Zinc in PDB 5kl3: Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Dna

The structure of Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Dna, PDB code: 5kl3 was solved by H.Hashimoto, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.22 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.223, 66.069, 35.646, 90.00, 91.75, 90.00
R / Rfree (%)	16.2 / 18.2

The binding sites of Zinc atom in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Dna (pdb code 5kl3). 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) ZNF2-4 Q369H in Complex with Dna, PDB code: 5kl3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with 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) ZNF2-4 Q369H in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:21.9 occ:1.00 NE2 A:HIS377 2.0 22.4 1.0 NE2 A:HIS373 2.1 24.2 1.0 SG A:CYS360 2.3 26.7 1.0 SG A:CYS355 2.3 21.7 1.0 CD2 A:HIS377 3.0 21.4 1.0 CD2 A:HIS373 3.0 22.9 1.0 CE1 A:HIS377 3.0 24.1 1.0 CE1 A:HIS373 3.1 24.5 1.0 HB3 A:CYS355 3.1 32.1 1.0 CB A:CYS360 3.1 28.0 1.0 HD2 A:HIS377 3.2 25.7 1.0 HB2 A:CYS360 3.2 33.5 1.0 HB3 A:CYS360 3.2 33.5 1.0 CB A:CYS355 3.2 26.7 1.0 HD2 A:HIS373 3.2 27.4 1.0 HE1 A:HIS377 3.2 29.0 1.0 HE1 A:HIS373 3.3 29.4 1.0 HB2 A:CYS355 3.4 32.1 1.0 HB2 A:PHE357 3.4 26.0 1.0 HB2 A:ARG362 3.7 33.8 1.0 O A:HOH693 4.1 37.0 1.0 ND1 A:HIS377 4.1 28.4 1.0 CG A:HIS377 4.2 23.1 1.0 ND1 A:HIS373 4.2 20.9 1.0 CG A:HIS373 4.2 20.8 1.0 HG2 A:GLN374 4.3 23.7 1.0 HG3 A:ARG362 4.3 44.1 1.0 CB A:PHE357 4.4 21.7 1.0 H A:PHE357 4.4 29.1 1.0 HD1 A:PHE357 4.4 26.0 1.0 H A:ARG362 4.5 32.5 1.0 HA A:GLN374 4.5 20.7 1.0 CB A:ARG362 4.6 28.2 1.0 CA A:CYS355 4.6 22.7 1.0 CA A:CYS360 4.6 37.3 1.0 HB3 A:PHE357 4.7 26.0 1.0 HA A:CYS360 4.9 44.8 1.0 CG A:ARG362 4.9 36.8 1.0 CD1 A:PHE357 4.9 21.7 1.0 HD1 A:HIS377 4.9 34.0 1.0 HA A:CYS355 4.9 27.2 1.0 HD1 A:HIS373 4.9 25.0 1.0 CG A:PHE357 4.9 21.6 1.0 HG3 A:GLN374 5.0 23.7 1.0 C A:CYS355 5.0 28.7 1.0

Zinc binding site 2 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with 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) ZNF2-4 Q369H in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:20.5 occ:1.00 NE2 A:HIS405 2.0 24.9 1.0 NE2 A:HIS401 2.1 19.0 1.0 SG A:CYS388 2.3 21.7 1.0 SG A:CYS385 2.3 20.4 1.0 CD2 A:HIS405 3.0 20.7 1.0 CD2 A:HIS401 3.0 18.1 1.0 CE1 A:HIS405 3.0 29.6 1.0 HB3 A:CYS385 3.1 21.2 1.0 CE1 A:HIS401 3.1 15.9 1.0 HB3 A:CYS388 3.1 28.6 1.0 H A:CYS388 3.1 30.6 1.0 HD2 A:HIS401 3.1 21.7 1.0 CB A:CYS385 3.2 17.7 1.0 HD2 A:HIS405 3.2 24.9 1.0 HE1 A:HIS405 3.2 35.5 1.0 HB2 A:CYS385 3.3 21.2 1.0 CB A:CYS388 3.3 23.8 1.0 HE1 A:HIS401 3.3 19.1 1.0 HB A:THR387 3.5 39.6 1.0 N A:CYS388 3.7 25.5 1.0 CA A:CYS388 4.1 25.6 1.0 HB2 A:CYS388 4.1 28.6 1.0 ND1 A:HIS405 4.1 26.6 1.0 CG A:HIS405 4.2 26.1 1.0 CG A:HIS401 4.2 15.3 1.0 ND1 A:HIS401 4.2 17.7 1.0 HB3 A:ARG390 4.2 24.5 1.0 H A:ARG390 4.3 24.4 1.0 H A:THR387 4.4 32.9 1.0 HA A:THR402 4.4 31.6 1.0 CB A:THR387 4.5 33.0 1.0 HE2 A:PHE392 4.6 22.6 1.0 H A:GLN389 4.6 30.2 1.0 CA A:CYS385 4.6 17.3 1.0 HZ A:PHE392 4.7 20.5 1.0 C A:CYS388 4.7 22.7 1.0 C A:THR387 4.7 32.0 1.0 HG22 A:THR402 4.8 27.3 1.0 HG1 A:THR404 4.9 34.6 1.0 HG22 A:THR387 4.9 37.6 1.0 HA A:CYS388 4.9 30.7 1.0 HB2 A:ARG390 4.9 24.5 1.0 N A:GLN389 4.9 25.2 1.0 HD1 A:HIS405 4.9 31.9 1.0 HD1 A:HIS401 5.0 21.3 1.0 HA A:CYS385 5.0 20.8 1.0 CB A:ARG390 5.0 20.4 1.0

Zinc binding site 3 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with 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) ZNF2-4 Q369H in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:21.8 occ:1.00 NE2 A:HIS431 2.0 23.6 1.0 NE2 A:HIS435 2.0 23.2 1.0 SG A:CYS413 2.2 20.8 1.0 SG A:CYS418 2.3 24.5 1.0 HB3 A:CYS418 3.0 29.1 1.0 CD2 A:HIS431 3.0 18.7 1.0 CD2 A:HIS435 3.0 21.6 1.0 CE1 A:HIS431 3.0 22.1 1.0 CE1 A:HIS435 3.1 29.2 1.0 HB2 A:CYS413 3.1 25.5 1.0 CB A:CYS418 3.1 24.2 1.0 HD2 A:HIS435 3.1 25.9 1.0 HD2 A:HIS431 3.1 22.4 1.0 CB A:CYS413 3.1 21.3 1.0 HE1 A:HIS431 3.3 26.5 1.0 HB2 A:CYS418 3.3 29.1 1.0 HB3 A:CYS413 3.3 25.5 1.0 HE1 A:HIS435 3.3 35.1 1.0 HB2 A:TRP415 3.3 44.8 1.0 HB2 A:LYS420 3.5 26.7 1.0 CG A:HIS431 4.1 20.9 1.0 ND1 A:HIS431 4.1 21.1 1.0 CG A:HIS435 4.1 23.5 1.0 ND1 A:HIS435 4.1 28.4 1.0 CB A:TRP415 4.2 37.3 1.0 H A:LYS420 4.3 32.5 1.0 H A:TRP415 4.3 25.4 1.0 HB3 A:TRP415 4.4 44.8 1.0 CB A:LYS420 4.4 22.2 1.0 HG3 A:LYS420 4.5 35.3 1.0 HG2 A:LYS420 4.5 35.3 1.0 CA A:CYS418 4.5 26.0 1.0 CA A:CYS413 4.6 19.0 1.0 HD1 A:TRP415 4.6 67.5 1.0 HE1 A:MET434 4.6 37.0 1.0 HD2 A:HIS432 4.6 23.1 1.0 CG A:LYS420 4.7 29.4 1.0 HA A:CYS413 4.8 22.9 1.0 CG A:TRP415 4.9 45.4 1.0 HA A:CYS418 4.9 31.2 1.0 HD1 A:HIS431 4.9 25.3 1.0 C A:CYS418 4.9 31.0 1.0 HD1 A:HIS435 4.9 34.1 1.0 HB3 A:LYS420 4.9 26.7 1.0 CD1 A:TRP415 5.0 56.2 1.0 HE2 A:PHE422 5.0 21.6 1.0

H.Hashimoto, X.Zhang, Y.Zheng, G.G.Wilson, X.Cheng. Denys-Drash Syndrome Associated WT1 Glutamine 369 Mutants Have Altered Sequence-Preferences and Altered Responses to Epigenetic Modifications. Nucleic Acids Res. V. 44 10165 2016.
ISSN: ESSN 1362-4962
PubMed: 27596598
DOI: 10.1093/NAR/GKW766