Calcium 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:

Zinc	(Zn)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna, PDB code: 5kl4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca504 b:42.0 occ:1.00 O A:HOH633 2.3 56.0 1.0 O A:CYS360 2.3 34.6 1.0 O A:HOH627 2.4 48.1 1.0 O A:CYS355 2.4 33.6 1.0 HA A:GLU361 3.2 59.6 1.0 HA A:ASP356 3.3 42.6 1.0 C A:CYS360 3.5 36.8 1.0 C A:CYS355 3.6 31.5 1.0 CA A:GLU361 4.0 49.7 1.0 CA A:ASP356 4.1 35.5 1.0 N A:GLU361 4.2 43.1 1.0 HB2 A:GLN354 4.2 57.0 1.0 O A:HOH644 4.3 49.4 1.0 N A:ASP356 4.3 32.1 1.0 HG2 A:GLU361 4.3 76.8 1.0 HB3 A:CYS360 4.4 38.8 1.0 H A:CYS360 4.5 44.2 1.0 OD1 A:ASP356 4.5 41.6 1.0 O A:PHE357 4.5 37.1 1.0 HB3 A:CYS355 4.6 32.0 1.0 H A:CYS355 4.6 36.4 1.0 C A:ASP356 4.6 34.5 1.0 CA A:CYS360 4.6 33.7 1.0 CA A:CYS355 4.7 28.8 1.0 N A:CYS355 4.7 30.3 1.0 H A:ARG362 4.8 51.5 1.0 N A:CYS360 4.8 36.8 1.0 HG3 A:GLU361 4.8 76.8 1.0 HG3 A:GLN354 4.8 65.9 1.0 C A:GLU361 4.9 47.4 1.0 CG A:GLU361 4.9 64.0 1.0 CB A:GLU361 5.0 57.6 1.0

Calcium binding site 2 out of 2 in the Wilms Tumor Protein (WT1) ZNF2-4 Q369H in Complex with Formylated Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 D:Ca504 b:42.8 occ:1.00 O D:CYS355 2.4 34.2 1.0 O D:HOH626 2.4 36.3 1.0 O D:CYS360 2.4 40.1 1.0 O D:HOH620 2.4 29.9 1.0 HA D:GLU361 3.2 61.6 1.0 HA D:ASP356 3.5 41.5 1.0 C D:CYS355 3.6 31.9 1.0 C D:CYS360 3.6 41.2 1.0 HB3 D:GLN354 4.0 55.2 1.0 OE1 D:GLN354 4.0 59.1 1.0 CA D:GLU361 4.1 51.4 1.0 H D:CYS355 4.3 38.0 1.0 CA D:ASP356 4.3 34.5 1.0 N D:GLU361 4.3 45.9 1.0 N D:ASP356 4.3 31.7 1.0 HB3 D:CYS360 4.4 44.3 1.0 HG2 D:GLN354 4.4 62.2 1.0 HB3 D:CYS355 4.4 34.0 1.0 N D:CYS355 4.5 31.7 1.0 CA D:CYS355 4.6 29.6 1.0 CD D:GLN354 4.6 58.5 1.0 HG2 D:GLU361 4.7 80.2 1.0 H D:CYS360 4.7 48.4 1.0 OD1 D:ASP356 4.7 39.5 1.0 C D:GLU361 4.7 48.0 1.0 O D:PHE357 4.7 38.7 1.0 CA D:CYS360 4.8 38.6 1.0 CG D:GLN354 4.8 51.8 1.0 CB D:GLN354 4.8 46.0 1.0 C D:ASP356 4.8 34.2 1.0 O D:ARG362 4.9 37.5 1.0 N D:CYS360 5.0 40.3 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