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Zinc in PDB 6blw: Zinc Finger Domain of WT1(+Kts Form) with M342R Mutation and 17+1MER Oligonucleotide with Triplet Ggt

Protein crystallography data

The structure of Zinc Finger Domain of WT1(+Kts Form) with M342R Mutation and 17+1MER Oligonucleotide with Triplet Ggt, PDB code: 6blw 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) 29.69 / 1.84
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 63.552, 95.572, 83.340, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Zinc Finger Domain of WT1(+Kts Form) with M342R Mutation and 17+1MER Oligonucleotide with Triplet Ggt (pdb code 6blw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Zinc Finger Domain of WT1(+Kts Form) with M342R Mutation and 17+1MER Oligonucleotide with Triplet Ggt, PDB code: 6blw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6blw

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Zinc binding site 1 out of 4 in the Zinc Finger Domain of WT1(+Kts Form) with M342R Mutation and 17+1MER Oligonucleotide with 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 M342R Mutation and 17+1MER Oligonucleotide with Triplet Ggt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:34.4
occ:1.00
NE2 A:HIS373 2.0 43.4 1.0
NE2 A:HIS377 2.0 51.4 1.0
SG A:CYS360 2.3 46.6 1.0
SG A:CYS355 2.3 36.3 1.0
CD2 A:HIS377 2.8 48.1 1.0
CE1 A:HIS373 3.0 41.9 1.0
CD2 A:HIS373 3.0 37.8 1.0
CE1 A:HIS377 3.1 52.8 1.0
CB A:CYS355 3.2 39.2 1.0
CB A:CYS360 3.3 49.7 1.0
CG A:HIS377 4.0 46.9 1.0
ND1 A:HIS373 4.1 39.2 1.0
ND1 A:HIS377 4.1 51.3 1.0
CG A:HIS373 4.1 36.5 1.0
CB A:PHE357 4.3 40.3 1.0
CA A:CYS355 4.6 42.4 1.0
CA A:CYS360 4.7 58.1 1.0
CG A:PHE357 4.8 38.4 1.0
CB A:ARG362 4.9 57.8 1.0
C A:CYS355 5.0 49.4 1.0

Zinc binding site 2 out of 4 in 6blw

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Zinc binding site 2 out of 4 in the Zinc Finger Domain of WT1(+Kts Form) with M342R Mutation and 17+1MER Oligonucleotide with 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 M342R Mutation and 17+1MER Oligonucleotide with Triplet Ggt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:35.1
occ:1.00
NE2 A:HIS405 2.0 52.5 1.0
NE2 A:HIS401 2.0 52.2 1.0
SG A:CYS388 2.3 45.5 1.0
SG A:CYS385 2.3 46.1 1.0
CD2 A:HIS401 2.9 53.0 1.0
CD2 A:HIS405 3.0 52.1 1.0
CE1 A:HIS405 3.0 55.4 1.0
CE1 A:HIS401 3.1 53.5 1.0
CB A:CYS385 3.2 42.0 1.0
CB A:CYS388 3.4 55.7 1.0
N A:CYS388 3.7 59.0 1.0
CG A:HIS401 4.0 52.1 1.0
ND1 A:HIS401 4.1 53.4 1.0
CA A:CYS388 4.1 59.9 1.0
ND1 A:HIS405 4.1 57.0 1.0
CG A:HIS405 4.1 54.2 1.0
CB A:THR387 4.4 58.0 1.0
CA A:CYS385 4.7 43.1 1.0
C A:THR387 4.7 59.9 1.0
C A:CYS388 4.8 58.2 1.0
CB A:ARG390 4.9 47.8 1.0
CA A:THR387 4.9 59.1 1.0
CG2 A:THR387 5.0 63.1 1.0
N A:THR387 5.0 53.9 1.0
N A:GLN389 5.0 53.9 1.0

Zinc binding site 3 out of 4 in 6blw

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Zinc binding site 3 out of 4 in the Zinc Finger Domain of WT1(+Kts Form) with M342R Mutation and 17+1MER Oligonucleotide with 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 M342R Mutation and 17+1MER Oligonucleotide with Triplet Ggt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:44.9
occ:1.00
NE2 A:HIS347 2.0 64.6 1.0
NE2 A:HIS343 2.0 68.5 1.0
SG A:CYS330 2.3 62.5 1.0
SG A:CYS325 2.3 57.5 1.0
CE1 A:HIS347 3.0 64.9 1.0
CD2 A:HIS343 3.0 66.4 1.0
CE1 A:HIS343 3.0 66.5 1.0
CD2 A:HIS347 3.0 68.1 1.0
CB A:CYS325 3.2 55.0 1.0
CB A:CYS330 3.2 69.1 1.0
CB A:TYR327 4.0 65.0 1.0
ND1 A:HIS347 4.1 71.0 1.0
ND1 A:HIS343 4.1 64.5 1.0
CG A:HIS343 4.1 62.8 1.0
CG A:HIS347 4.2 71.7 1.0
CB A:LYS332 4.3 57.1 1.0
CG A:LYS332 4.3 59.0 1.0
CA A:CYS325 4.6 55.9 1.0
CA A:CYS330 4.6 75.1 1.0
CG A:TYR327 4.8 69.8 1.0
CD2 A:TYR327 5.0 73.7 1.0
N A:TYR327 5.0 64.1 1.0

Zinc binding site 4 out of 4 in 6blw

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Zinc binding site 4 out of 4 in the Zinc Finger Domain of WT1(+Kts Form) with M342R Mutation and 17+1MER Oligonucleotide with 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 M342R Mutation and 17+1MER Oligonucleotide with Triplet Ggt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:78.4
occ:1.00
CE1 A:HIS434 1.8 0.2 1.0
NE2 A:HIS434 2.0 0.8 1.0
NE2 A:HIS438 2.0 0.7 1.0
SG A:CYS421 2.2 0.8 1.0
SG A:CYS416 2.4 94.2 1.0
CB A:CYS421 2.4 0.7 1.0
CE1 A:HIS438 2.6 96.7 1.0
ND1 A:HIS434 3.1 0.3 1.0
CD2 A:HIS438 3.3 0.8 1.0
CD2 A:HIS434 3.4 0.3 1.0
CB A:CYS416 3.8 95.1 1.0
ND1 A:HIS438 3.8 94.6 1.0
CG A:HIS434 3.9 0.5 1.0
CA A:CYS421 3.9 0.1 1.0
CB A:TRP418 3.9 95.1 1.0
CG A:HIS438 4.2 95.3 1.0
C A:CYS421 4.4 0.8 1.0
CG A:TRP418 4.5 88.7 1.0
N A:CYS421 4.7 1.0 1.0
CD1 A:TRP418 4.7 83.5 1.0
O A:CYS421 4.8 0.2 1.0
O A:TRP418 4.9 0.2 1.0
CA A:TRP418 4.9 0.3 1.0
N A:TRP418 5.0 96.7 1.0
N A:GLN422 5.0 0.3 1.0

Reference:

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
Page generated: Wed Dec 16 11:32:20 2020

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