Zinc in PDB 6b0q: Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt

The structure of Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt, PDB code: 6b0q was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.83 / 2.79
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	161.664, 161.664, 42.172, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 24.1

The binding sites of Zinc atom in the Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt (pdb code 6b0q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt, PDB code: 6b0q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:45.3 occ:1.00 NE2 D:HIS343 2.0 88.5 1.0 NE2 D:HIS347 2.0 87.7 1.0 SG D:CYS330 2.3 78.7 1.0 SG D:CYS325 2.3 67.9 1.0 CD2 D:HIS347 2.7 84.1 1.0 CB D:CYS330 2.8 82.1 1.0 CD2 D:HIS343 2.8 85.4 1.0 CB D:CYS325 3.1 66.9 1.0 CE1 D:HIS343 3.1 92.1 1.0 CE1 D:HIS347 3.3 90.4 1.0 CG D:HIS347 3.9 84.5 1.0 CG D:HIS343 4.0 84.9 1.0 CB D:TYR327 4.1 74.9 1.0 ND1 D:HIS343 4.1 90.5 1.0 ND1 D:HIS347 4.2 89.8 1.0 CA D:CYS330 4.3 85.5 1.0 O D:CYS330 4.5 81.4 1.0 CA D:CYS325 4.6 64.7 1.0 C D:CYS330 4.7 83.9 1.0 O D:HIS343 4.8 71.0 1.0 O D:HOH605 4.8 33.7 1.0

Zinc binding site 2 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:23.2 occ:1.00 NE2 D:HIS377 2.0 40.3 1.0 NE2 D:HIS373 2.0 38.6 1.0 SG D:CYS360 2.3 36.8 1.0 SG D:CYS355 2.3 38.8 1.0 CE1 D:HIS373 2.9 38.9 1.0 CE1 D:HIS377 2.9 42.0 1.0 CD2 D:HIS377 3.1 41.0 1.0 CD2 D:HIS373 3.1 38.7 1.0 CB D:CYS360 3.1 40.3 1.0 CB D:CYS355 3.2 39.3 1.0 ND1 D:HIS373 4.0 38.0 1.0 ND1 D:HIS377 4.1 42.6 1.0 CG D:HIS377 4.2 41.2 1.0 CG D:HIS373 4.2 37.1 1.0 CB D:PHE357 4.3 41.9 1.0 CA D:CYS360 4.6 43.8 1.0 CA D:CYS355 4.7 40.9 1.0 CB D:ARG362 5.0 35.5 1.0 C D:CYS360 5.0 44.7 1.0

Zinc binding site 3 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn503 b:35.6 occ:1.00 NE2 D:HIS401 2.0 63.9 1.0 NE2 D:HIS405 2.0 71.6 1.0 SG D:CYS388 2.3 61.2 1.0 SG D:CYS385 2.3 51.9 1.0 CD2 D:HIS405 2.5 72.9 1.0 CD2 D:HIS401 2.8 63.0 1.0 CE1 D:HIS401 3.1 63.9 1.0 CE1 D:HIS405 3.2 73.0 1.0 CB D:CYS385 3.2 50.8 1.0 CB D:CYS388 3.2 66.6 1.0 N D:CYS388 3.6 66.8 1.0 CG D:HIS405 3.8 72.6 1.0 CG D:HIS401 4.0 58.2 1.0 CA D:CYS388 4.0 68.9 1.0 ND1 D:HIS405 4.0 73.5 1.0 ND1 D:HIS401 4.1 61.2 1.0 CB D:THR387 4.4 65.7 1.0 C D:THR387 4.7 68.7 1.0 CA D:CYS385 4.7 51.9 1.0 C D:CYS388 4.7 68.8 1.0 O D:HIS401 4.8 54.8 1.0 CA D:THR387 4.9 67.1 1.0 N D:THR387 4.9 63.6 1.0

Zinc binding site 4 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn504 b:34.2 occ:1.00 NE2 D:HIS435 2.0 71.8 1.0 NE2 D:HIS431 2.0 66.6 1.0 SG D:CYS418 2.3 69.0 1.0 SG D:CYS413 2.3 61.8 1.0 CD2 D:HIS431 2.7 65.1 1.0 CE1 D:HIS435 2.8 75.2 1.0 CD2 D:HIS435 3.1 71.2 1.0 CE1 D:HIS431 3.2 66.8 1.0 CB D:CYS413 3.4 56.6 1.0 CB D:CYS418 3.6 71.8 1.0 ND1 D:HIS435 3.9 75.6 1.0 CG D:HIS431 4.0 61.9 1.0 CG D:HIS435 4.1 72.6 1.0 ND1 D:HIS431 4.1 64.3 1.0 CB D:TRP415 4.4 69.5 1.0 CB D:LYS420 4.6 64.5 1.0 CA D:CYS413 4.8 56.8 1.0 O D:CYS418 4.8 71.2 1.0 CA D:CYS418 4.9 73.3 1.0 CG D:TRP415 5.0 69.6 1.0

Zinc binding site 5 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:32.8 occ:1.00 NE2 A:HIS343 2.0 60.4 1.0 NE2 A:HIS347 2.0 72.3 1.0 SG A:CYS330 2.3 45.5 1.0 SG A:CYS325 2.4 46.4 1.0 CE1 A:HIS347 2.8 72.4 1.0 CE1 A:HIS343 2.9 61.4 1.0 CD2 A:HIS343 3.0 61.4 1.0 CD2 A:HIS347 3.2 69.6 1.0 CB A:CYS330 3.2 47.9 1.0 CB A:CYS325 3.4 46.2 1.0 ND1 A:HIS343 4.0 61.7 1.0 ND1 A:HIS347 4.0 69.5 1.0 CG A:HIS343 4.1 61.0 1.0 CG A:HIS347 4.2 66.6 1.0 CB A:TYR327 4.3 53.6 1.0 CD2 A:TYR327 4.5 56.4 1.0 CA A:CYS330 4.6 48.6 1.0 CG A:TYR327 4.7 56.2 1.0 N A:ASN331 4.8 48.2 1.0 CA A:CYS325 4.8 47.8 1.0 C A:CYS330 4.9 47.9 1.0

Zinc binding site 6 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:22.9 occ:1.00 NE2 A:HIS377 2.0 43.0 1.0 NE2 A:HIS373 2.0 41.2 1.0 SG A:CYS360 2.3 39.9 1.0 SG A:CYS355 2.3 41.4 1.0 CE1 A:HIS377 2.8 44.7 1.0 CE1 A:HIS373 2.9 41.4 1.0 CD2 A:HIS373 3.1 41.5 1.0 CD2 A:HIS377 3.1 43.6 1.0 CB A:CYS355 3.3 42.2 1.0 CB A:CYS360 3.5 43.5 1.0 ND1 A:HIS377 4.0 45.4 1.0 ND1 A:HIS373 4.0 40.3 1.0 CG A:HIS377 4.1 43.8 1.0 CG A:HIS373 4.2 39.6 1.0 CB A:ARG362 4.5 42.6 1.0 CA A:CYS355 4.7 44.4 1.0 CB A:PHE357 4.8 43.2 1.0 CA A:CYS360 4.9 46.4 1.0 CD2 A:PHE357 4.9 41.1 1.0 CG A:ARG362 5.0 40.7 1.0

Zinc binding site 7 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:37.0 occ:1.00 NE2 A:HIS405 2.0 68.8 1.0 NE2 A:HIS401 2.0 61.2 1.0 SG A:CYS388 2.3 51.8 1.0 SG A:CYS385 2.3 48.6 1.0 CD2 A:HIS405 2.6 70.0 1.0 CD2 A:HIS401 2.8 60.1 1.0 CE1 A:HIS401 3.1 60.9 1.0 CE1 A:HIS405 3.2 71.7 1.0 CB A:CYS385 3.2 47.4 1.0 CB A:CYS388 3.4 55.9 1.0 N A:CYS388 3.5 58.7 1.0 CG A:HIS405 3.8 70.8 1.0 CG A:HIS401 4.0 57.2 1.0 CA A:CYS388 4.0 58.5 1.0 ND1 A:HIS405 4.0 72.7 1.0 ND1 A:HIS401 4.1 58.7 1.0 CB A:THR387 4.2 60.8 1.0 C A:THR387 4.5 61.4 1.0 CA A:CYS385 4.7 48.6 1.0 N A:THR387 4.7 58.4 1.0 CA A:THR387 4.7 61.1 1.0 C A:CYS388 4.7 57.9 1.0 CG2 A:THR387 4.9 62.7 1.0 N A:GLN389 4.9 57.3 1.0 O A:HIS401 5.0 50.5 1.0

Zinc binding site 8 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zinc Finger Domain of WT1(-Kts Form) with 13+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:31.6 occ:1.00 NE2 A:HIS431 2.0 60.9 1.0 NE2 A:HIS435 2.0 65.3 1.0 SG A:CYS418 2.3 52.1 1.0 SG A:CYS413 2.3 48.2 1.0 CD2 A:HIS435 2.9 64.3 1.0 CD2 A:HIS431 2.9 59.3 1.0 CE1 A:HIS435 3.0 68.0 1.0 CE1 A:HIS431 3.1 61.6 1.0 CB A:CYS418 3.1 55.6 1.0 CB A:CYS413 3.3 48.4 1.0 CB A:TRP415 4.0 51.7 1.0 CG A:HIS435 4.0 64.8 1.0 ND1 A:HIS435 4.1 67.7 1.0 CG A:HIS431 4.1 56.9 1.0 ND1 A:HIS431 4.1 59.3 1.0 CA A:CYS418 4.6 58.9 1.0 CB A:LYS420 4.7 58.5 1.0 CA A:CYS413 4.8 48.8 1.0 CG A:TRP415 4.8 51.9 1.0

D.Wang, J.R.Horton, Y.Zheng, R.M.Blumenthal, X.Zhang, X.Cheng. Role For First Zinc Finger of WT1 in Dna Sequence Specificity: Denys-Drash Syndrome-Associated WT1 Mutant in ZF1 Enhances Affinity For A Subset of WT1 Binding Sites. Nucleic Acids Res. V. 46 3864 2018.
ISSN: ESSN 1362-4962
PubMed: 29294058
DOI: 10.1093/NAR/GKX1274