.5
|
1.0
|
|
N
|
C:THR77
|
5.0
|
22.6
|
1.0
|
|
HG13
|
C:VAL79
|
5.0
|
67.5
|
1.0
|
|
HB
|
C:THR47
|
5.0
|
18.6
|
1.0
|
|
C
|
C:ARG41
|
5.0
|
24.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 6xtf
Go back to
Iron Binding Sites List in 6xtf
Iron binding site 3 out
of 4 in the Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe5202
b:27.8
occ:1.00
|
FE1
|
D:FES5202
|
0.0
|
27.8
|
1.0
|
|
SG
|
D:CYS40
|
2.1
|
35.0
|
1.0
|
|
S1
|
D:FES5202
|
2.2
|
35.4
|
1.0
|
|
S2
|
D:FES5202
|
2.2
|
38.2
|
1.0
|
|
SG
|
D:CYS45
|
2.4
|
46.2
|
1.0
|
|
FE2
|
D:FES5202
|
2.7
|
46.0
|
1.0
|
|
H
|
D:CYS40
|
2.8
|
34.5
|
1.0
|
|
HG
|
D:CYS78
|
3.1
|
48.3
|
1.0
|
|
H
|
D:ARG41
|
3.2
|
52.8
|
1.0
|
|
H
|
D:CYS45
|
3.2
|
34.8
|
1.0
|
|
CB
|
D:CYS40
|
3.4
|
25.4
|
1.0
|
|
N
|
D:CYS40
|
3.6
|
28.1
|
1.0
|
|
HB3
|
D:CYS40
|
3.6
|
31.3
|
1.0
|
|
H
|
D:SER39
|
3.7
|
54.0
|
1.0
|
|
CB
|
D:CYS45
|
3.7
|
30.9
|
1.0
|
|
H
|
D:ALA42
|
3.7
|
55.1
|
1.0
|
|
H
|
D:ALA44
|
3.8
|
46.6
|
1.0
|
|
HB2
|
D:SER39
|
3.8
|
40.2
|
1.0
|
|
H
|
D:GLY43
|
3.8
|
42.9
|
1.0
|
|
N
|
D:CYS45
|
3.8
|
32.4
|
1.0
|
|
N
|
D:ARG41
|
3.8
|
43.4
|
1.0
|
|
HB3
|
D:CYS45
|
3.8
|
33.0
|
1.0
|
|
HB
|
D:THR47
|
3.9
|
31.2
|
1.0
|
|
H
|
D:THR47
|
3.9
|
41.3
|
1.0
|
|
CA
|
D:CYS40
|
4.0
|
23.9
|
1.0
|
|
CA
|
D:CYS45
|
4.1
|
35.0
|
1.0
|
|
H
|
D:CYS48
|
4.1
|
51.7
|
1.0
|
|
C
|
D:CYS45
|
4.1
|
38.8
|
1.0
|
|
HB2
|
D:CYS40
|
4.2
|
31.3
|
1.0
|
|
SG
|
D:CYS78
|
4.3
|
39.6
|
1.0
|
|
C
|
D:CYS40
|
4.3
|
49.3
|
1.0
|
|
SG
|
D:CYS48
|
4.4
|
43.8
|
1.0
|
|
HB3
|
D:CYS48
|
4.4
|
44.5
|
1.0
|
|
O
|
D:CYS45
|
4.4
|
55.8
|
1.0
|
|
N
|
D:ALA44
|
4.4
|
38.1
|
1.0
|
|
HA
|
D:ARG41
|
4.4
|
43.6
|
1.0
|
|
N
|
D:SER39
|
4.4
|
44.3
|
1.0
|
|
N
|
D:GLY43
|
4.5
|
35.0
|
1.0
|
|
HB2
|
D:CYS45
|
4.5
|
33.0
|
1.0
|
|
N
|
D:ALA42
|
4.5
|
45.2
|
1.0
|
|
N
|
D:THR47
|
4.5
|
33.8
|
1.0
|
|
N
|
D:SER46
|
4.6
|
32.8
|
1.0
|
|
HG1
|
D:THR47
|
4.6
|
56.5
|
1.0
|
|
C
|
D:SER39
|
4.6
|
38.2
|
1.0
|
|
HA2
|
D:GLY43
|
4.6
|
48.6
|
1.0
|
|
CB
|
D:SER39
|
4.6
|
32.8
|
1.0
|
|
CA
|
D:ARG41
|
4.7
|
35.7
|
1.0
|
|
HD13
|
D:LEU76
|
4.7
|
43.5
|
1.0
|
|
CB
|
D:THR47
|
4.7
|
29.4
|
1.0
|
|
C
|
D:ALA44
|
4.8
|
40.8
|
1.0
|
|
H
|
D:SER46
|
4.8
|
37.6
|
1.0
|
|
CA
|
D:SER39
|
4.8
|
39.0
|
1.0
|
|
HA
|
D:CYS40
|
4.9
|
29.4
|
1.0
|
|
N
|
D:CYS48
|
4.9
|
42.4
|
1.0
|
|
CB
|
D:CYS48
|
4.9
|
36.4
|
1.0
|
|
CA
|
D:GLY43
|
4.9
|
39.9
|
1.0
|
|
HA
|
D:PHE38
|
4.9
|
33.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 6xtf
Go back to
Iron Binding Sites List in 6xtf
Iron binding site 4 out
of 4 in the Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor
 Mono view
 Stereo pair view
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|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe5202
b:46.0
occ:1.00
|
FE2
|
D:FES5202
|
0.0
|
46.0
|
1.0
|
|
HG
|
D:CYS78
|
1.5
|
48.3
|
1.0
|
|
SG
|
D:CYS78
|
2.1
|
39.6
|
1.0
|
|
S1
|
D:FES5202
|
2.2
|
35.4
|
1.0
|
|
S2
|
D:FES5202
|
2.2
|
38.2
|
1.0
|
|
SG
|
D:CYS48
|
2.2
|
43.8
|
1.0
|
|
HB3
|
D:CYS48
|
2.7
|
44.5
|
1.0
|
|
FE1
|
D:FES5202
|
2.7
|
27.8
|
1.0
|
|
HB3
|
D:CYS78
|
2.9
|
36.4
|
1.0
|
|
CB
|
D:CYS48
|
3.0
|
36.4
|
1.0
|
|
CB
|
D:CYS78
|
3.1
|
29.6
|
1.0
|
|
HB3
|
D:LEU76
|
3.3
|
37.9
|
1.0
|
|
H
|
D:CYS78
|
3.5
|
39.3
|
1.0
|
|
HB2
|
D:CYS48
|
3.5
|
44.5
|
1.0
|
|
H
|
D:CYS48
|
3.5
|
51.7
|
1.0
|
|
H
|
D:GLY43
|
3.6
|
42.9
|
1.0
|
|
HB2
|
D:CYS78
|
3.7
|
36.4
|
1.0
|
|
HA
|
D:ARG41
|
3.9
|
43.6
|
1.0
|
|
H
|
D:ARG41
|
3.9
|
52.8
|
1.0
|
|
HA2
|
D:GLY43
|
4.0
|
48.6
|
1.0
|
|
N
|
D:CYS78
|
4.2
|
32.0
|
1.0
|
|
SG
|
D:CYS40
|
4.2
|
35.0
|
1.0
|
|
N
|
D:CYS48
|
4.2
|
42.4
|
1.0
|
|
CA
|
D:CYS48
|
4.2
|
32.2
|
1.0
|
|
CA
|
D:CYS78
|
4.2
|
42.8
|
1.0
|
|
HD13
|
D:LEU76
|
4.2
|
43.5
|
1.0
|
|
H
|
D:ALA42
|
4.3
|
55.1
|
1.0
|
|
CB
|
D:LEU76
|
4.3
|
30.9
|
1.0
|
|
N
|
D:GLY43
|
4.4
|
35.0
|
1.0
|
|
HD22
|
D:LEU76
|
4.4
|
41.1
|
1.0
|
|
N
|
D:ARG41
|
4.5
|
43.4
|
1.0
|
|
CA
|
D:ARG41
|
4.6
|
35.7
|
1.0
|
|
H
|
D:SER39
|
4.6
|
54.0
|
1.0
|
|
HA
|
D:LEU76
|
4.6
|
49.3
|
1.0
|
|
HA
|
D:PHE38
|
4.7
|
33.5
|
1.0
|
|
CA
|
D:GLY43
|
4.7
|
39.9
|
1.0
|
|
H
|
D:CYS45
|
4.8
|
34.8
|
1.0
|
|
N
|
D:ALA42
|
4.8
|
45.2
|
1.0
|
|
HG22
|
D:VAL79
|
4.8
|
40.8
|
1.0
|
|
HD12
|
D:LEU76
|
4.8
|
43.5
|
1.0
|
|
HB2
|
D:LEU76
|
4.8
|
37.9
|
1.0
|
|
SG
|
D:CYS45
|
4.8
|
46.2
|
1.0
|
|
HB
|
D:THR47
|
4.8
|
31.2
|
1.0
|
|
H
|
D:THR77
|
4.9
|
48.8
|
1.0
|
|
CD1
|
D:LEU76
|
4.9
|
35.6
|
1.0
|
|
HA
|
D:CYS48
|
4.9
|
39.4
|
1.0
|
|
CA
|
D:LEU76
|
4.9
|
40.4
|
1.0
|
|
HD22
|
D:LEU26
|
4.9
|
50.9
|
1.0
|
|
H
|
D:CYS40
|
4.9
|
34.5
|
1.0
|
|
HA
|
D:CYS78
|
4.9
|
52.1
|
1.0
|
|
C
|
D:LEU76
|
5.0
|
38.1
|
1.0
|
|
C
|
D:CYS48
|
5.0
|
32.4
|
1.0
|
|
C
|
D:ARG41
|
5.0
|
39.9
|
1.0
|
|
HB2
|
D:PHE38
|
5.0
|
39.5
|
1.0
|
|
H
|
D:ALA44
|
5.0
|
46.6
|
1.0
|
|
H
|
D:THR47
|
5.0
|
41.3
|
1.0
|
|
Reference:
R.M.Buey,
G.Gonzalez-Holgado,
D.Fernandez-Justel,
M.Balsera.
Crystal Structure A Thioredoxin Reductase From Gloeobacter Violaceus Bound to Its Electron Donor To Be Published.
Page generated: Wed Aug 7 15:38:26 2024
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