Zinc in PDB 5kl7: Wilms Tumor Protein (WT1) ZNF2-4Q369R in Complex with Carboxylated Dna

The structure of Wilms Tumor Protein (WT1) ZNF2-4Q369R in Complex with Carboxylated Dna, PDB code: 5kl7 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)	29.23 / 1.58
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.458, 77.797, 35.683, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.4

The binding sites of Zinc atom in the Wilms Tumor Protein (WT1) ZNF2-4Q369R in Complex with Carboxylated Dna (pdb code 5kl7). 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) ZNF2-4Q369R in Complex with Carboxylated Dna, PDB code: 5kl7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4Q369R 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) ZNF2-4Q369R in Complex with Carboxylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:16.3 occ:1.00 NE2 A:HIS373 2.0 13.9 1.0 NE2 A:HIS377 2.1 15.7 1.0 SG A:CYS360 2.3 16.8 1.0 SG A:CYS355 2.3 17.0 1.0 CE1 A:HIS373 2.9 14.9 1.0 CD2 A:HIS373 3.0 14.5 1.0 CD2 A:HIS377 3.0 16.4 1.0 CE1 A:HIS377 3.1 20.8 1.0 HB3 A:CYS355 3.1 21.7 1.0 HE1 A:HIS373 3.1 17.9 1.0 HB3 A:CYS360 3.1 21.6 1.0 CB A:CYS360 3.1 18.0 1.0 HD2 A:HIS377 3.2 19.6 1.0 CB A:CYS355 3.2 18.1 1.0 HD2 A:HIS373 3.2 17.4 1.0 HB2 A:CYS360 3.2 21.6 1.0 HE1 A:HIS377 3.3 25.0 1.0 HB2 A:CYS355 3.3 21.7 1.0 HB2 A:PHE357 3.5 20.6 1.0 HB2 A:ARG362 3.7 20.6 1.0 O A:HOH604 4.0 30.7 0.5 HG3 A:ARG362 4.0 23.9 1.0 ND1 A:HIS373 4.1 14.6 1.0 CG A:HIS373 4.1 13.3 1.0 ND1 A:HIS377 4.2 22.1 1.0 CG A:HIS377 4.2 15.7 1.0 H A:ARG362 4.3 21.0 1.0 H A:PHE357 4.4 25.3 1.0 CB A:PHE357 4.4 17.2 1.0 HG2 A:GLN374 4.5 17.9 1.0 HG2 A:ARG362 4.5 23.9 1.0 CB A:ARG362 4.5 17.2 1.0 CG A:ARG362 4.5 20.0 1.0 CA A:CYS360 4.6 19.6 1.0 CA A:CYS355 4.6 18.6 1.0 HA A:GLN374 4.7 17.7 1.0 HD1 A:PHE357 4.7 32.6 1.0 HB3 A:PHE357 4.8 20.6 1.0 HD1 A:HIS373 4.8 17.5 1.0 HA A:CYS360 4.9 23.5 1.0 HA A:CYS355 4.9 22.4 1.0 CG A:PHE357 4.9 18.0 1.0 HD3 A:ARG376 4.9 63.3 1.0 HD1 A:HIS377 5.0 26.5 1.0 HG3 A:GLN374 5.0 17.9 1.0 HG2 A:ARG376 5.0 34.3 1.0 C A:CYS355 5.0 19.8 1.0 CD1 A:PHE357 5.0 27.2 1.0

Zinc binding site 2 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4Q369R 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) ZNF2-4Q369R in Complex with Carboxylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:18.8 occ:1.00 NE2 A:HIS405 2.0 18.2 1.0 NE2 A:HIS401 2.1 17.0 1.0 SG A:CYS388 2.3 20.1 1.0 SG A:CYS385 2.3 19.8 1.0 CD2 A:HIS405 3.0 20.7 1.0 CD2 A:HIS401 3.0 16.6 1.0 CE1 A:HIS405 3.0 26.2 1.0 HB3 A:CYS388 3.1 27.2 1.0 CE1 A:HIS401 3.1 19.8 1.0 HB3 A:CYS385 3.1 21.0 1.0 HD2 A:HIS401 3.1 19.9 1.0 HD2 A:HIS405 3.1 24.8 1.0 CB A:CYS385 3.2 17.5 1.0 H A:CYS388 3.2 28.7 1.0 HE1 A:HIS405 3.2 31.4 1.0 CB A:CYS388 3.3 22.6 1.0 HB2 A:CYS385 3.3 21.0 1.0 HE1 A:HIS401 3.3 23.8 1.0 HB A:THR387 3.6 29.9 1.0 N A:CYS388 3.8 23.9 1.0 HB2 A:CYS388 4.1 27.2 1.0 CA A:CYS388 4.1 22.4 1.0 ND1 A:HIS405 4.1 25.5 1.0 CG A:HIS405 4.1 21.5 1.0 CG A:HIS401 4.2 13.5 1.0 ND1 A:HIS401 4.2 16.0 1.0 HB3 A:ARG390 4.2 20.5 1.0 H A:ARG390 4.3 23.8 1.0 H A:THR387 4.4 26.1 1.0 CB A:THR387 4.5 24.9 1.0 HE2 A:PHE392 4.5 20.6 1.0 H A:GLN389 4.5 27.0 1.0 HA A:THR402 4.6 21.1 1.0 HG22 A:THR387 4.6 30.8 1.0 CA A:CYS385 4.6 19.1 1.0 C A:CYS388 4.7 27.0 1.0 C A:THR387 4.8 27.0 1.0 HZ A:PHE392 4.8 23.0 1.0 HG1 A:THR404 4.9 31.2 1.0 HA A:CYS388 4.9 26.9 1.0 N A:GLN389 4.9 22.5 1.0 HD1 A:HIS405 4.9 30.6 1.0 CG2 A:THR387 4.9 25.7 1.0 HG21 A:THR387 5.0 30.8 1.0 HA A:CYS385 5.0 22.9 1.0 HD1 A:HIS401 5.0 19.2 1.0 HB2 A:ARG390 5.0 20.5 1.0 HG22 A:THR402 5.0 20.6 1.0

Zinc binding site 3 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4Q369R 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) ZNF2-4Q369R in Complex with Carboxylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:22.9 occ:1.00 NE2 A:HIS435 2.0 25.4 1.0 NE2 A:HIS431 2.0 18.9 1.0 SG A:CYS418 2.2 28.1 1.0 SG A:CYS413 2.3 23.0 1.0 CD2 A:HIS431 3.0 19.7 1.0 CD2 A:HIS435 3.0 22.1 1.0 HB3 A:CYS418 3.0 33.3 1.0 CE1 A:HIS435 3.0 35.5 1.0 CE1 A:HIS431 3.1 22.3 1.0 HD2 A:HIS431 3.1 23.7 1.0 HB2 A:CYS413 3.1 28.2 1.0 CB A:CYS418 3.1 27.8 1.0 HD2 A:HIS435 3.2 26.5 1.0 CB A:CYS413 3.2 23.5 1.0 HE1 A:HIS435 3.2 42.6 1.0 HB3 A:CYS413 3.3 28.2 1.0 HE1 A:HIS431 3.3 26.8 1.0 HB2 A:CYS418 3.4 33.3 1.0 HB2 A:TRP415 3.4 39.4 1.0 HB2 A:LYS420 3.7 23.9 1.0 HG3 A:LYS420 4.1 39.1 1.0 CG A:HIS431 4.1 18.2 1.0 ND1 A:HIS435 4.1 33.4 1.0 ND1 A:HIS431 4.1 20.2 1.0 CG A:HIS435 4.1 26.4 1.0 HD1 A:TRP415 4.2 78.1 1.0 H A:LYS420 4.3 41.3 1.0 CB A:TRP415 4.4 32.9 1.0 H A:TRP415 4.4 27.6 1.0 HG2 A:LYS420 4.4 39.1 1.0 HE1 A:MET434 4.5 42.9 1.0 CB A:LYS420 4.5 19.9 1.0 CG A:LYS420 4.5 32.6 1.0 CA A:CYS418 4.5 29.5 1.0 CA A:CYS413 4.6 17.6 1.0 HD2 A:HIS432 4.7 24.0 1.0 HB3 A:TRP415 4.7 39.4 1.0 CD1 A:TRP415 4.8 65.1 1.0 O A:CYS418 4.8 45.6 1.0 HA A:CYS413 4.8 21.1 1.0 C A:CYS418 4.9 31.5 1.0 CG A:TRP415 4.9 38.0 1.0 HA A:CYS418 4.9 35.4 1.0 HD1 A:HIS435 4.9 40.0 1.0 HD1 A:HIS431 4.9 24.3 1.0 HE3 A:MET434 4.9 42.9 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