Zinc in PDB 6b0r: Zinc Finger Domain of WT1(-Kts Form) with M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg

The structure of Zinc Finger Domain of WT1(-Kts Form) with M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg, PDB code: 6b0r 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)	31.32 / 1.82
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	153.940, 35.113, 87.148, 90.00, 110.03, 90.00
R / Rfree (%)	20.8 / 23.4

The binding sites of Zinc atom in the Zinc Finger Domain of WT1(-Kts Form) with M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg (pdb code 6b0r). 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 M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg, PDB code: 6b0r:
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 M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg


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 M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:45.2 occ:1.00 NE2 D:HIS347 2.0 43.0 1.0 NE2 D:HIS343 2.0 39.3 1.0 SG D:CYS330 2.3 43.4 1.0 SG D:CYS325 2.3 42.5 1.0 CD2 D:HIS347 3.0 41.5 1.0 CD2 D:HIS343 3.0 36.1 1.0 CE1 D:HIS343 3.0 40.1 1.0 CE1 D:HIS347 3.0 49.4 1.0 CB D:CYS330 3.2 43.1 1.0 CB D:CYS325 3.2 38.2 1.0 ND1 D:HIS343 4.1 35.2 1.0 CG D:HIS343 4.1 31.6 1.0 CG D:HIS347 4.1 48.6 1.0 ND1 D:HIS347 4.1 48.2 1.0 CB D:TYR327 4.2 39.9 1.0 O D:HOH665 4.2 58.6 1.0 CA D:CYS330 4.6 49.1 1.0 CB D:LYS332 4.6 42.8 1.0 CA D:CYS325 4.7 39.1 1.0 CD D:LYS332 4.7 56.4 1.0 CG D:LYS332 5.0 51.3 1.0

Zinc binding site 2 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg


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 M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:35.3 occ:1.00 NE2 D:HIS373 2.0 33.2 1.0 NE2 D:HIS377 2.0 38.5 1.0 SG D:CYS360 2.3 38.1 1.0 SG D:CYS355 2.3 35.9 1.0 CD2 D:HIS373 3.0 28.5 1.0 CD2 D:HIS377 3.0 40.8 1.0 CE1 D:HIS377 3.0 40.0 1.0 CE1 D:HIS373 3.0 34.9 1.0 CB D:CYS355 3.2 28.9 1.0 CB D:CYS360 3.3 40.6 1.0 O D:HOH666 4.1 45.1 1.0 ND1 D:HIS377 4.1 42.9 1.0 ND1 D:HIS373 4.1 33.1 1.0 CG D:HIS377 4.1 37.5 1.0 CG D:HIS373 4.1 33.6 1.0 CB D:ARG362 4.5 41.0 1.0 CB D:PHE357 4.6 32.6 1.0 CA D:CYS355 4.6 39.4 1.0 CA D:CYS360 4.7 41.6 1.0 CG D:ARG362 4.9 46.2 1.0

Zinc binding site 3 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg


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 M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn503 b:51.8 occ:1.00 NE2 D:HIS405 2.0 65.1 1.0 NE2 D:HIS401 2.0 60.4 1.0 SG D:CYS388 2.3 63.6 1.0 SG D:CYS385 2.3 47.2 1.0 CD2 D:HIS405 2.8 60.0 1.0 CE1 D:HIS401 3.0 53.6 1.0 CD2 D:HIS401 3.0 46.6 1.0 CE1 D:HIS405 3.1 64.3 1.0 CB D:CYS385 3.2 38.2 1.0 CB D:CYS388 3.4 64.6 1.0 N D:CYS388 3.7 56.5 1.0 CG D:HIS405 4.0 60.7 1.0 ND1 D:HIS401 4.1 51.7 1.0 ND1 D:HIS405 4.1 64.0 1.0 CG D:HIS401 4.1 46.3 1.0 CA D:CYS388 4.1 53.2 1.0 CB D:THR387 4.5 60.8 1.0 CA D:CYS385 4.6 38.0 1.0 C D:THR387 4.7 62.3 1.0 C D:CYS388 4.8 55.2 1.0 CA D:THR387 5.0 60.9 1.0 N D:THR387 5.0 58.7 1.0 CB D:ARG390 5.0 52.2 1.0

Zinc binding site 4 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg


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 M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn504 b:48.1 occ:1.00 NE2 D:HIS435 2.0 67.2 1.0 NE2 D:HIS431 2.0 58.2 1.0 SG D:CYS418 2.3 45.8 1.0 SG D:CYS413 2.3 38.8 1.0 CD2 D:HIS431 2.9 54.5 1.0 CD2 D:HIS435 3.0 62.9 1.0 CE1 D:HIS435 3.0 63.8 1.0 CB D:CYS418 3.1 51.1 1.0 CE1 D:HIS431 3.1 61.5 1.0 CB D:CYS413 3.2 34.4 1.0 CB D:TRP415 4.0 49.1 1.0 CG D:HIS431 4.1 55.1 1.0 ND1 D:HIS435 4.1 61.6 1.0 CG D:HIS435 4.1 62.1 1.0 ND1 D:HIS431 4.1 55.0 1.0 CA D:CYS418 4.6 58.5 1.0 CA D:CYS413 4.7 33.6 1.0 CG D:TRP415 4.8 53.2 1.0 N D:TRP415 5.0 35.4 1.0

Zinc binding site 5 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg


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 M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:58.2 occ:1.00 NE2 A:HIS343 2.0 53.9 1.0 NE2 A:HIS347 2.0 66.4 1.0 SG A:CYS330 2.3 56.9 1.0 SG A:CYS325 2.3 55.7 1.0 CE1 A:HIS343 2.9 49.0 1.0 CD2 A:HIS347 3.0 64.8 1.0 CD2 A:HIS343 3.0 48.5 1.0 CE1 A:HIS347 3.1 65.0 1.0 CB A:CYS330 3.2 67.5 1.0 CB A:CYS325 3.2 52.3 1.0 ND1 A:HIS343 4.0 45.1 1.0 CG A:HIS343 4.1 44.3 1.0 CG A:HIS347 4.1 62.8 1.0 ND1 A:HIS347 4.1 63.0 1.0 CB A:TYR327 4.2 74.3 1.0 CB A:LYS332 4.5 55.7 1.0 CA A:CYS330 4.6 76.0 1.0 CG A:LYS332 4.6 59.8 1.0 CA A:CYS325 4.7 54.4 1.0 C A:CYS330 5.0 66.2 1.0

Zinc binding site 6 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg


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 M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:39.5 occ:1.00 NE2 A:HIS377 2.0 52.0 1.0 NE2 A:HIS373 2.0 48.4 1.0 SG A:CYS360 2.3 47.0 1.0 SG A:CYS355 2.3 38.2 1.0 CD2 A:HIS377 2.9 36.5 1.0 CD2 A:HIS373 3.0 35.8 1.0 CE1 A:HIS373 3.1 40.2 1.0 CE1 A:HIS377 3.1 39.5 1.0 CB A:CYS355 3.2 44.9 1.0 CB A:CYS360 3.3 49.5 1.0 CG A:HIS377 4.1 34.2 1.0 CG A:HIS373 4.1 37.2 1.0 ND1 A:HIS373 4.1 37.4 1.0 ND1 A:HIS377 4.1 40.4 1.0 CB A:PHE357 4.2 40.0 1.0 CB A:ARG362 4.6 58.0 1.0 CA A:CYS355 4.6 37.1 1.0 CA A:CYS360 4.7 55.6 1.0 CG A:ARG362 4.7 60.8 1.0 N A:PHE357 5.0 40.3 1.0

Zinc binding site 7 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg


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 M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:71.2 occ:1.00 NE2 A:HIS405 2.0 84.8 1.0 NE2 A:HIS401 2.0 75.9 1.0 SG A:CYS388 2.3 72.2 1.0 SG A:CYS385 2.3 57.5 1.0 CD2 A:HIS405 2.8 83.0 1.0 CD2 A:HIS401 2.9 66.4 1.0 CB A:CYS388 3.1 70.2 1.0 CE1 A:HIS401 3.1 69.6 1.0 CE1 A:HIS405 3.2 83.2 1.0 CB A:CYS385 3.2 60.6 1.0 N A:CYS388 3.6 78.4 1.0 CA A:CYS388 3.9 71.7 1.0 CG A:HIS405 4.0 86.4 1.0 CG A:HIS401 4.0 63.4 1.0 ND1 A:HIS401 4.1 63.6 1.0 ND1 A:HIS405 4.2 86.7 1.0 CB A:THR387 4.5 77.9 1.0 C A:THR387 4.6 80.3 1.0 CA A:CYS385 4.7 60.8 1.0 C A:CYS388 4.7 70.4 1.0 N A:THR387 4.9 84.3 1.0 CA A:THR387 4.9 81.0 1.0 O A:HIS401 4.9 64.3 1.0 N A:GLN389 5.0 84.3 1.0

Zinc binding site 8 out of 8 in the Zinc Finger Domain of WT1(-Kts Form) with M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg


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 M342R Mutation and 14+1MER Oligonucleotide with 3' Triplet Tgg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:47.6 occ:1.00 NE2 A:HIS431 2.0 51.1 1.0 NE2 A:HIS435 2.0 41.5 1.0 SG A:CYS418 2.3 49.4 1.0 SG A:CYS413 2.3 45.9 1.0 CD2 A:HIS431 2.9 52.2 1.0 CD2 A:HIS435 3.0 41.9 1.0 CE1 A:HIS435 3.0 42.2 1.0 CE1 A:HIS431 3.1 50.5 1.0 CB A:CYS413 3.2 45.7 1.0 CB A:CYS418 3.3 48.6 1.0 CG A:HIS431 4.1 49.8 1.0 ND1 A:HIS435 4.1 41.7 1.0 CG A:HIS435 4.1 42.8 1.0 ND1 A:HIS431 4.1 45.0 1.0 CB A:TRP415 4.1 51.8 1.0 CB A:LYS420 4.6 55.8 1.0 CG A:TRP415 4.6 64.1 1.0 CA A:CYS413 4.7 55.8 1.0 CD1 A:TRP415 4.7 72.4 1.0 CA A:CYS418 4.7 59.4 1.0 CG A:LYS420 4.9 69.8 1.0 N A:TRP415 5.0 41.1 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