Zinc in PDB 6b0p: Zinc Finger Domain of WT1(-Kts Form) with 12+1MER Oligonucleotide with 3' Triplet Ggt

The structure of Zinc Finger Domain of WT1(-Kts Form) with 12+1MER Oligonucleotide with 3' Triplet Ggt, PDB code: 6b0p 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)	37.88 / 2.08
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	75.798, 84.402, 85.968, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.6

The binding sites of Zinc atom in the Zinc Finger Domain of WT1(-Kts Form) with 12+1MER Oligonucleotide with 3' Triplet Ggt (pdb code 6b0p). 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 Ggt, PDB code: 6b0p:
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 Ggt


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 Ggt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:20.7 occ:1.00 NE2 D:HIS343 2.0 23.1 1.0 NE2 D:HIS347 2.0 22.1 1.0 SG D:CYS325 2.2 21.0 1.0 SG D:CYS330 2.3 22.1 1.0 CE1 D:HIS343 2.9 23.8 1.0 CD2 D:HIS347 3.0 20.8 1.0 CE1 D:HIS347 3.1 21.8 1.0 CD2 D:HIS343 3.1 18.2 1.0 CB D:CYS330 3.1 18.1 1.0 CB D:CYS325 3.2 20.9 1.0 ND1 D:HIS343 4.0 18.8 1.0 ND1 D:HIS347 4.1 18.7 1.0 CG D:HIS347 4.1 20.1 1.0 CG D:HIS343 4.2 19.1 1.0 O D:HOH632 4.3 43.7 1.0 CB D:TYR327 4.3 19.5 1.0 CB D:LYS332 4.5 22.4 1.0 CA D:CYS330 4.6 18.0 1.0 CA D:CYS325 4.6 21.1 1.0 CG D:LYS332 4.6 26.5 1.0 C D:CYS330 4.9 20.7 1.0 N D:LYS332 4.9 21.1 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 Ggt


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 Ggt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:31.4 occ:1.00 NE2 D:HIS373 2.0 34.5 1.0 NE2 D:HIS377 2.1 40.5 1.0 SG D:CYS360 2.3 32.2 1.0 SG D:CYS355 2.3 32.3 1.0 CD2 D:HIS377 2.8 32.7 1.0 CE1 D:HIS373 3.0 30.5 1.0 CD2 D:HIS373 3.0 30.0 1.0 CB D:CYS355 3.1 25.9 1.0 CB D:CYS360 3.3 36.6 1.0 CE1 D:HIS377 3.3 41.5 1.0 CG D:HIS377 4.1 39.0 1.0 ND1 D:HIS373 4.1 28.5 1.0 CG D:HIS373 4.2 29.6 1.0 ND1 D:HIS377 4.3 41.1 1.0 CB D:PHE357 4.4 32.3 1.0 CB D:ARG362 4.5 28.8 1.0 CA D:CYS355 4.6 31.1 1.0 CA D:CYS360 4.7 46.0 1.0 CD1 D:PHE357 4.9 25.6 1.0 CG D:GLN374 4.9 32.7 1.0 CG D:ARG362 5.0 44.7 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 Ggt


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 Ggt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn503 b:44.6 occ:1.00 NE2 D:HIS405 2.1 48.2 1.0 NE2 D:HIS401 2.1 44.1 1.0 SG D:CYS388 2.4 44.5 1.0 SG D:CYS385 2.4 38.9 1.0 CD2 D:HIS405 3.0 42.0 1.0 CE1 D:HIS401 3.1 35.4 1.0 CD2 D:HIS401 3.1 34.0 1.0 CE1 D:HIS405 3.1 47.4 1.0 CB D:CYS385 3.2 38.5 1.0 CB D:CYS388 3.4 48.8 1.0 N D:CYS388 3.8 52.7 1.0 CA D:CYS388 4.1 52.2 1.0 CG D:HIS405 4.2 48.0 1.0 ND1 D:HIS401 4.2 32.6 1.0 ND1 D:HIS405 4.2 51.7 1.0 CG D:HIS401 4.2 33.9 1.0 CB D:THR387 4.5 51.1 1.0 CA D:CYS385 4.7 39.5 1.0 C D:THR387 4.8 51.1 1.0 C D:CYS388 4.8 49.4 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 Ggt


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 Ggt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn504 b:37.0 occ:1.00 NE2 D:HIS435 2.0 39.1 1.0 NE2 D:HIS431 2.1 37.0 1.0 SG D:CYS418 2.3 46.8 1.0 SG D:CYS413 2.3 32.5 1.0 CD2 D:HIS435 2.9 42.4 1.0 CD2 D:HIS431 3.0 29.4 1.0 CE1 D:HIS435 3.0 43.6 1.0 CE1 D:HIS431 3.1 35.0 1.0 CB D:CYS413 3.3 31.8 1.0 CB D:CYS418 3.3 40.0 1.0 CG D:HIS435 4.1 47.0 1.0 ND1 D:HIS435 4.1 48.2 1.0 CB D:TRP415 4.1 39.9 1.0 ND1 D:HIS431 4.1 30.0 1.0 CG D:HIS431 4.2 32.9 1.0 CB D:LYS420 4.5 44.6 1.0 CG D:TRP415 4.6 42.3 1.0 CD1 D:TRP415 4.7 48.2 1.0 CG D:LYS420 4.7 48.7 1.0 CA D:CYS413 4.7 35.5 1.0 CA D:CYS418 4.8 46.4 1.0 N D:TRP415 5.0 38.4 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 Ggt


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 Ggt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:19.7 occ:1.00 NE2 A:HIS347 2.0 17.1 1.0 NE2 A:HIS343 2.1 24.6 1.0 SG A:CYS325 2.3 18.8 1.0 SG A:CYS330 2.4 20.6 1.0 CE1 A:HIS347 2.9 24.1 1.0 CE1 A:HIS343 3.0 24.8 1.0 CD2 A:HIS347 3.1 19.2 1.0 CD2 A:HIS343 3.1 17.8 1.0 CB A:CYS325 3.1 19.5 1.0 CB A:CYS330 3.2 18.3 1.0 O A:HOH681 3.9 44.9 1.0 ND1 A:HIS347 4.0 21.1 1.0 ND1 A:HIS343 4.1 22.7 1.0 CG A:HIS347 4.2 19.3 1.0 CG A:HIS343 4.2 19.2 1.0 CB A:LYS332 4.6 26.0 1.0 CA A:CYS325 4.6 19.9 1.0 CG A:LYS332 4.6 35.6 1.0 CA A:CYS330 4.7 17.9 1.0 CB A:TYR327 4.7 23.4 1.0 CA A:SER344 5.0 22.5 0.5 CA A:SER344 5.0 22.5 0.5

Zinc binding site 6 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with 12+1MER Oligonucleotide with 3' Triplet Ggt


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 Ggt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:34.9 occ:1.00 NE2 A:HIS373 2.0 29.6 1.0 NE2 A:HIS377 2.1 46.6 1.0 SG A:CYS360 2.3 36.7 1.0 SG A:CYS355 2.3 32.5 1.0 CD2 A:HIS373 2.9 27.4 1.0 CD2 A:HIS377 2.9 39.9 1.0 CB A:CYS355 3.1 31.4 1.0 CE1 A:HIS373 3.1 33.5 1.0 CE1 A:HIS377 3.2 41.7 1.0 CB A:CYS360 3.3 39.9 1.0 CG A:HIS373 4.0 27.5 1.0 ND1 A:HIS373 4.1 28.2 1.0 CG A:HIS377 4.1 41.8 1.0 ND1 A:HIS377 4.2 45.5 1.0 CB A:PHE357 4.5 44.6 1.0 CA A:CYS355 4.5 41.6 1.0 CA A:CYS360 4.7 44.1 1.0 CB A:ARG362 4.8 39.0 1.0 CD1 A:PHE357 4.9 37.4 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 Ggt


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 Ggt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:46.1 occ:1.00 NE2 A:HIS401 2.1 39.9 1.0 NE2 A:HIS405 2.1 55.0 1.0 SG A:CYS388 2.3 51.4 1.0 SG A:CYS385 2.4 43.9 1.0 CD2 A:HIS405 2.8 48.9 1.0 CE1 A:HIS401 3.0 29.4 1.0 CD2 A:HIS401 3.1 30.1 1.0 CB A:CYS385 3.2 47.3 1.0 CE1 A:HIS405 3.3 49.3 1.0 CB A:CYS388 3.4 55.0 1.0 N A:CYS388 3.7 61.3 1.0 CG A:HIS405 4.1 49.0 1.0 CA A:CYS388 4.1 64.3 1.0 ND1 A:HIS401 4.2 28.1 1.0 CG A:HIS401 4.2 28.5 1.0 ND1 A:HIS405 4.2 52.3 1.0 CB A:THR387 4.5 61.3 1.0 CA A:CYS385 4.7 53.5 1.0 C A:CYS388 4.7 61.8 1.0 C A:THR387 4.7 64.8 1.0 N A:GLN389 5.0 63.9 1.0 CB A:ARG390 5.0 49.8 1.0 CA A:THR387 5.0 63.3 1.0 N A:THR387 5.0 68.2 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 Ggt


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 Ggt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:35.6 occ:1.00 NE2 A:HIS435 2.0 35.0 1.0 NE2 A:HIS431 2.1 36.7 1.0 SG A:CYS418 2.3 39.2 1.0 SG A:CYS413 2.3 31.3 1.0 CD2 A:HIS435 3.0 34.3 1.0 CD2 A:HIS431 3.0 28.6 1.0 CE1 A:HIS431 3.0 29.7 1.0 CE1 A:HIS435 3.0 36.6 1.0 CB A:CYS413 3.3 34.1 1.0 CB A:CYS418 3.3 36.3 1.0 ND1 A:HIS431 4.1 30.3 1.0 CG A:HIS431 4.1 30.5 1.0 ND1 A:HIS435 4.1 37.9 1.0 CG A:HIS435 4.1 36.5 1.0 CB A:TRP415 4.2 35.8 1.0 CB A:LYS420 4.5 30.1 1.0 CG A:TRP415 4.6 44.2 1.0 CA A:CYS413 4.7 37.5 1.0 CA A:CYS418 4.7 37.6 1.0 CD1 A:TRP415 4.7 43.3 1.0 CG A:LYS420 4.8 45.1 1.0 N A:TRP415 5.0 34.9 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