Zinc in PDB 5kl5: Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Carboxylated Dna

The structure of Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Carboxylated Dna, PDB code: 5kl5 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)	29.26 / 2.29
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.493, 77.211, 35.794, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.6

The binding sites of Zinc atom in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Carboxylated Dna (pdb code 5kl5). 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 Carboxylated Dna, PDB code: 5kl5:
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 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) ZNF2-4 Q369H in Complex with Carboxylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:28.0 occ:1.00 NE2 A:HIS373 2.0 27.0 1.0 NE2 A:HIS377 2.1 28.5 1.0 SG A:CYS360 2.3 24.9 1.0 SG A:CYS355 2.3 25.2 1.0 CE1 A:HIS373 2.9 30.4 1.0 CD2 A:HIS377 3.0 23.8 1.0 HE1 A:HIS373 3.0 36.5 1.0 HB3 A:CYS355 3.0 34.1 1.0 CE1 A:HIS377 3.1 28.2 1.0 HD2 A:HIS377 3.1 28.6 1.0 CD2 A:HIS373 3.1 29.4 1.0 CB A:CYS355 3.2 28.4 1.0 HB3 A:CYS360 3.2 31.7 1.0 CB A:CYS360 3.2 26.4 1.0 HB2 A:PHE357 3.3 43.9 1.0 HE1 A:HIS377 3.3 33.9 1.0 HB2 A:CYS360 3.3 31.7 1.0 HD2 A:HIS373 3.4 35.4 1.0 HB2 A:CYS355 3.4 34.1 1.0 HB2 A:ARG362 3.7 43.6 1.0 ND1 A:HIS373 4.0 28.8 1.0 HG2 A:ARG362 4.1 42.9 1.0 HG3 A:ARG362 4.1 42.9 1.0 CG A:HIS377 4.1 27.7 1.0 ND1 A:HIS377 4.2 30.7 1.0 CG A:HIS373 4.2 30.6 1.0 CB A:PHE357 4.2 36.6 1.0 H A:PHE357 4.3 49.4 1.0 H A:ARG362 4.4 39.9 1.0 CG A:ARG362 4.4 35.7 1.0 CB A:ARG362 4.5 36.3 1.0 HD1 A:PHE357 4.5 48.0 1.0 HB3 A:PHE357 4.6 43.9 1.0 HA A:GLN374 4.6 34.3 1.0 HG2 A:GLN374 4.6 39.6 1.0 CA A:CYS355 4.6 33.0 1.0 CA A:CYS360 4.7 32.8 1.0 CG A:PHE357 4.7 36.6 1.0 HD1 A:HIS373 4.8 34.6 1.0 CD1 A:PHE357 4.8 40.0 1.0 HA A:CYS360 4.9 39.3 1.0 HD1 A:HIS377 4.9 36.9 1.0 HE2 A:PHE364 4.9 37.1 1.0 C A:CYS355 5.0 33.9 1.0

Zinc binding site 2 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H 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) ZNF2-4 Q369H in Complex with Carboxylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:28.1 occ:1.00 NE2 A:HIS405 2.0 37.1 1.0 NE2 A:HIS401 2.0 33.7 1.0 SG A:CYS388 2.3 31.2 1.0 SG A:CYS385 2.3 31.4 1.0 CD2 A:HIS405 2.9 26.1 1.0 H A:CYS388 3.0 49.3 1.0 CE1 A:HIS401 3.0 31.6 1.0 HD2 A:HIS405 3.0 31.4 1.0 CD2 A:HIS401 3.0 28.0 1.0 HB3 A:CYS385 3.0 34.2 1.0 CE1 A:HIS405 3.1 31.3 1.0 CB A:CYS385 3.1 28.4 1.0 HD2 A:HIS401 3.2 33.6 1.0 HE1 A:HIS401 3.2 38.0 1.0 HB3 A:CYS388 3.2 43.6 1.0 HB2 A:CYS385 3.3 34.2 1.0 HE1 A:HIS405 3.3 37.6 1.0 CB A:CYS388 3.4 36.3 1.0 HB A:THR387 3.4 43.1 1.0 N A:CYS388 3.7 41.1 1.0 CG A:HIS405 4.1 30.4 1.0 CA A:CYS388 4.1 35.7 1.0 ND1 A:HIS401 4.1 30.3 1.0 ND1 A:HIS405 4.1 30.0 1.0 CG A:HIS401 4.1 30.5 1.0 HB2 A:CYS388 4.1 43.6 1.0 HB3 A:ARG390 4.2 37.8 1.0 H A:THR387 4.2 43.4 1.0 H A:ARG390 4.3 41.6 1.0 CB A:THR387 4.3 35.9 1.0 HE2 A:PHE392 4.4 37.2 1.0 CA A:CYS385 4.6 29.4 1.0 HZ A:PHE392 4.6 33.1 1.0 HA A:THR402 4.6 34.5 1.0 H A:GLN389 4.7 43.9 1.0 C A:THR387 4.7 35.1 1.0 C A:CYS388 4.8 38.4 1.0 HG22 A:THR387 4.8 44.0 1.0 CA A:THR387 4.9 34.0 1.0 HD1 A:HIS401 4.9 36.4 1.0 HA A:CYS388 4.9 42.9 1.0 N A:THR387 4.9 36.2 1.0 HD1 A:HIS405 4.9 36.0 1.0 HG1 A:THR404 5.0 39.1 1.0 N A:GLN389 5.0 36.6 1.0 HA A:CYS385 5.0 35.3 1.0 CG2 A:THR387 5.0 36.6 1.0

Zinc binding site 3 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H 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) ZNF2-4 Q369H in Complex with Carboxylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:34.9 occ:1.00 NE2 A:HIS431 2.0 31.5 1.0 NE2 A:HIS435 2.0 38.1 1.0 SG A:CYS413 2.3 34.8 1.0 SG A:CYS418 2.3 35.1 1.0 CE1 A:HIS435 2.8 37.9 1.0 CD2 A:HIS431 2.9 26.8 1.0 HE1 A:HIS435 2.9 45.5 1.0 HD2 A:HIS431 3.0 32.2 1.0 HB3 A:CYS418 3.1 41.9 1.0 CE1 A:HIS431 3.1 27.1 1.0 CD2 A:HIS435 3.2 38.9 1.0 HB2 A:CYS413 3.2 43.9 1.0 CB A:CYS418 3.2 34.9 1.0 CB A:CYS413 3.3 36.6 1.0 HB3 A:CYS413 3.4 43.9 1.0 HE1 A:HIS431 3.4 32.5 1.0 HB2 A:TRP415 3.5 51.5 1.0 HD2 A:HIS435 3.5 46.7 1.0 HB2 A:CYS418 3.6 41.9 1.0 H A:LYS420 3.7 62.9 1.0 HD1 A:TRP415 3.8 57.8 1.0 HB2 A:LYS420 3.9 54.1 1.0 H A:GLN419 3.9 63.3 1.0 ND1 A:HIS435 4.0 39.5 1.0 CG A:HIS431 4.0 27.2 1.0 ND1 A:HIS431 4.1 25.8 1.0 HG2 A:LYS420 4.1 57.1 1.0 HG3 A:LYS420 4.2 57.1 1.0 CG A:HIS435 4.2 39.2 1.0 CB A:TRP415 4.4 42.9 1.0 N A:GLN419 4.4 52.7 1.0 CD1 A:TRP415 4.4 48.1 1.0 H A:TRP415 4.5 47.6 1.0 CG A:LYS420 4.5 47.6 1.0 N A:LYS420 4.5 52.4 1.0 HE1 A:MET434 4.5 75.1 1.0 CA A:CYS418 4.6 40.5 1.0 CB A:LYS420 4.6 45.0 1.0 CA A:CYS413 4.7 37.4 1.0 HD1 A:HIS435 4.7 47.4 1.0 HD2 A:HIS432 4.7 30.7 1.0 HB3 A:TRP415 4.7 51.5 1.0 CG A:TRP415 4.7 41.6 1.0 C A:CYS418 4.8 38.8 1.0 HE3 A:MET434 4.9 75.1 1.0 HD1 A:HIS431 4.9 31.0 1.0 HE2 A:PHE422 4.9 37.2 1.0 HA A:CYS413 4.9 44.9 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