Zinc in PDB 6b0o: Zinc Finger Domain of WT1(-Kts Form) with 12+1MER Oligonucleotide with 3' Triplet Tgt

The structure of Zinc Finger Domain of WT1(-Kts Form) with 12+1MER Oligonucleotide with 3' Triplet Tgt, PDB code: 6b0o 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)	29.59 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.927, 42.657, 71.821, 88.28, 77.71, 85.81
R / Rfree (%)	19.3 / 20.6

The binding sites of Zinc atom in the Zinc Finger Domain of WT1(-Kts Form) with 12+1MER Oligonucleotide with 3' Triplet Tgt (pdb code 6b0o). 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 12+1MER Oligonucleotide with 3' Triplet Tgt, PDB code: 6b0o:
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 12+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 12+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:17.4 occ:1.00 NE2 A:HIS377 2.0 20.9 1.0 NE2 A:HIS373 2.0 15.2 1.0 SG A:CYS355 2.3 18.2 1.0 SG A:CYS360 2.3 18.1 1.0 CD2 A:HIS377 3.0 20.3 1.0 CD2 A:HIS373 3.0 15.4 1.0 CB A:CYS360 3.0 19.7 1.0 CE1 A:HIS373 3.0 17.8 1.0 CE1 A:HIS377 3.0 23.9 1.0 CB A:CYS355 3.1 18.6 1.0 O A:HOH709 4.0 44.9 1.0 ND1 A:HIS377 4.1 23.2 1.0 CG A:HIS377 4.1 22.5 1.0 ND1 A:HIS373 4.1 16.3 1.0 CG A:HIS373 4.2 14.6 1.0 CB A:ARG362 4.4 19.9 1.0 CA A:CYS360 4.5 20.6 1.0 CA A:CYS355 4.6 19.2 1.0 O A:PHE357 4.6 25.6 1.0 CB A:PHE357 4.7 19.6 1.0 CG A:ARG362 4.8 26.6 1.0 C A:CYS355 5.0 20.5 1.0 O A:HOH718 5.0 38.5 1.0

Zinc binding site 2 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 12+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 12+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:24.9 occ:1.00 NE2 A:HIS405 2.1 31.9 1.0 NE2 A:HIS401 2.1 18.3 1.0 SG A:CYS388 2.3 28.4 1.0 SG A:CYS385 2.3 24.1 1.0 CD2 A:HIS405 3.0 28.3 1.0 CD2 A:HIS401 3.1 22.5 1.0 CE1 A:HIS405 3.1 31.4 1.0 CE1 A:HIS401 3.1 22.8 1.0 CB A:CYS385 3.1 22.9 1.0 CB A:CYS388 3.3 31.1 1.0 N A:CYS388 3.6 31.0 1.0 CA A:CYS388 4.0 29.0 1.0 CG A:HIS405 4.2 30.3 1.0 ND1 A:HIS405 4.2 31.7 1.0 ND1 A:HIS401 4.2 19.9 1.0 CG A:HIS401 4.2 20.8 1.0 O A:HOH712 4.3 50.3 1.0 CB A:THR387 4.5 28.8 1.0 CA A:CYS385 4.6 22.9 1.0 C A:CYS388 4.6 30.7 1.0 C A:THR387 4.7 32.9 1.0 N A:GLN389 4.8 31.1 1.0 CB A:ARG390 4.9 25.9 1.0 CA A:THR387 5.0 29.4 1.0 N A:THR387 5.0 28.5 1.0 N A:ARG390 5.0 28.7 1.0

Zinc binding site 3 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 12+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 12+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:37.2 occ:1.00 NE2 A:HIS431 2.1 41.3 1.0 NE2 A:HIS435 2.1 57.3 1.0 SG A:CYS413 2.3 45.9 1.0 SG A:CYS418 2.4 57.2 1.0 CB A:CYS418 2.7 63.9 1.0 CD2 A:HIS431 3.0 36.0 1.0 CD2 A:HIS435 3.0 53.1 1.0 CE1 A:HIS431 3.0 37.5 1.0 CE1 A:HIS435 3.1 55.8 1.0 CB A:CYS413 3.2 41.5 1.0 CB A:TRP415 3.9 71.2 1.0 ND1 A:HIS431 4.1 36.9 1.0 CG A:HIS431 4.1 35.3 1.0 CA A:CYS418 4.2 73.2 1.0 ND1 A:HIS435 4.2 55.4 1.0 CG A:HIS435 4.2 54.0 1.0 CG A:TRP415 4.6 73.4 1.0 CA A:CYS413 4.7 46.6 1.0 C A:CYS418 4.7 71.9 1.0 N A:CYS418 5.0 82.5 1.0 O A:CYS418 5.0 78.1 1.0

Zinc binding site 4 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 12+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 12+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:28.6 occ:1.00 NE2 A:HIS347 2.1 29.6 1.0 NE2 A:HIS343 2.1 29.1 1.0 SG A:CYS325 2.3 33.8 1.0 SG A:CYS330 2.3 35.6 1.0 CD2 A:HIS347 3.0 29.4 1.0 CE1 A:HIS343 3.0 31.6 1.0 CE1 A:HIS347 3.1 29.1 1.0 CD2 A:HIS343 3.1 31.5 1.0 CB A:CYS325 3.2 34.3 1.0 CB A:CYS330 3.3 40.3 1.0 CB A:TYR327 4.0 33.7 1.0 ND1 A:HIS343 4.1 28.2 1.0 ND1 A:HIS347 4.2 28.1 1.0 CG A:HIS347 4.2 28.2 1.0 CG A:HIS343 4.2 28.4 1.0 O A:HOH630 4.3 41.5 1.0 O A:HOH696 4.3 49.6 1.0 CB A:LYS332 4.6 35.7 1.0 CA A:CYS325 4.7 36.4 1.0 CA A:CYS330 4.7 41.6 1.0 CG A:LYS332 4.8 38.9 1.0 CG A:TYR327 4.9 32.7 1.0 N A:TYR327 5.0 40.0 1.0

Zinc binding site 5 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 12+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 12+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:22.2 occ:1.00 NE2 D:HIS377 2.1 22.1 1.0 NE2 D:HIS373 2.1 21.2 1.0 SG D:CYS360 2.3 25.9 1.0 SG D:CYS355 2.3 20.9 1.0 CD2 D:HIS377 3.0 22.9 1.0 CD2 D:HIS373 3.0 22.8 1.0 CE1 D:HIS377 3.1 28.1 1.0 CE1 D:HIS373 3.1 23.7 1.0 CB D:CYS355 3.2 21.1 1.0 CB D:CYS360 3.2 29.0 1.0 ND1 D:HIS377 4.2 27.3 1.0 CG D:HIS377 4.2 24.7 1.0 CG D:HIS373 4.2 21.6 1.0 ND1 D:HIS373 4.2 22.1 1.0 O D:HOH672 4.3 46.4 1.0 CB D:PHE357 4.3 21.4 1.0 CA D:CYS360 4.6 28.8 1.0 CA D:CYS355 4.6 21.0 1.0 CB D:ARG362 4.8 30.4 1.0 C D:CYS360 5.0 31.7 1.0

Zinc binding site 6 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 12+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 12+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:27.6 occ:1.00 NE2 D:HIS405 2.1 32.5 1.0 NE2 D:HIS401 2.1 23.7 1.0 SG D:CYS388 2.3 31.8 1.0 SG D:CYS385 2.3 28.0 1.0 CD2 D:HIS405 2.8 31.2 1.0 CE1 D:HIS401 3.1 24.8 1.0 CD2 D:HIS401 3.1 21.4 1.0 CB D:CYS385 3.1 25.1 1.0 CE1 D:HIS405 3.2 35.7 1.0 CB D:CYS388 3.3 30.9 1.0 N D:CYS388 3.6 35.4 1.0 CA D:CYS388 4.0 32.5 1.0 CG D:HIS405 4.1 31.9 1.0 ND1 D:HIS401 4.2 20.0 1.0 CG D:HIS401 4.2 21.0 1.0 ND1 D:HIS405 4.2 34.2 1.0 CB D:THR387 4.4 36.4 1.0 CA D:CYS385 4.6 25.9 1.0 C D:THR387 4.7 39.2 1.0 C D:CYS388 4.7 34.1 1.0 N D:GLN389 4.9 34.6 1.0 N D:THR387 4.9 36.5 1.0 CA D:THR387 4.9 36.4 1.0 CB D:ARG390 4.9 28.6 1.0

Zinc binding site 7 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 12+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 12+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn503 b:42.4 occ:1.00 NE2 D:HIS431 2.1 55.0 1.0 NE2 D:HIS435 2.1 74.0 1.0 SG D:CYS418 2.3 54.0 1.0 SG D:CYS413 2.4 49.5 1.0 CE1 D:HIS435 2.9 74.2 1.0 CD2 D:HIS431 3.0 46.4 1.0 CE1 D:HIS431 3.1 51.1 1.0 CB D:CYS413 3.2 50.0 1.0 CD2 D:HIS435 3.3 70.9 1.0 CB D:CYS418 3.3 57.6 1.0 ND1 D:HIS435 4.0 74.3 1.0 ND1 D:HIS431 4.1 48.4 1.0 CG D:HIS431 4.1 45.0 1.0 CB D:LYS420 4.2 48.2 1.0 CG D:HIS435 4.3 72.5 1.0 CB D:TRP415 4.3 60.9 1.0 CA D:CYS413 4.7 47.0 1.0 CA D:CYS418 4.7 63.8 1.0 O D:CYS418 4.9 63.6 1.0 C D:CYS418 4.9 63.1 1.0

Zinc binding site 8 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 12+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 12+1MER Oligonucleotide with 3' Triplet Tgt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn504 b:33.7 occ:1.00 NE2 D:HIS343 2.1 28.2 1.0 NE2 D:HIS347 2.1 40.0 1.0 SG D:CYS330 2.3 41.8 1.0 SG D:CYS325 2.4 34.1 1.0 CD2 D:HIS347 3.0 35.9 1.0 CE1 D:HIS343 3.1 29.8 1.0 CD2 D:HIS343 3.1 30.6 1.0 CB D:CYS325 3.1 34.1 1.0 CE1 D:HIS347 3.2 39.8 1.0 CB D:CYS330 3.2 47.2 1.0 ND1 D:HIS343 4.1 29.7 1.0 CG D:HIS343 4.2 28.2 1.0 CG D:HIS347 4.2 37.0 1.0 ND1 D:HIS347 4.2 39.0 1.0 CB D:TYR327 4.3 45.6 1.0 CB D:LYS332 4.5 39.4 1.0 CA D:CYS325 4.6 30.2 1.0 CA D:CYS330 4.7 47.5 1.0 CG D:LYS332 4.7 47.0 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