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Zinc in PDB 4r2r: Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Carboxylated Dna

Protein crystallography data

The structure of Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Carboxylated Dna, PDB code: 4r2r 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) 29.12 / 2.09
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.957, 77.518, 35.585, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Carboxylated Dna (pdb code 4r2r). 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 Carboxylated Dna, PDB code: 4r2r:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4r2r

Go back to Zinc Binding Sites List in 4r2r
Zinc binding site 1 out of 3 in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Carboxylated 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 Carboxylated Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:24.4
occ:1.00
NE2 A:HIS373 2.0 23.1 1.0
NE2 A:HIS377 2.1 24.7 1.0
SG A:CYS360 2.3 25.2 1.0
SG A:CYS355 2.3 24.5 1.0
CD2 A:HIS377 2.9 23.7 1.0
CE1 A:HIS373 3.0 24.6 1.0
CD2 A:HIS373 3.0 22.4 1.0
CE1 A:HIS377 3.1 28.1 1.0
CB A:CYS360 3.2 26.4 1.0
CB A:CYS355 3.2 26.0 1.0
ND1 A:HIS373 4.1 22.8 1.0
CG A:HIS377 4.1 25.9 1.0
CG A:HIS373 4.1 25.4 1.0
ND1 A:HIS377 4.2 28.1 1.0
CB A:PHE357 4.3 26.6 1.0
CB A:ARG362 4.4 24.8 1.0
O A:HOH666 4.6 38.8 1.0
CG A:ARG362 4.6 27.4 1.0
CA A:CYS355 4.6 29.0 1.0
CA A:CYS360 4.6 33.7 1.0
CG A:PHE357 4.8 28.6 1.0
CD1 A:PHE357 4.8 33.3 1.0
C A:CYS355 5.0 29.4 1.0

Zinc binding site 2 out of 3 in 4r2r

Go back to Zinc Binding Sites List in 4r2r
Zinc binding site 2 out of 3 in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Carboxylated 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 Carboxylated Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:24.4
occ:1.00
NE2 A:HIS405 2.0 23.1 1.0
NE2 A:HIS401 2.0 25.6 1.0
SG A:CYS385 2.3 25.3 1.0
SG A:CYS388 2.3 26.5 1.0
CD2 A:HIS405 2.9 25.2 1.0
CD2 A:HIS401 3.0 17.8 1.0
CE1 A:HIS401 3.0 20.7 1.0
CE1 A:HIS405 3.1 23.9 1.0
CB A:CYS385 3.1 25.1 1.0
CB A:CYS388 3.4 24.8 1.0
N A:CYS388 3.7 26.1 1.0
CA A:CYS388 4.1 25.9 1.0
ND1 A:HIS401 4.1 18.7 1.0
CG A:HIS405 4.1 22.0 1.0
CG A:HIS401 4.1 23.6 1.0
ND1 A:HIS405 4.2 24.5 1.0
CB A:THR387 4.3 21.8 1.0
CA A:CYS385 4.6 25.9 1.0
C A:THR387 4.7 30.8 1.0
C A:CYS388 4.7 25.5 1.0
CA A:THR387 4.9 20.4 1.0
N A:GLN389 4.9 26.1 1.0
N A:THR387 4.9 27.7 1.0
CB A:ARG390 5.0 25.5 1.0

Zinc binding site 3 out of 3 in 4r2r

Go back to Zinc Binding Sites List in 4r2r
Zinc binding site 3 out of 3 in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Carboxylated 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 Carboxylated Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:31.0
occ:1.00
NE2 A:HIS431 2.0 26.3 1.0
NE2 A:HIS435 2.0 30.5 1.0
SG A:CYS413 2.3 33.4 1.0
SG A:CYS418 2.3 34.0 1.0
CD2 A:HIS431 2.9 21.5 1.0
CD2 A:HIS435 2.9 35.8 1.0
CE1 A:HIS435 3.0 35.4 1.0
CE1 A:HIS431 3.1 24.1 1.0
CB A:CYS413 3.2 25.4 1.0
CB A:CYS418 3.3 44.8 1.0
CG A:HIS431 4.1 23.3 1.0
CG A:HIS435 4.1 37.8 1.0
ND1 A:HIS435 4.1 32.7 1.0
ND1 A:HIS431 4.1 25.5 1.0
CB A:TRP415 4.3 30.6 1.0
CB A:LYS420 4.4 27.8 1.0
CG A:LYS420 4.5 33.4 1.0
CA A:CYS413 4.6 28.3 1.0
CA A:CYS418 4.7 45.1 1.0
CE A:MET434 4.9 32.2 1.0
CG A:TRP415 5.0 35.3 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: Wed Dec 16 05:44:38 2020

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