Zinc in PDB 4r2p: Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Hydroxymethylated Dna

The structure of Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Hydroxymethylated Dna, PDB code: 4r2p 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)	29.24 / 1.79
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.852, 78.591, 35.718, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21

The binding sites of Zinc atom in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Hydroxymethylated Dna (pdb code 4r2p). 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 Hydroxymethylated Dna, PDB code: 4r2p:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Hydroxymethylated 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 Hydroxymethylated 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 18.7 1.0 NE2 A:HIS373 2.1 18.5 1.0 SG A:CYS360 2.2 19.5 1.0 SG A:CYS355 2.3 18.5 1.0 CD2 A:HIS377 3.0 16.6 1.0 CD2 A:HIS373 3.0 20.4 1.0 CE1 A:HIS377 3.1 29.7 1.0 CE1 A:HIS373 3.1 18.3 1.0 CB A:CYS360 3.1 24.2 1.0 CB A:CYS355 3.2 15.6 1.0 CG A:HIS377 4.1 19.2 1.0 ND1 A:HIS377 4.2 19.3 1.0 CG A:HIS373 4.2 16.5 1.0 ND1 A:HIS373 4.2 19.3 1.0 CB A:PHE357 4.4 20.2 1.0 CA A:CYS360 4.6 22.9 1.0 CA A:CYS355 4.6 18.8 1.0 CB A:ARG362 4.7 16.8 1.0 CG A:ARG362 4.9 20.7 1.0 CG A:PHE357 5.0 20.8 1.0 CD1 A:PHE357 5.0 22.6 1.0 C A:CYS355 5.0 23.2 1.0

Zinc binding site 2 out of 3 in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Hydroxymethylated 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 Hydroxymethylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:22.9 occ:1.00 NE2 A:HIS405 2.0 21.3 1.0 NE2 A:HIS401 2.1 20.1 1.0 SG A:CYS385 2.2 22.4 1.0 SG A:CYS388 2.3 24.1 1.0 CD2 A:HIS401 2.9 14.5 1.0 CD2 A:HIS405 3.0 21.8 1.0 CE1 A:HIS405 3.0 23.8 1.0 CB A:CYS385 3.1 21.1 1.0 CE1 A:HIS401 3.2 17.5 1.0 CB A:CYS388 3.3 31.6 1.0 N A:CYS388 3.7 32.6 1.0 CA A:CYS388 4.1 19.8 1.0 CG A:HIS401 4.1 15.5 1.0 ND1 A:HIS405 4.1 21.9 1.0 CG A:HIS405 4.2 21.7 1.0 ND1 A:HIS401 4.2 22.1 1.0 O A:HOH616 4.4 33.9 1.0 CB A:THR387 4.5 25.7 1.0 CA A:CYS385 4.5 19.2 1.0 C A:THR387 4.7 32.4 1.0 C A:CYS388 4.7 20.0 1.0 N A:GLN389 4.9 24.7 1.0 N A:THR387 4.9 26.1 1.0 CA A:THR387 4.9 22.5 1.0 CB A:ARG390 5.0 20.1 1.0 C A:CYS385 5.0 26.7 1.0

Zinc binding site 3 out of 3 in the Wilms Tumor Protein (WT1) Zinc Fingers in Complex with Hydroxymethylated 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 Hydroxymethylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:21.5 occ:1.00 NE2 A:HIS435 2.0 21.4 1.0 NE2 A:HIS431 2.0 18.7 1.0 SG A:CYS413 2.2 19.4 1.0 SG A:CYS418 2.3 22.6 1.0 CD2 A:HIS435 2.9 25.0 1.0 CD2 A:HIS431 2.9 18.0 1.0 CE1 A:HIS431 3.0 20.8 1.0 CE1 A:HIS435 3.0 24.7 1.0 CB A:CYS418 3.1 25.1 1.0 CB A:CYS413 3.1 20.1 1.0 CB A:TRP415 4.1 27.9 1.0 CG A:HIS431 4.1 18.4 1.0 ND1 A:HIS431 4.1 19.3 1.0 CG A:HIS435 4.1 28.6 1.0 ND1 A:HIS435 4.1 25.7 1.0 CB A:LYS420 4.4 16.8 1.0 CG A:LYS420 4.4 30.1 1.0 CA A:CYS418 4.5 25.0 1.0 CA A:CYS413 4.6 18.9 1.0 CG A:TRP415 4.8 31.9 1.0

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