Zinc in PDB 5kl6: Wilms Tumor Protein (WT1) Q369R ZNF2-4 in Complex with Dna

The structure of Wilms Tumor Protein (WT1) Q369R ZNF2-4 in Complex with Dna, PDB code: 5kl6 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)	29.03 / 1.64
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.982, 66.008, 35.567, 90.00, 90.52, 90.00
R / Rfree (%)	17.3 / 20.6

The binding sites of Zinc atom in the Wilms Tumor Protein (WT1) Q369R ZNF2-4 in Complex with Dna (pdb code 5kl6). 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) Q369R ZNF2-4 in Complex with Dna, PDB code: 5kl6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Wilms Tumor Protein (WT1) Q369R ZNF2-4 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) Q369R ZNF2-4 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:28.6 occ:1.00 NE2 A:HIS373 2.0 26.9 1.0 NE2 A:HIS377 2.1 26.4 1.0 SG A:CYS360 2.3 34.5 1.0 SG A:CYS355 2.3 29.0 1.0 CD2 A:HIS377 3.0 26.4 1.0 CD2 A:HIS373 3.0 25.5 1.0 CE1 A:HIS373 3.0 28.3 1.0 HB3 A:CYS355 3.1 34.8 1.0 HD2 A:HIS377 3.1 31.7 1.0 CE1 A:HIS377 3.1 33.5 1.0 CB A:CYS355 3.1 29.0 1.0 HD2 A:HIS373 3.2 30.6 1.0 CB A:CYS360 3.2 32.7 1.0 HB3 A:CYS360 3.2 39.2 1.0 HB2 A:CYS360 3.2 39.2 1.0 HE1 A:HIS373 3.2 34.0 1.0 HB2 A:CYS355 3.3 34.8 1.0 HE1 A:HIS377 3.4 40.1 1.0 HB2 A:PHE357 3.5 38.0 1.0 HB2 A:ARG362 3.8 41.2 1.0 O A:HOH663 4.0 44.7 1.0 ND1 A:HIS373 4.1 26.0 1.0 CG A:HIS373 4.1 23.8 1.0 CG A:HIS377 4.2 27.2 1.0 ND1 A:HIS377 4.2 30.2 1.0 HG2 A:GLN374 4.2 29.0 1.0 CB A:PHE357 4.4 31.7 1.0 H A:ARG362 4.4 44.9 1.0 HD1 A:PHE357 4.5 37.9 1.0 HA A:GLN374 4.5 24.6 1.0 H A:PHE357 4.5 42.1 1.0 HG3 A:ARG362 4.5 47.8 1.0 CA A:CYS355 4.6 30.9 1.0 CA A:CYS360 4.6 39.3 1.0 HB3 A:PHE357 4.7 38.0 1.0 CB A:ARG362 4.7 34.3 1.0 CD1 A:PHE357 4.9 31.6 1.0 HA A:CYS355 4.9 37.0 1.0 CG A:PHE357 4.9 30.5 1.0 HA A:CYS360 4.9 47.1 1.0 HD1 A:HIS373 4.9 31.1 1.0 HE2 A:PHE364 4.9 46.6 1.0 HG3 A:GLN374 4.9 29.0 1.0 HD1 A:HIS377 5.0 36.2 1.0

Zinc binding site 2 out of 3 in the Wilms Tumor Protein (WT1) Q369R ZNF2-4 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) Q369R ZNF2-4 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:33.1 occ:1.00 NE2 A:HIS401 2.0 31.4 1.0 NE2 A:HIS405 2.0 35.1 1.0 SG A:CYS388 2.3 38.1 1.0 SG A:CYS385 2.3 34.8 1.0 CD2 A:HIS405 2.9 41.9 1.0 CD2 A:HIS401 3.0 29.9 1.0 HD2 A:HIS405 3.0 50.3 1.0 CE1 A:HIS401 3.0 29.1 1.0 CE1 A:HIS405 3.1 51.5 1.0 HD2 A:HIS401 3.1 35.9 1.0 H A:CYS388 3.1 48.7 1.0 HB3 A:CYS385 3.2 39.8 1.0 HB3 A:CYS388 3.2 45.0 1.0 CB A:CYS385 3.2 33.2 1.0 HE1 A:HIS401 3.3 34.9 1.0 HB2 A:CYS385 3.3 39.8 1.0 CB A:CYS388 3.3 37.5 1.0 HE1 A:HIS405 3.4 61.8 1.0 HB A:THR387 3.6 57.3 1.0 N A:CYS388 3.8 40.6 1.0 O A:HOH665 4.0 45.3 1.0 CG A:HIS405 4.1 39.8 1.0 HB2 A:CYS388 4.1 45.0 1.0 CG A:HIS401 4.1 35.1 1.0 CA A:CYS388 4.1 41.5 1.0 ND1 A:HIS401 4.1 27.8 1.0 ND1 A:HIS405 4.2 42.9 1.0 HB3 A:ARG390 4.3 41.5 1.0 H A:ARG390 4.4 48.1 1.0 H A:THR387 4.4 63.0 1.0 HA A:THR402 4.5 48.2 1.0 HE2 A:PHE392 4.5 34.8 1.0 CB A:THR387 4.6 47.8 1.0 HZ A:PHE392 4.6 32.6 1.0 CA A:CYS385 4.6 36.7 1.0 H A:GLN389 4.7 47.1 1.0 C A:CYS388 4.8 43.2 1.0 C A:THR387 4.8 36.2 1.0 HB2 A:ARG390 4.9 41.5 1.0 HG22 A:THR387 4.9 56.3 1.0 HD1 A:HIS401 4.9 33.3 1.0 HA A:CYS385 4.9 44.0 1.0 HA A:CYS388 4.9 49.8 1.0 HD1 A:HIS405 5.0 51.5 1.0 HG1 A:THR404 5.0 47.9 1.0 N A:GLN389 5.0 39.2 1.0

Zinc binding site 3 out of 3 in the Wilms Tumor Protein (WT1) Q369R ZNF2-4 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) Q369R ZNF2-4 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:28.4 occ:1.00 NE2 A:HIS435 1.9 30.5 1.0 NE2 A:HIS431 2.0 28.1 1.0 SG A:CYS413 2.3 26.8 1.0 SG A:CYS418 2.3 34.4 1.0 CD2 A:HIS435 2.9 33.7 1.0 CD2 A:HIS431 2.9 22.1 1.0 HB3 A:CYS418 3.0 44.6 1.0 CE1 A:HIS435 3.0 44.1 1.0 HD2 A:HIS435 3.0 40.4 1.0 CE1 A:HIS431 3.0 29.4 1.0 HD2 A:HIS431 3.1 26.5 1.0 HB2 A:CYS413 3.1 36.3 1.0 CB A:CYS418 3.1 37.2 1.0 CB A:CYS413 3.1 30.2 1.0 HE1 A:HIS435 3.3 53.0 1.0 HB3 A:CYS413 3.3 36.3 1.0 HE1 A:HIS431 3.3 35.3 1.0 HB2 A:CYS418 3.3 44.6 1.0 HB3 A:TRP415 3.5 45.8 1.0 HB2 A:LYS420 3.8 36.7 1.0 HB2 A:TRP415 3.8 45.8 1.0 HG3 A:LYS420 4.0 43.4 1.0 CG A:HIS435 4.0 34.5 1.0 ND1 A:HIS435 4.1 34.7 1.0 CG A:HIS431 4.1 24.3 1.0 ND1 A:HIS431 4.1 29.4 1.0 CB A:TRP415 4.1 38.1 1.0 H A:LYS420 4.3 48.0 1.0 H A:TRP415 4.4 36.2 1.0 CA A:CYS418 4.6 45.9 1.0 CA A:CYS413 4.6 28.0 1.0 CB A:LYS420 4.6 30.6 1.0 CG A:LYS420 4.6 36.2 1.0 HG2 A:LYS420 4.6 43.4 1.0 HD2 A:HIS432 4.6 36.1 1.0 HE1 A:MET434 4.6 63.8 1.0 HA A:CYS413 4.8 33.6 1.0 HD1 A:HIS435 4.9 41.7 1.0 HE3 A:MET434 4.9 63.8 1.0 HD1 A:HIS431 4.9 35.3 1.0 HA A:CYS418 4.9 55.0 1.0 C A:CYS418 4.9 48.2 1.0 CG A:TRP415 5.0 71.9 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