Iron in PDB 8d5v: WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
Enzymatic activity of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
All present enzymatic activity of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera:
2.7.7.6;
Protein crystallography data
The structure of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera, PDB code: 8d5v
was solved by
T.Wan,
L.M.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.27 /
1.80
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.983,
66.54,
158.805,
90,
90,
90
|
R / Rfree (%)
|
21 /
23.1
|
Iron Binding Sites:
The binding sites of Iron atom in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
(pdb code 8d5v). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera, PDB code: 8d5v:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 8d5v
Go back to
Iron Binding Sites List in 8d5v
Iron binding site 1 out
of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:38.3
occ:1.00
|
FE1
|
A:SF4201
|
0.0
|
38.3
|
1.0
|
S4
|
A:SF4201
|
2.3
|
37.2
|
1.0
|
S2
|
A:SF4201
|
2.3
|
35.9
|
1.0
|
SG
|
A:CYS14
|
2.3
|
33.4
|
1.0
|
S3
|
A:SF4201
|
2.3
|
38.0
|
1.0
|
FE3
|
A:SF4201
|
2.7
|
33.8
|
1.0
|
FE2
|
A:SF4201
|
2.7
|
42.7
|
1.0
|
FE4
|
A:SF4201
|
2.7
|
32.8
|
1.0
|
CB
|
A:CYS14
|
3.2
|
34.0
|
1.0
|
S1
|
A:SF4201
|
3.9
|
37.7
|
1.0
|
N
|
A:CYS14
|
4.2
|
38.0
|
1.0
|
CA
|
A:GLY12
|
4.2
|
45.8
|
1.0
|
NE1
|
A:TRP21
|
4.2
|
34.9
|
1.0
|
CA
|
A:CYS14
|
4.3
|
36.5
|
1.0
|
CD1
|
A:TRP21
|
4.3
|
32.5
|
1.0
|
CE1
|
B:HIS516
|
4.4
|
41.3
|
1.0
|
C
|
A:GLY12
|
4.6
|
46.2
|
1.0
|
CG
|
B:PRO517
|
4.6
|
41.1
|
1.0
|
SG
|
A:CYS42
|
4.8
|
32.1
|
1.0
|
N
|
A:VAL13
|
4.8
|
43.5
|
1.0
|
SG
|
A:CYS33
|
4.8
|
35.1
|
1.0
|
SG
|
A:CYS36
|
4.8
|
39.9
|
1.0
|
CE2
|
A:TRP21
|
4.9
|
36.1
|
1.0
|
CB
|
B:PRO517
|
4.9
|
40.0
|
1.0
|
NE2
|
B:HIS516
|
5.0
|
42.7
|
1.0
|
|
Iron binding site 2 out
of 8 in 8d5v
Go back to
Iron Binding Sites List in 8d5v
Iron binding site 2 out
of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:42.7
occ:1.00
|
FE2
|
A:SF4201
|
0.0
|
42.7
|
1.0
|
S3
|
A:SF4201
|
2.3
|
38.0
|
1.0
|
SG
|
A:CYS36
|
2.3
|
39.9
|
1.0
|
S1
|
A:SF4201
|
2.3
|
37.7
|
1.0
|
S4
|
A:SF4201
|
2.3
|
37.2
|
1.0
|
FE4
|
A:SF4201
|
2.7
|
32.8
|
1.0
|
FE1
|
A:SF4201
|
2.7
|
38.3
|
1.0
|
FE3
|
A:SF4201
|
2.7
|
33.8
|
1.0
|
CB
|
A:CYS36
|
3.1
|
39.7
|
1.0
|
S2
|
A:SF4201
|
3.9
|
35.9
|
1.0
|
CA
|
A:GLY12
|
4.0
|
45.8
|
1.0
|
CG
|
A:ARG38
|
4.2
|
47.9
|
1.0
|
O
|
A:HOH323
|
4.3
|
43.2
|
1.0
|
CA
|
A:CYS36
|
4.6
|
42.3
|
1.0
|
SG
|
A:CYS14
|
4.8
|
33.4
|
1.0
|
CA
|
A:CYS33
|
4.8
|
38.8
|
1.0
|
SG
|
A:CYS42
|
4.8
|
32.1
|
1.0
|
SG
|
A:CYS33
|
4.8
|
35.1
|
1.0
|
CB
|
A:CYS42
|
4.9
|
33.1
|
1.0
|
N
|
A:ARG39
|
4.9
|
37.5
|
1.0
|
CA
|
A:ARG39
|
4.9
|
35.3
|
1.0
|
C
|
A:GLY12
|
4.9
|
46.2
|
1.0
|
C
|
A:ARG38
|
4.9
|
45.3
|
1.0
|
CD
|
A:ARG38
|
5.0
|
50.0
|
1.0
|
N
|
A:GLY12
|
5.0
|
47.4
|
1.0
|
N
|
A:VAL13
|
5.0
|
43.5
|
1.0
|
|
Iron binding site 3 out
of 8 in 8d5v
Go back to
Iron Binding Sites List in 8d5v
Iron binding site 3 out
of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:33.8
occ:1.00
|
FE3
|
A:SF4201
|
0.0
|
33.8
|
1.0
|
S4
|
A:SF4201
|
2.3
|
37.2
|
1.0
|
S2
|
A:SF4201
|
2.3
|
35.9
|
1.0
|
SG
|
A:CYS33
|
2.3
|
35.1
|
1.0
|
S1
|
A:SF4201
|
2.3
|
37.7
|
1.0
|
FE1
|
A:SF4201
|
2.7
|
38.3
|
1.0
|
FE2
|
A:SF4201
|
2.7
|
42.7
|
1.0
|
FE4
|
A:SF4201
|
2.8
|
32.8
|
1.0
|
CB
|
A:CYS33
|
3.3
|
36.8
|
1.0
|
NE1
|
A:TRP21
|
3.6
|
34.9
|
1.0
|
CA
|
A:CYS33
|
3.6
|
38.8
|
1.0
|
S3
|
A:SF4201
|
3.9
|
38.0
|
1.0
|
CD1
|
A:TRP21
|
3.9
|
32.5
|
1.0
|
N
|
A:ALA57
|
4.0
|
31.8
|
1.0
|
N
|
A:CYS33
|
4.5
|
41.0
|
1.0
|
CA
|
A:ALA57
|
4.5
|
31.9
|
1.0
|
CB
|
A:CYS36
|
4.6
|
39.7
|
1.0
|
SG
|
A:CYS36
|
4.7
|
39.9
|
1.0
|
CE2
|
A:TRP21
|
4.7
|
36.1
|
1.0
|
SG
|
A:CYS42
|
4.7
|
32.1
|
1.0
|
N
|
A:GLY58
|
4.7
|
30.2
|
1.0
|
C
|
A:CYS33
|
4.8
|
40.3
|
1.0
|
SG
|
A:CYS14
|
4.8
|
33.4
|
1.0
|
O
|
A:CYS33
|
4.9
|
39.6
|
1.0
|
CB
|
A:CYS14
|
4.9
|
34.0
|
1.0
|
|
Iron binding site 4 out
of 8 in 8d5v
Go back to
Iron Binding Sites List in 8d5v
Iron binding site 4 out
of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:32.8
occ:1.00
|
FE4
|
A:SF4201
|
0.0
|
32.8
|
1.0
|
S3
|
A:SF4201
|
2.2
|
38.0
|
1.0
|
SG
|
A:CYS42
|
2.3
|
32.1
|
1.0
|
S1
|
A:SF4201
|
2.3
|
37.7
|
1.0
|
S2
|
A:SF4201
|
2.4
|
35.9
|
1.0
|
FE2
|
A:SF4201
|
2.7
|
42.7
|
1.0
|
FE1
|
A:SF4201
|
2.7
|
38.3
|
1.0
|
FE3
|
A:SF4201
|
2.8
|
33.8
|
1.0
|
CB
|
A:CYS42
|
3.0
|
33.1
|
1.0
|
N
|
A:ALA57
|
3.9
|
31.8
|
1.0
|
S4
|
A:SF4201
|
3.9
|
37.2
|
1.0
|
CG
|
B:PRO517
|
4.1
|
41.1
|
1.0
|
CA
|
A:ALA57
|
4.5
|
31.9
|
1.0
|
CA
|
A:CYS42
|
4.5
|
34.6
|
1.0
|
NH1
|
A:ARG38
|
4.6
|
46.3
|
1.0
|
SG
|
A:CYS14
|
4.8
|
33.4
|
1.0
|
SG
|
A:CYS36
|
4.8
|
39.9
|
1.0
|
SG
|
A:CYS33
|
4.8
|
35.1
|
1.0
|
CA
|
A:TRP56
|
4.9
|
31.8
|
1.0
|
C
|
A:TRP56
|
4.9
|
31.6
|
1.0
|
CB
|
B:PRO517
|
4.9
|
40.0
|
1.0
|
|
Iron binding site 5 out
of 8 in 8d5v
Go back to
Iron Binding Sites List in 8d5v
Iron binding site 5 out
of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:50.0
occ:1.00
|
FE1
|
C:SF4201
|
0.0
|
50.0
|
1.0
|
S3
|
C:SF4201
|
2.2
|
48.9
|
1.0
|
S2
|
C:SF4201
|
2.3
|
51.6
|
1.0
|
S4
|
C:SF4201
|
2.3
|
48.3
|
1.0
|
SG
|
C:CYS14
|
2.4
|
48.8
|
1.0
|
FE2
|
C:SF4201
|
2.6
|
46.5
|
1.0
|
FE4
|
C:SF4201
|
2.7
|
45.7
|
1.0
|
FE3
|
C:SF4201
|
2.7
|
48.4
|
1.0
|
CB
|
C:CYS14
|
3.2
|
53.3
|
1.0
|
S1
|
C:SF4201
|
3.9
|
47.2
|
1.0
|
N
|
C:CYS14
|
4.1
|
57.8
|
1.0
|
CA
|
C:CYS14
|
4.3
|
58.1
|
1.0
|
NE1
|
C:TRP21
|
4.4
|
61.7
|
1.0
|
CG
|
D:PRO517
|
4.5
|
47.0
|
1.0
|
CA
|
C:GLY12
|
4.5
|
49.7
|
1.0
|
CD1
|
C:TRP21
|
4.5
|
61.0
|
1.0
|
CE1
|
D:HIS516
|
4.5
|
48.9
|
1.0
|
C
|
C:GLY12
|
4.7
|
53.5
|
1.0
|
CB
|
D:PRO517
|
4.8
|
46.3
|
1.0
|
SG
|
C:CYS36
|
4.8
|
51.5
|
1.0
|
SG
|
C:CYS42
|
4.8
|
45.5
|
1.0
|
NE2
|
D:GLN521
|
4.8
|
61.6
|
1.0
|
N
|
C:VAL13
|
4.8
|
60.1
|
1.0
|
SG
|
C:CYS33
|
4.9
|
52.7
|
1.0
|
|
Iron binding site 6 out
of 8 in 8d5v
Go back to
Iron Binding Sites List in 8d5v
Iron binding site 6 out
of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:46.5
occ:1.00
|
FE2
|
C:SF4201
|
0.0
|
46.5
|
1.0
|
S4
|
C:SF4201
|
2.2
|
48.3
|
1.0
|
S1
|
C:SF4201
|
2.3
|
47.2
|
1.0
|
S3
|
C:SF4201
|
2.3
|
48.9
|
1.0
|
SG
|
C:CYS36
|
2.3
|
51.5
|
1.0
|
FE1
|
C:SF4201
|
2.6
|
50.0
|
1.0
|
FE3
|
C:SF4201
|
2.7
|
48.4
|
1.0
|
FE4
|
C:SF4201
|
2.7
|
45.7
|
1.0
|
CB
|
C:CYS36
|
3.2
|
52.2
|
1.0
|
S2
|
C:SF4201
|
3.8
|
51.6
|
1.0
|
CA
|
C:GLY12
|
4.3
|
49.7
|
1.0
|
CG
|
C:ARG38
|
4.3
|
56.1
|
1.0
|
CA
|
C:CYS36
|
4.7
|
53.9
|
1.0
|
SG
|
C:CYS14
|
4.8
|
48.8
|
1.0
|
CA
|
C:CYS33
|
4.8
|
53.1
|
1.0
|
SG
|
C:CYS42
|
4.8
|
45.5
|
1.0
|
SG
|
C:CYS33
|
4.9
|
52.7
|
1.0
|
CB
|
C:CYS42
|
4.9
|
44.3
|
1.0
|
CD
|
C:ARG38
|
4.9
|
59.2
|
1.0
|
N
|
C:VAL13
|
4.9
|
60.1
|
1.0
|
|
Iron binding site 7 out
of 8 in 8d5v
Go back to
Iron Binding Sites List in 8d5v
Iron binding site 7 out
of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:48.4
occ:1.00
|
FE3
|
C:SF4201
|
0.0
|
48.4
|
1.0
|
S2
|
C:SF4201
|
2.2
|
51.6
|
1.0
|
S4
|
C:SF4201
|
2.3
|
48.3
|
1.0
|
S1
|
C:SF4201
|
2.3
|
47.2
|
1.0
|
SG
|
C:CYS33
|
2.4
|
52.7
|
1.0
|
FE2
|
C:SF4201
|
2.7
|
46.5
|
1.0
|
FE1
|
C:SF4201
|
2.7
|
50.0
|
1.0
|
FE4
|
C:SF4201
|
2.7
|
45.7
|
1.0
|
CB
|
C:CYS33
|
3.4
|
52.0
|
1.0
|
CA
|
C:CYS33
|
3.7
|
53.1
|
1.0
|
NE1
|
C:TRP21
|
3.8
|
61.7
|
1.0
|
S3
|
C:SF4201
|
3.9
|
48.9
|
1.0
|
N
|
C:ALA57
|
4.0
|
50.3
|
1.0
|
CD1
|
C:TRP21
|
4.2
|
61.0
|
1.0
|
CA
|
C:ALA57
|
4.4
|
47.8
|
1.0
|
N
|
C:CYS33
|
4.5
|
56.6
|
1.0
|
N
|
C:GLY58
|
4.6
|
46.9
|
1.0
|
SG
|
C:CYS36
|
4.7
|
51.5
|
1.0
|
CB
|
C:CYS36
|
4.7
|
52.2
|
1.0
|
SG
|
C:CYS42
|
4.8
|
45.5
|
1.0
|
C
|
C:CYS33
|
4.8
|
52.4
|
1.0
|
O
|
C:LEU55
|
4.8
|
50.4
|
1.0
|
SG
|
C:CYS14
|
4.9
|
48.8
|
1.0
|
O
|
C:CYS33
|
4.9
|
50.1
|
1.0
|
CE2
|
C:TRP21
|
5.0
|
65.4
|
1.0
|
C
|
C:TRP56
|
5.0
|
43.9
|
1.0
|
C
|
C:ALA57
|
5.0
|
50.4
|
1.0
|
|
Iron binding site 8 out
of 8 in 8d5v
Go back to
Iron Binding Sites List in 8d5v
Iron binding site 8 out
of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:45.7
occ:1.00
|
FE4
|
C:SF4201
|
0.0
|
45.7
|
1.0
|
S2
|
C:SF4201
|
2.3
|
51.6
|
1.0
|
S3
|
C:SF4201
|
2.3
|
48.9
|
1.0
|
SG
|
C:CYS42
|
2.3
|
45.5
|
1.0
|
S1
|
C:SF4201
|
2.3
|
47.2
|
1.0
|
FE1
|
C:SF4201
|
2.7
|
50.0
|
1.0
|
FE3
|
C:SF4201
|
2.7
|
48.4
|
1.0
|
FE2
|
C:SF4201
|
2.7
|
46.5
|
1.0
|
CB
|
C:CYS42
|
3.1
|
44.3
|
1.0
|
N
|
C:ALA57
|
3.8
|
50.3
|
1.0
|
S4
|
C:SF4201
|
3.9
|
48.3
|
1.0
|
CG
|
D:PRO517
|
4.0
|
47.0
|
1.0
|
CA
|
C:ALA57
|
4.4
|
47.8
|
1.0
|
CA
|
C:CYS42
|
4.6
|
42.2
|
1.0
|
NH1
|
C:ARG38
|
4.6
|
58.9
|
1.0
|
CA
|
C:TRP56
|
4.8
|
45.7
|
1.0
|
C
|
C:TRP56
|
4.8
|
43.9
|
1.0
|
CB
|
D:PRO517
|
4.8
|
46.3
|
1.0
|
SG
|
C:CYS14
|
4.8
|
48.8
|
1.0
|
SG
|
C:CYS33
|
4.8
|
52.7
|
1.0
|
SG
|
C:CYS36
|
4.8
|
51.5
|
1.0
|
|
Reference:
T.Wan,
L.M.Zhang.
Crystal Structure of WHIB6 and SIGA4-Betatip Complex To Be Published.
Page generated: Fri Aug 9 23:15:48 2024
|