Zinc in PDB 5kl4: Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna

The structure of Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna, PDB code: 5kl4 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)	29.56 / 1.78
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.766, 43.853, 54.808, 81.95, 88.57, 88.51
R / Rfree (%)	21.7 / 24.6

The structure of Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna (pdb code 5kl4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna, PDB code: 5kl4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated 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 Formylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:24.6 occ:1.00 NE2 A:HIS373 2.0 32.4 1.0 NE2 A:HIS377 2.1 34.1 1.0 SG A:CYS360 2.2 35.7 1.0 SG A:CYS355 2.3 26.9 1.0 CD2 A:HIS377 2.9 28.7 1.0 CE1 A:HIS373 3.0 30.7 1.0 HD2 A:HIS377 3.0 34.5 1.0 HB3 A:CYS360 3.0 38.8 1.0 CB A:CYS360 3.1 32.3 1.0 CD2 A:HIS373 3.1 28.4 1.0 HB3 A:CYS355 3.1 32.0 1.0 HE1 A:HIS373 3.1 36.9 1.0 CB A:CYS355 3.2 26.7 1.0 HB2 A:CYS360 3.2 38.8 1.0 CE1 A:HIS377 3.2 32.5 1.0 HD2 A:HIS373 3.3 34.1 1.0 HB2 A:CYS355 3.3 32.0 1.0 HB2 A:PHE357 3.4 38.2 1.0 HE1 A:HIS377 3.5 39.0 1.0 HB2 A:ARG362 4.0 46.6 1.0 ND1 A:HIS373 4.1 29.2 1.0 CG A:HIS377 4.2 27.8 1.0 CG A:HIS373 4.2 27.4 1.0 HG3 A:ARG362 4.2 49.3 1.0 ND1 A:HIS377 4.3 32.1 1.0 CB A:PHE357 4.3 31.9 1.0 H A:PHE357 4.3 39.0 1.0 HD1 A:PHE357 4.5 36.6 1.0 CA A:CYS360 4.5 33.7 1.0 CA A:CYS355 4.6 28.8 1.0 H A:ARG362 4.6 51.5 1.0 HB3 A:PHE357 4.7 38.2 1.0 HG2 A:GLN374 4.7 33.8 1.0 HA A:GLN374 4.7 29.8 1.0 HA A:CYS360 4.8 40.5 1.0 CG A:PHE357 4.9 31.7 1.0 CD1 A:PHE357 4.9 30.5 1.0 HD1 A:HIS373 4.9 35.0 1.0 CB A:ARG362 4.9 38.9 1.0 HE2 A:PHE364 4.9 29.6 1.0 CG A:ARG362 4.9 41.1 1.0 HD3 A:ARG362 4.9 48.6 1.0 HA A:CYS355 4.9 34.5 1.0 C A:CYS355 5.0 31.5 1.0 N A:PHE357 5.0 32.5 1.0

Zinc binding site 2 out of 6 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated 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 Formylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:20.7 occ:1.00 NE2 A:HIS405 2.0 28.1 1.0 NE2 A:HIS401 2.1 26.2 1.0 SG A:CYS388 2.2 30.8 1.0 SG A:CYS385 2.2 30.8 1.0 CD2 A:HIS405 2.9 25.4 1.0 CE1 A:HIS401 3.0 24.5 1.0 HD2 A:HIS405 3.1 30.4 1.0 CE1 A:HIS405 3.1 26.5 1.0 CD2 A:HIS401 3.1 24.6 1.0 HB3 A:CYS385 3.1 32.2 1.0 HB3 A:CYS388 3.1 34.5 1.0 CB A:CYS385 3.2 26.8 1.0 HE1 A:HIS401 3.2 29.4 1.0 H A:CYS388 3.2 34.5 1.0 CB A:CYS388 3.3 28.8 1.0 HD2 A:HIS401 3.3 29.5 1.0 HE1 A:HIS405 3.3 31.8 1.0 HB2 A:CYS385 3.4 32.2 1.0 HB A:THR387 3.5 32.7 1.0 N A:CYS388 3.7 28.8 1.0 HB2 A:CYS388 4.0 34.5 1.0 CA A:CYS388 4.0 29.2 1.0 CG A:HIS405 4.1 24.3 1.0 ND1 A:HIS405 4.1 26.3 1.0 ND1 A:HIS401 4.1 23.7 1.0 HB3 A:ARG390 4.2 28.9 1.0 CG A:HIS401 4.2 23.0 1.0 H A:ARG390 4.4 31.4 1.0 H A:THR387 4.4 33.5 1.0 CB A:THR387 4.4 27.2 1.0 HE2 A:PHE392 4.5 29.4 1.0 HA A:THR402 4.5 28.4 1.0 H A:GLN389 4.6 36.1 1.0 HZ A:PHE392 4.6 27.9 1.0 CA A:CYS385 4.6 26.0 1.0 HG22 A:THR387 4.7 33.8 1.0 C A:THR387 4.7 30.2 1.0 C A:CYS388 4.7 29.8 1.0 HG22 A:THR402 4.7 29.5 1.0 HB2 A:ARG390 4.8 28.9 1.0 HA A:CYS388 4.9 35.1 1.0 N A:GLN389 4.9 30.1 1.0 CB A:ARG390 4.9 24.1 1.0 HD1 A:HIS401 4.9 28.4 1.0 CA A:THR387 4.9 29.1 1.0 HD1 A:HIS405 4.9 31.6 1.0 CG2 A:THR387 5.0 28.1 1.0 HA A:CYS385 5.0 31.2 1.0 N A:THR387 5.0 27.9 1.0 HG21 A:THR387 5.0 33.8 1.0

Zinc binding site 3 out of 6 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated 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 Formylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:25.9 occ:1.00 NE2 A:HIS431 2.0 37.3 1.0 NE2 A:HIS435 2.0 38.1 1.0 SG A:CYS413 2.2 28.3 1.0 SG A:CYS418 2.2 34.2 1.0 CD2 A:HIS431 2.9 32.4 1.0 HD2 A:HIS431 3.0 38.8 1.0 CE1 A:HIS435 3.0 37.2 1.0 HB3 A:CYS418 3.0 44.3 1.0 CD2 A:HIS435 3.0 34.0 1.0 CE1 A:HIS431 3.1 35.8 1.0 CB A:CYS418 3.1 36.9 1.0 HB2 A:CYS413 3.1 34.2 1.0 CB A:CYS413 3.1 28.5 1.0 HB3 A:CYS413 3.2 34.2 1.0 HE1 A:HIS435 3.2 44.7 1.0 HB2 A:CYS418 3.2 44.3 1.0 HD2 A:HIS435 3.2 40.8 1.0 HE1 A:HIS431 3.3 42.9 1.0 HB2 A:LYS420 3.4 38.6 1.0 HB3 A:TRP415 3.4 40.9 1.0 HB2 A:TRP415 3.6 40.9 1.0 HG3 A:LYS420 4.0 42.4 1.0 CB A:TRP415 4.0 34.1 1.0 CG A:HIS431 4.1 31.2 1.0 ND1 A:HIS431 4.1 34.0 1.0 ND1 A:HIS435 4.1 37.5 1.0 CG A:HIS435 4.2 35.9 1.0 H A:TRP415 4.2 39.6 1.0 H A:LYS420 4.3 45.4 1.0 CB A:LYS420 4.3 32.2 1.0 HG2 A:LYS420 4.4 42.4 1.0 CG A:LYS420 4.4 35.3 1.0 HD2 A:HIS432 4.5 35.3 1.0 CA A:CYS418 4.5 42.2 1.0 CA A:CYS413 4.5 28.2 1.0 HA A:CYS413 4.8 33.9 1.0 HB3 A:LYS420 4.8 38.6 1.0 HA A:CYS418 4.8 50.6 1.0 CG A:TRP415 4.8 37.1 1.0 HD1 A:HIS435 4.9 45.0 1.0 HD1 A:HIS431 4.9 40.8 1.0 N A:TRP415 4.9 33.0 1.0

Zinc binding site 4 out of 6 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:25.4 occ:1.00 NE2 D:HIS373 2.0 32.3 1.0 SG D:CYS360 2.1 42.1 1.0 NE2 D:HIS377 2.1 41.7 1.0 SG D:CYS355 2.3 26.9 1.0 CE1 D:HIS373 3.0 28.1 1.0 CD2 D:HIS377 3.0 38.6 1.0 CB D:CYS360 3.0 37.0 1.0 HB3 D:CYS360 3.0 44.3 1.0 CD2 D:HIS373 3.1 28.4 1.0 HB3 D:CYS355 3.1 34.0 1.0 HD2 D:HIS377 3.1 46.4 1.0 HB2 D:CYS360 3.1 44.3 1.0 HE1 D:HIS373 3.1 33.7 1.0 CE1 D:HIS377 3.2 40.2 1.0 CB D:CYS355 3.2 28.3 1.0 HD2 D:HIS373 3.3 34.1 1.0 HB2 D:PHE357 3.3 40.2 1.0 HB2 D:CYS355 3.4 34.0 1.0 HE1 D:HIS377 3.4 48.3 1.0 HG3 D:ARG362 3.9 48.4 1.0 HB2 D:ARG362 4.0 45.6 1.0 ND1 D:HIS373 4.1 26.9 1.0 CG D:HIS373 4.2 27.0 1.0 CG D:HIS377 4.2 36.3 1.0 ND1 D:HIS377 4.2 39.0 1.0 H D:PHE357 4.3 40.0 1.0 CB D:PHE357 4.3 33.5 1.0 HD1 D:PHE357 4.4 36.8 1.0 CA D:CYS360 4.5 38.6 1.0 HG2 D:GLN374 4.5 34.1 1.0 CA D:CYS355 4.6 29.6 1.0 HB3 D:PHE357 4.7 40.2 1.0 H D:ARG362 4.7 51.9 1.0 CG D:ARG362 4.7 40.3 1.0 HA D:CYS360 4.7 46.4 1.0 HA D:GLN374 4.8 31.6 1.0 CD1 D:PHE357 4.8 30.6 1.0 CB D:ARG362 4.8 38.0 1.0 CG D:PHE357 4.8 32.3 1.0 HE2 D:PHE364 4.8 35.6 1.0 HD1 D:HIS373 4.9 32.2 1.0 HA D:CYS355 4.9 35.6 1.0 HG2 D:ARG362 5.0 48.4 1.0 C D:CYS355 5.0 31.9 1.0

Zinc binding site 5 out of 6 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:24.5 occ:1.00 NE2 D:HIS405 2.1 33.3 1.0 NE2 D:HIS401 2.1 30.1 1.0 SG D:CYS385 2.2 29.2 1.0 SG D:CYS388 2.3 28.9 1.0 CD2 D:HIS405 2.9 29.1 1.0 HD2 D:HIS405 3.0 34.9 1.0 CD2 D:HIS401 3.0 26.7 1.0 H D:CYS388 3.1 39.2 1.0 CE1 D:HIS401 3.1 27.3 1.0 HB3 D:CYS385 3.1 34.4 1.0 CE1 D:HIS405 3.2 30.9 1.0 CB D:CYS385 3.2 28.7 1.0 HB3 D:CYS388 3.2 37.7 1.0 HD2 D:HIS401 3.2 32.1 1.0 HB2 D:CYS385 3.3 34.4 1.0 CB D:CYS388 3.3 31.4 1.0 HE1 D:HIS401 3.3 32.8 1.0 HE1 D:HIS405 3.4 37.1 1.0 HB D:THR387 3.5 38.3 1.0 N D:CYS388 3.7 32.7 1.0 CA D:CYS388 4.1 32.5 1.0 HB2 D:CYS388 4.1 37.7 1.0 CG D:HIS405 4.1 27.2 1.0 ND1 D:HIS401 4.2 26.3 1.0 HB3 D:ARG390 4.2 29.8 1.0 CG D:HIS401 4.2 25.2 1.0 ND1 D:HIS405 4.2 30.6 1.0 O D:HOH654 4.3 40.3 1.0 H D:THR387 4.3 41.7 1.0 CB D:THR387 4.4 31.9 1.0 H D:ARG390 4.4 31.5 1.0 HG22 D:THR387 4.5 39.7 1.0 HA D:THR402 4.5 34.6 1.0 CA D:CYS385 4.6 29.1 1.0 HE2 D:PHE392 4.6 28.4 1.0 H D:GLN389 4.6 36.6 1.0 HZ D:PHE392 4.6 26.9 1.0 C D:THR387 4.7 34.4 1.0 HB2 D:ARG390 4.7 29.8 1.0 C D:CYS388 4.7 31.8 1.0 CG2 D:THR387 4.8 33.1 1.0 HG21 D:THR387 4.8 39.7 1.0 HG1 D:THR404 4.8 32.6 1.0 HA D:CYS388 4.9 39.0 1.0 CB D:ARG390 4.9 24.9 1.0 CA D:THR387 4.9 34.1 1.0 HA D:CYS385 4.9 34.9 1.0 N D:GLN389 4.9 30.5 1.0 N D:THR387 4.9 34.8 1.0 HG22 D:THR402 4.9 37.0 1.0 HD1 D:HIS401 5.0 31.6 1.0 HD1 D:HIS405 5.0 36.8 1.0

Zinc binding site 6 out of 6 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn503 b:25.3 occ:1.00 NE2 D:HIS431 2.0 31.2 1.0 NE2 D:HIS435 2.1 38.5 1.0 SG D:CYS413 2.2 31.5 1.0 SG D:CYS418 2.3 32.4 1.0 CD2 D:HIS431 2.9 26.7 1.0 HD2 D:HIS431 3.0 32.0 1.0 HB3 D:CYS418 3.0 41.3 1.0 CD2 D:HIS435 3.1 35.7 1.0 HB2 D:CYS413 3.1 30.7 1.0 CE1 D:HIS431 3.1 30.1 1.0 CE1 D:HIS435 3.1 39.6 1.0 CB D:CYS413 3.1 25.6 1.0 CB D:CYS418 3.2 34.4 1.0 HD2 D:HIS435 3.2 42.8 1.0 HB3 D:CYS413 3.3 30.7 1.0 HE1 D:HIS435 3.3 47.5 1.0 HB2 D:CYS418 3.3 41.3 1.0 HE1 D:HIS431 3.4 36.1 1.0 HB3 D:TRP415 3.4 38.7 1.0 HB2 D:LYS420 3.4 38.5 1.0 HB2 D:TRP415 3.6 38.7 1.0 CB D:TRP415 4.0 32.2 1.0 CG D:HIS431 4.1 26.1 1.0 ND1 D:HIS431 4.1 28.5 1.0 ND1 D:HIS435 4.2 40.1 1.0 CG D:HIS435 4.2 37.5 1.0 HG2 D:LYS420 4.2 43.0 1.0 HG3 D:LYS420 4.2 43.0 1.0 H D:LYS420 4.2 40.7 1.0 H D:TRP415 4.3 37.0 1.0 CB D:LYS420 4.3 32.1 1.0 CG D:LYS420 4.5 35.8 1.0 CA D:CYS413 4.5 24.0 1.0 HD2 D:HIS432 4.6 32.2 1.0 CA D:CYS418 4.6 38.3 1.0 HA D:CYS413 4.7 28.8 1.0 CG D:TRP415 4.8 35.8 1.0 HB3 D:LYS420 4.9 38.5 1.0 HA D:CYS418 4.9 45.9 1.0 HD1 D:HIS431 4.9 34.2 1.0 N D:TRP415 5.0 30.8 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