Nickel in PDB 8cwt: Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212
Enzymatic activity of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212
All present enzymatic activity of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212:
2.7.7.6;
Protein crystallography data
The structure of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212, PDB code: 8cwt
was solved by
T.Wan,
L.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.68 /
1.35
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
121.826,
121.826,
114.305,
90,
90,
90
|
R / Rfree (%)
|
15.2 /
17.4
|
Other elements in 8cwt:
The structure of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212
(pdb code 8cwt). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 7 binding sites of Nickel where determined in the
Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212, PDB code: 8cwt:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
Nickel binding site 1 out
of 7 in 8cwt
Go back to
Nickel Binding Sites List in 8cwt
Nickel binding site 1 out
of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni601
b:14.8
occ:1.00
|
NE2
|
F:HIS443
|
2.1
|
15.3
|
1.0
|
NE2
|
D:HIS445
|
2.1
|
14.7
|
1.0
|
NE2
|
B:HIS443
|
2.1
|
14.5
|
1.0
|
NE2
|
B:HIS445
|
2.1
|
15.1
|
1.0
|
NE2
|
F:HIS445
|
2.1
|
15.2
|
1.0
|
NE2
|
D:HIS443
|
2.1
|
14.7
|
1.0
|
CE1
|
B:HIS443
|
3.1
|
15.8
|
1.0
|
CE1
|
B:HIS445
|
3.1
|
15.9
|
1.0
|
CE1
|
F:HIS443
|
3.1
|
15.5
|
1.0
|
CE1
|
D:HIS445
|
3.1
|
15.6
|
1.0
|
CE1
|
D:HIS443
|
3.1
|
16.2
|
1.0
|
CE1
|
F:HIS445
|
3.1
|
15.9
|
1.0
|
CD2
|
D:HIS445
|
3.2
|
14.9
|
1.0
|
CD2
|
B:HIS443
|
3.2
|
14.6
|
1.0
|
CD2
|
F:HIS445
|
3.2
|
15.5
|
1.0
|
CD2
|
B:HIS445
|
3.2
|
14.9
|
1.0
|
CD2
|
F:HIS443
|
3.2
|
15.7
|
1.0
|
CD2
|
D:HIS443
|
3.2
|
15.1
|
1.0
|
ND1
|
B:HIS445
|
4.3
|
15.9
|
1.0
|
ND1
|
D:HIS445
|
4.3
|
15.8
|
1.0
|
ND1
|
B:HIS443
|
4.3
|
15.8
|
1.0
|
ND1
|
F:HIS445
|
4.3
|
16.4
|
1.0
|
ND1
|
F:HIS443
|
4.3
|
15.9
|
1.0
|
ND1
|
D:HIS443
|
4.3
|
16.4
|
1.0
|
CG
|
D:HIS445
|
4.3
|
15.5
|
1.0
|
CG
|
B:HIS445
|
4.3
|
15.1
|
1.0
|
CG
|
F:HIS445
|
4.3
|
15.7
|
1.0
|
CG
|
B:HIS443
|
4.3
|
14.8
|
1.0
|
CG
|
F:HIS443
|
4.3
|
15.5
|
1.0
|
CG
|
D:HIS443
|
4.3
|
14.8
|
1.0
|
|
Nickel binding site 2 out
of 7 in 8cwt
Go back to
Nickel Binding Sites List in 8cwt
Nickel binding site 2 out
of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni602
b:18.8
occ:1.00
|
NE2
|
F:HIS440
|
2.1
|
24.5
|
1.0
|
NE2
|
B:HIS444
|
2.1
|
18.6
|
1.0
|
NE2
|
B:HIS442
|
2.1
|
18.6
|
1.0
|
O2
|
F:TRS607
|
2.1
|
26.0
|
1.0
|
O3
|
F:TRS607
|
2.1
|
21.2
|
1.0
|
O1
|
F:TRS607
|
2.2
|
23.7
|
1.0
|
CE1
|
F:HIS440
|
3.0
|
27.2
|
1.0
|
C3
|
F:TRS607
|
3.0
|
29.1
|
1.0
|
CE1
|
B:HIS442
|
3.1
|
20.0
|
1.0
|
CE1
|
B:HIS444
|
3.1
|
20.6
|
1.0
|
C1
|
F:TRS607
|
3.1
|
30.2
|
1.0
|
CD2
|
B:HIS444
|
3.1
|
17.4
|
1.0
|
CD2
|
F:HIS440
|
3.1
|
25.3
|
1.0
|
CD2
|
B:HIS442
|
3.1
|
17.4
|
1.0
|
C
|
F:TRS607
|
3.2
|
30.3
|
1.0
|
C2
|
F:TRS607
|
3.2
|
38.3
|
1.0
|
OE2
|
F:GLU537
|
4.0
|
19.7
|
1.0
|
ND1
|
F:HIS440
|
4.1
|
28.6
|
1.0
|
ND1
|
B:HIS442
|
4.2
|
19.7
|
1.0
|
ND1
|
B:HIS444
|
4.2
|
20.7
|
1.0
|
OE1
|
F:GLU537
|
4.2
|
20.2
|
1.0
|
CG
|
B:HIS444
|
4.2
|
18.5
|
1.0
|
CG
|
F:HIS440
|
4.3
|
25.2
|
1.0
|
CG
|
B:HIS442
|
4.3
|
17.4
|
1.0
|
O
|
F:HOH727
|
4.3
|
45.3
|
1.0
|
CD
|
F:GLU537
|
4.5
|
19.2
|
1.0
|
OE1
|
B:GLN457
|
4.6
|
32.2
|
1.0
|
N
|
F:TRS607
|
4.7
|
37.4
|
1.0
|
|
Nickel binding site 3 out
of 7 in 8cwt
Go back to
Nickel Binding Sites List in 8cwt
Nickel binding site 3 out
of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni603
b:25.2
occ:1.00
|
N
|
B:HIS440
|
1.8
|
25.1
|
1.0
|
ND1
|
B:HIS441
|
1.8
|
13.0
|
1.0
|
N
|
B:ALA439
|
1.9
|
28.1
|
1.0
|
N
|
B:HIS441
|
1.9
|
20.3
|
1.0
|
C
|
B:HIS440
|
2.7
|
23.1
|
1.0
|
C
|
B:ALA439
|
2.7
|
31.2
|
1.0
|
CE1
|
B:HIS441
|
2.7
|
23.3
|
1.0
|
CA
|
B:HIS440
|
2.8
|
25.8
|
1.0
|
CA
|
B:ALA439
|
2.8
|
33.4
|
1.0
|
CG
|
B:HIS441
|
3.0
|
21.0
|
1.0
|
O
|
B:HOH799
|
3.1
|
32.8
|
1.0
|
CA
|
B:HIS441
|
3.1
|
18.7
|
1.0
|
CB
|
B:HIS441
|
3.4
|
19.8
|
1.0
|
CD2
|
B:HIS440
|
3.6
|
26.3
|
1.0
|
CB
|
B:ALA439
|
3.8
|
36.7
|
1.0
|
O
|
B:ALA439
|
3.9
|
33.5
|
1.0
|
CB
|
B:HIS440
|
3.9
|
27.8
|
1.0
|
O
|
B:HIS440
|
3.9
|
26.9
|
1.0
|
CE1
|
D:HIS442
|
4.0
|
20.8
|
1.0
|
CG
|
B:HIS440
|
4.0
|
28.6
|
1.0
|
NE2
|
B:HIS441
|
4.0
|
25.6
|
1.0
|
N
|
B:HIS442
|
4.0
|
16.6
|
1.0
|
C
|
B:HIS441
|
4.0
|
19.4
|
1.0
|
CD2
|
B:HIS441
|
4.1
|
22.5
|
1.0
|
O1
|
D:SO4603
|
4.1
|
37.8
|
0.5
|
ND1
|
D:HIS442
|
4.3
|
21.2
|
1.0
|
NE2
|
B:HIS440
|
4.7
|
24.4
|
1.0
|
NE2
|
D:HIS442
|
4.8
|
19.4
|
1.0
|
O
|
B:HOH780
|
4.8
|
33.3
|
1.0
|
O2
|
D:SO4603
|
5.0
|
34.4
|
0.5
|
|
Nickel binding site 4 out
of 7 in 8cwt
Go back to
Nickel Binding Sites List in 8cwt
Nickel binding site 4 out
of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni601
b:25.3
occ:1.00
|
ND1
|
D:HIS441
|
1.8
|
12.4
|
1.0
|
N
|
D:HIS440
|
1.8
|
26.0
|
1.0
|
N
|
D:HIS441
|
1.9
|
20.2
|
1.0
|
N
|
D:ALA439
|
1.9
|
30.6
|
1.0
|
C
|
D:HIS440
|
2.7
|
24.1
|
1.0
|
C
|
D:ALA439
|
2.7
|
34.2
|
1.0
|
CE1
|
D:HIS441
|
2.8
|
24.6
|
1.0
|
CA
|
D:HIS440
|
2.8
|
27.0
|
1.0
|
CA
|
D:ALA439
|
2.8
|
35.7
|
1.0
|
CG
|
D:HIS441
|
3.0
|
21.4
|
1.0
|
O
|
D:HOH788
|
3.1
|
32.5
|
1.0
|
CA
|
D:HIS441
|
3.1
|
19.5
|
1.0
|
CB
|
D:HIS441
|
3.4
|
21.5
|
1.0
|
CD2
|
D:HIS440
|
3.6
|
24.8
|
1.0
|
CB
|
D:ALA439
|
3.7
|
36.0
|
1.0
|
CB
|
D:HIS440
|
3.9
|
26.7
|
1.0
|
O
|
D:ALA439
|
3.9
|
35.9
|
1.0
|
O
|
D:HIS440
|
3.9
|
24.9
|
1.0
|
CE1
|
F:HIS442
|
4.0
|
21.1
|
1.0
|
CG
|
D:HIS440
|
4.0
|
26.7
|
1.0
|
N
|
D:HIS442
|
4.0
|
17.0
|
1.0
|
NE2
|
D:HIS441
|
4.0
|
25.7
|
1.0
|
C
|
D:HIS441
|
4.0
|
19.1
|
1.0
|
CD2
|
D:HIS441
|
4.1
|
21.2
|
1.0
|
O
|
D:HOH701
|
4.1
|
48.8
|
1.0
|
O4
|
F:SO4603
|
4.2
|
37.4
|
0.5
|
ND1
|
F:HIS442
|
4.3
|
21.3
|
1.0
|
NE2
|
D:HIS440
|
4.7
|
23.8
|
1.0
|
NE2
|
F:HIS442
|
4.8
|
19.8
|
1.0
|
O
|
D:HOH771
|
4.9
|
33.3
|
1.0
|
|
Nickel binding site 5 out
of 7 in 8cwt
Go back to
Nickel Binding Sites List in 8cwt
Nickel binding site 5 out
of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni602
b:19.0
occ:1.00
|
NE2
|
D:HIS444
|
2.1
|
19.1
|
1.0
|
NE2
|
B:HIS440
|
2.1
|
24.4
|
1.0
|
NE2
|
D:HIS442
|
2.1
|
19.4
|
1.0
|
O2
|
B:TRS610
|
2.1
|
20.1
|
1.0
|
O1
|
B:TRS610
|
2.1
|
21.6
|
1.0
|
O3
|
B:TRS610
|
2.1
|
24.6
|
1.0
|
CE1
|
B:HIS440
|
3.0
|
27.5
|
1.0
|
C2
|
B:TRS610
|
3.0
|
30.3
|
1.0
|
CE1
|
D:HIS442
|
3.0
|
20.8
|
1.0
|
CE1
|
D:HIS444
|
3.0
|
21.0
|
1.0
|
C1
|
B:TRS610
|
3.1
|
29.3
|
1.0
|
CD2
|
D:HIS444
|
3.1
|
17.8
|
1.0
|
CD2
|
D:HIS442
|
3.1
|
18.4
|
1.0
|
CD2
|
B:HIS440
|
3.1
|
26.3
|
1.0
|
C
|
B:TRS610
|
3.2
|
33.4
|
1.0
|
C3
|
B:TRS610
|
3.3
|
36.4
|
1.0
|
OE2
|
B:GLU537
|
4.0
|
19.7
|
1.0
|
ND1
|
B:HIS440
|
4.1
|
29.4
|
1.0
|
ND1
|
D:HIS442
|
4.1
|
21.2
|
1.0
|
ND1
|
D:HIS444
|
4.2
|
20.2
|
1.0
|
OE1
|
B:GLU537
|
4.2
|
20.2
|
1.0
|
CG
|
D:HIS444
|
4.2
|
18.8
|
1.0
|
CG
|
D:HIS442
|
4.2
|
18.8
|
1.0
|
CG
|
B:HIS440
|
4.3
|
28.6
|
1.0
|
O
|
B:HOH749
|
4.4
|
49.7
|
1.0
|
CD
|
B:GLU537
|
4.5
|
19.9
|
1.0
|
OE1
|
D:GLN457
|
4.7
|
33.9
|
1.0
|
N
|
B:TRS610
|
4.7
|
35.8
|
1.0
|
O
|
D:HOH726
|
5.0
|
51.5
|
1.0
|
|
Nickel binding site 6 out
of 7 in 8cwt
Go back to
Nickel Binding Sites List in 8cwt
Nickel binding site 6 out
of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni601
b:19.1
occ:1.00
|
NE2
|
D:HIS440
|
2.0
|
23.8
|
1.0
|
NE2
|
F:HIS442
|
2.1
|
19.8
|
1.0
|
NE2
|
F:HIS444
|
2.1
|
19.3
|
1.0
|
O2
|
D:TRS609
|
2.1
|
21.0
|
1.0
|
O3
|
D:TRS609
|
2.1
|
21.7
|
1.0
|
O1
|
D:TRS609
|
2.1
|
38.7
|
1.0
|
C1
|
D:TRS609
|
2.3
|
25.5
|
1.0
|
C
|
D:TRS609
|
2.9
|
30.3
|
1.0
|
CE1
|
D:HIS440
|
3.0
|
26.6
|
1.0
|
C3
|
D:TRS609
|
3.0
|
27.1
|
1.0
|
CE1
|
F:HIS442
|
3.0
|
21.1
|
1.0
|
CE1
|
F:HIS444
|
3.1
|
20.7
|
1.0
|
C2
|
D:TRS609
|
3.1
|
28.7
|
1.0
|
CD2
|
F:HIS444
|
3.1
|
17.5
|
1.0
|
CD2
|
F:HIS442
|
3.1
|
17.7
|
1.0
|
CD2
|
D:HIS440
|
3.1
|
24.8
|
1.0
|
OE2
|
D:GLU537
|
4.0
|
20.9
|
1.0
|
ND1
|
D:HIS440
|
4.1
|
29.6
|
1.0
|
ND1
|
F:HIS442
|
4.1
|
21.3
|
1.0
|
OE1
|
D:GLU537
|
4.2
|
20.7
|
1.0
|
ND1
|
F:HIS444
|
4.2
|
20.4
|
1.0
|
CG
|
F:HIS442
|
4.2
|
18.3
|
1.0
|
CG
|
D:HIS440
|
4.2
|
26.7
|
1.0
|
CG
|
F:HIS444
|
4.2
|
18.6
|
1.0
|
N
|
D:TRS609
|
4.4
|
34.4
|
1.0
|
CD
|
D:GLU537
|
4.5
|
21.0
|
1.0
|
OE1
|
F:GLN457
|
4.6
|
34.8
|
1.0
|
O
|
F:HOH722
|
4.9
|
47.9
|
1.0
|
|
Nickel binding site 7 out
of 7 in 8cwt
Go back to
Nickel Binding Sites List in 8cwt
Nickel binding site 7 out
of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni602
b:24.6
occ:1.00
|
ND1
|
F:HIS441
|
1.8
|
14.2
|
1.0
|
N
|
F:HIS440
|
1.9
|
24.9
|
1.0
|
N
|
F:ALA439
|
1.9
|
29.1
|
1.0
|
N
|
F:HIS441
|
1.9
|
20.2
|
1.0
|
CE1
|
F:HIS441
|
2.7
|
24.7
|
1.0
|
C
|
F:HIS440
|
2.7
|
23.1
|
1.0
|
C
|
F:ALA439
|
2.7
|
29.8
|
1.0
|
CA
|
F:HIS440
|
2.8
|
27.0
|
1.0
|
CA
|
F:ALA439
|
2.8
|
31.4
|
1.0
|
O
|
F:HOH778
|
3.0
|
34.8
|
1.0
|
CG
|
F:HIS441
|
3.0
|
20.4
|
1.0
|
CA
|
F:HIS441
|
3.1
|
19.5
|
1.0
|
CB
|
F:HIS441
|
3.4
|
20.1
|
1.0
|
CD2
|
F:HIS440
|
3.6
|
25.3
|
1.0
|
CB
|
F:ALA439
|
3.7
|
33.3
|
1.0
|
O
|
F:ALA439
|
3.9
|
32.4
|
1.0
|
O
|
F:HIS440
|
3.9
|
25.8
|
1.0
|
CE1
|
B:HIS442
|
3.9
|
20.0
|
1.0
|
CB
|
F:HIS440
|
3.9
|
26.9
|
1.0
|
NE2
|
F:HIS441
|
3.9
|
26.4
|
1.0
|
N
|
F:HIS442
|
4.0
|
17.3
|
1.0
|
CG
|
F:HIS440
|
4.0
|
25.2
|
1.0
|
C
|
F:HIS441
|
4.0
|
18.4
|
1.0
|
CD2
|
F:HIS441
|
4.1
|
21.4
|
1.0
|
O2
|
B:SO4605
|
4.1
|
36.4
|
0.6
|
ND1
|
B:HIS442
|
4.2
|
19.7
|
1.0
|
NE2
|
F:HIS440
|
4.8
|
24.5
|
1.0
|
NE2
|
B:HIS442
|
4.8
|
18.6
|
1.0
|
O
|
F:HOH758
|
4.9
|
31.7
|
1.0
|
O4
|
B:SO4605
|
4.9
|
31.7
|
0.6
|
|
Reference:
T.Wan,
M.Horova,
V.Khetrapal,
S.Li,
C.Jones,
A.Schacht,
X.Sun,
L.Zhang.
Structural Basis of Dna Binding By the Whib-Like Transcription Factor WHIB3 in Mycobacterium Tuberculosis. J.Biol.Chem. 04777 2023.
ISSN: ESSN 1083-351X
PubMed: 37142222
DOI: 10.1016/J.JBC.2023.104777
Page generated: Thu Oct 10 09:39:10 2024
|