Sodium in PDB 5kl2: Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna

The structure of Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna, PDB code: 5kl2 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)	29.12 / 1.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.107, 65.089, 35.702, 90.00, 93.42, 90.00
R / Rfree (%)	16.4 / 19.3

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

Zinc

(Zn)

3 atoms

The binding sites of Sodium atom in the Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna (pdb code 5kl2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna, PDB code: 5kl2:

Sodium binding site 1 out of 1 in the Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:41.4 occ:1.00 OP2 C:DC3 2.1 56.7 1.0 O A:HOH637 2.7 32.6 1.0 OG A:SER395 2.8 21.8 1.0 H6 C:DC3 3.0 23.5 1.0 O5' C:DC3 3.1 56.9 1.0 H2'' C:DA2 3.1 44.4 1.0 P C:DC3 3.1 67.0 1.0 H2' C:DC3 3.2 29.8 1.0 HB3 A:SER395 3.3 29.9 1.0 H71 C:DT4 3.3 27.4 1.0 HG A:SER395 3.5 26.2 1.0 HZ A:PHE383 3.6 36.3 1.0 CB A:SER395 3.6 25.0 1.0 C2' C:DA2 3.7 37.0 1.0 H2' C:DA2 3.8 44.4 1.0 C6 C:DC3 3.8 19.6 1.0 H A:SER395 3.9 21.3 1.0 H3' C:DA2 3.9 39.0 1.0 O3' C:DA2 4.1 54.9 1.0 C3' C:DA2 4.1 32.5 1.0 C7 C:DT4 4.1 22.8 1.0 H5 C:DC3 4.1 26.0 1.0 C2' C:DC3 4.2 24.9 1.0 H73 C:DT4 4.2 27.4 1.0 HB2 A:SER395 4.2 29.9 1.0 CZ A:PHE383 4.2 30.2 1.0 O A:HOH655 4.3 31.9 1.0 H3' C:DC3 4.3 38.7 1.0 OP1 C:DC3 4.3 80.8 1.0 O C:HOH213 4.3 42.2 1.0 H72 C:DT4 4.4 27.4 1.0 C5 C:DC3 4.4 21.6 1.0 C5' C:DC3 4.4 41.8 1.0 N A:SER395 4.6 17.8 1.0 C3' C:DC3 4.7 32.2 1.0 HE1 A:PHE383 4.7 36.0 1.0 CA A:SER395 4.7 19.2 1.0 H2'' C:DC3 4.7 29.8 1.0 O A:HOH605 4.8 31.6 1.0 H5' C:DC3 4.8 50.1 1.0 N1 C:DC3 4.8 22.9 1.0 CE1 A:PHE383 4.8 30.0 1.0 O4' C:DC3 4.9 27.5 1.0 C1' C:DC3 4.9 30.4 1.0 C4' C:DC3 4.9 31.0 1.0 HE2 A:PHE383 4.9 33.3 1.0 CE2 A:PHE383 5.0 27.7 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