Zinc in PDB 4r2q: Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Formylated Dna
Protein crystallography data
The structure of Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Formylated Dna, PDB code: 4r2q
was solved by
H.Hashimoto,
Y.O.Olanrewaju,
Y.Zheng,
G.G.Wilson,
X.Zhang,
X.Cheng,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.45 /
1.54
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.116,
78.675,
35.705,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.1 /
19.3
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Formylated Dna
(pdb code 4r2q). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Formylated Dna, PDB code: 4r2q:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 4r2q
Go back to
Zinc Binding Sites List in 4r2q
Zinc binding site 1 out
of 3 in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Formylated Dna
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Formylated Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:19.2
occ:1.00
|
NE2
|
A:HIS377
|
2.0
|
19.1
|
1.0
|
NE2
|
A:HIS373
|
2.0
|
16.0
|
1.0
|
SG
|
A:CYS355
|
2.3
|
18.8
|
1.0
|
SG
|
A:CYS360
|
2.3
|
21.8
|
1.0
|
CD2
|
A:HIS377
|
3.0
|
18.8
|
1.0
|
CD2
|
A:HIS373
|
3.0
|
16.7
|
1.0
|
CE1
|
A:HIS373
|
3.0
|
18.2
|
1.0
|
CE1
|
A:HIS377
|
3.1
|
22.4
|
1.0
|
CB
|
A:CYS355
|
3.1
|
18.8
|
1.0
|
CB
|
A:CYS360
|
3.2
|
26.4
|
1.0
|
ND1
|
A:HIS373
|
4.1
|
15.8
|
1.0
|
CG
|
A:HIS377
|
4.1
|
19.0
|
1.0
|
ND1
|
A:HIS377
|
4.2
|
21.7
|
1.0
|
CG
|
A:HIS373
|
4.2
|
15.7
|
1.0
|
O
|
A:HOH687
|
4.3
|
40.8
|
1.0
|
CB
|
A:PHE357
|
4.4
|
21.1
|
1.0
|
CA
|
A:CYS355
|
4.6
|
20.4
|
1.0
|
CB
|
A:ARG362
|
4.6
|
20.4
|
1.0
|
CA
|
A:CYS360
|
4.6
|
30.5
|
1.0
|
CG
|
A:ARG362
|
4.7
|
23.1
|
1.0
|
CD1
|
A:PHE357
|
4.9
|
22.2
|
1.0
|
CG
|
A:PHE357
|
4.9
|
22.1
|
1.0
|
C
|
A:CYS355
|
5.0
|
22.2
|
1.0
|
|
Zinc binding site 2 out
of 3 in 4r2q
Go back to
Zinc Binding Sites List in 4r2q
Zinc binding site 2 out
of 3 in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Formylated Dna
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Formylated Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:21.6
occ:1.00
|
NE2
|
A:HIS405
|
2.0
|
21.1
|
1.0
|
NE2
|
A:HIS401
|
2.1
|
19.5
|
1.0
|
SG
|
A:CYS385
|
2.3
|
21.1
|
1.0
|
SG
|
A:CYS388
|
2.3
|
22.8
|
1.0
|
CD2
|
A:HIS405
|
3.0
|
21.5
|
1.0
|
CE1
|
A:HIS401
|
3.0
|
18.5
|
1.0
|
CE1
|
A:HIS405
|
3.0
|
22.7
|
1.0
|
CD2
|
A:HIS401
|
3.1
|
16.2
|
1.0
|
CB
|
A:CYS385
|
3.1
|
21.2
|
1.0
|
CB
|
A:CYS388
|
3.3
|
24.4
|
1.0
|
N
|
A:CYS388
|
3.6
|
26.5
|
1.0
|
CA
|
A:CYS388
|
4.0
|
25.3
|
1.0
|
ND1
|
A:HIS405
|
4.1
|
23.3
|
1.0
|
ND1
|
A:HIS401
|
4.1
|
16.8
|
1.0
|
CG
|
A:HIS405
|
4.2
|
22.2
|
1.0
|
CG
|
A:HIS401
|
4.2
|
15.8
|
1.0
|
O
|
A:HOH670
|
4.3
|
47.5
|
1.0
|
CB
|
A:THR387
|
4.4
|
25.2
|
1.0
|
CA
|
A:CYS385
|
4.6
|
20.9
|
1.0
|
C
|
A:THR387
|
4.7
|
27.9
|
1.0
|
C
|
A:CYS388
|
4.7
|
25.5
|
1.0
|
N
|
A:GLN389
|
4.8
|
25.0
|
1.0
|
CA
|
A:THR387
|
4.9
|
26.1
|
1.0
|
N
|
A:THR387
|
5.0
|
25.6
|
1.0
|
CG2
|
A:THR387
|
5.0
|
23.8
|
1.0
|
|
Zinc binding site 3 out
of 3 in 4r2q
Go back to
Zinc Binding Sites List in 4r2q
Zinc binding site 3 out
of 3 in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Formylated Dna
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Formylated Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:21.9
occ:1.00
|
NE2
|
A:HIS435
|
2.1
|
22.3
|
1.0
|
NE2
|
A:HIS431
|
2.1
|
19.9
|
1.0
|
SG
|
A:CYS413
|
2.2
|
20.5
|
1.0
|
SG
|
A:CYS418
|
2.3
|
23.8
|
1.0
|
CD2
|
A:HIS435
|
3.0
|
23.4
|
1.0
|
CD2
|
A:HIS431
|
3.0
|
18.8
|
1.0
|
CE1
|
A:HIS435
|
3.1
|
24.5
|
1.0
|
CE1
|
A:HIS431
|
3.1
|
19.9
|
1.0
|
CB
|
A:CYS418
|
3.1
|
25.8
|
1.0
|
CB
|
A:CYS413
|
3.1
|
19.7
|
1.0
|
CB
|
A:TRP415
|
4.0
|
27.8
|
1.0
|
CG
|
A:HIS435
|
4.1
|
24.3
|
1.0
|
CG
|
A:HIS431
|
4.1
|
16.5
|
1.0
|
ND1
|
A:HIS435
|
4.2
|
25.0
|
1.0
|
ND1
|
A:HIS431
|
4.2
|
18.6
|
1.0
|
CB
|
A:LYS420
|
4.4
|
20.5
|
0.6
|
CB
|
A:LYS420
|
4.4
|
20.8
|
0.4
|
CG
|
A:LYS420
|
4.5
|
22.9
|
0.4
|
CG
|
A:LYS420
|
4.5
|
25.7
|
0.6
|
CA
|
A:CYS418
|
4.5
|
25.9
|
1.0
|
O
|
A:HOH697
|
4.5
|
37.4
|
1.0
|
CA
|
A:CYS413
|
4.6
|
17.6
|
1.0
|
O
|
A:HOH678
|
4.6
|
41.0
|
1.0
|
CG
|
A:TRP415
|
4.8
|
31.2
|
1.0
|
C
|
A:CYS418
|
5.0
|
26.8
|
1.0
|
N
|
A:TRP415
|
5.0
|
22.0
|
1.0
|
|
Reference:
H.Hashimoto,
Y.O.Olanrewaju,
Y.Zheng,
G.G.Wilson,
X.Zhang,
X.Cheng.
Wilms Tumor Protein Recognizes 5-Carboxylcytosine Within A Specific Dna Sequence. Genes Dev. 2014.
ISSN: ISSN 0890-9369
PubMed: 25258363
DOI: 10.1101/GAD.250746.114
Page generated: Sun Oct 27 06:50:20 2024
|