Atomistry » Zinc » PDB 6av1-6bd4 » 6b0p
Atomistry »
  Zinc »
    PDB 6av1-6bd4 »
      6b0p »

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

Protein crystallography data

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

Zinc Binding Sites:

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 6b0p

Go back to Zinc Binding Sites List in 6b0p
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 6b0p

Go back to Zinc Binding Sites List in 6b0p
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 6b0p

Go back to Zinc Binding Sites List in 6b0p
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 6b0p

Go back to Zinc Binding Sites List in 6b0p
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 6b0p

Go back to Zinc Binding Sites List in 6b0p
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 6b0p

Go back to Zinc Binding Sites List in 6b0p
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 6b0p

Go back to Zinc Binding Sites List in 6b0p
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 6b0p

Go back to Zinc Binding Sites List in 6b0p
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

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: Mon Oct 28 17:46:50 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy