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Zinc in PDB 5keb: Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form II

Protein crystallography data

The structure of Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form II, PDB code: 5keb was solved by H.Hashimoto, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.64 / 2.45
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 51.110, 51.110, 131.580, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 28.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form II (pdb code 5keb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form II, PDB code: 5keb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5keb

Go back to Zinc Binding Sites List in 5keb
Zinc binding site 1 out of 3 in the Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:63.9
occ:1.00
NE2 A:HIS478 2.0 68.3 1.0
NE2 A:HIS482 2.1 97.8 1.0
HB2 A:CYS465 2.3 1.0 1.0
SG A:CYS462 2.3 62.3 1.0
SG A:CYS465 2.3 96.2 1.0
CB A:CYS465 2.7 88.4 1.0
CD2 A:HIS478 2.7 58.8 1.0
HD2 A:HIS478 2.8 70.4 1.0
CE1 A:HIS482 3.0 96.5 1.0
HB3 A:CYS462 3.1 78.3 1.0
CD2 A:HIS482 3.1 93.9 1.0
CB A:CYS462 3.1 65.4 1.0
CE1 A:HIS478 3.2 63.5 1.0
HE1 A:HIS482 3.2 0.7 1.0
HB2 A:CYS462 3.3 78.3 1.0
HD2 A:HIS482 3.3 0.5 1.0
HB3 A:CYS465 3.4 1.0 1.0
HE1 A:HIS478 3.5 76.1 1.0
N A:CYS465 3.8 86.1 1.0
CA A:CYS465 3.9 88.7 1.0
HB2 A:LYS464 3.9 99.3 1.0
CG A:HIS478 4.0 58.0 1.0
C A:LYS464 4.0 76.9 1.0
H A:CYS465 4.1 0.2 1.0
HB2 A:ARG467 4.1 90.3 1.0
ND1 A:HIS482 4.2 96.0 1.0
ND1 A:HIS478 4.2 60.0 1.0
CG A:HIS482 4.2 93.9 1.0
O A:LYS464 4.2 74.5 1.0
H A:LYS464 4.3 88.2 1.0
HA A:CYS465 4.4 0.3 1.0
CA A:CYS462 4.6 65.7 1.0
CB A:LYS464 4.7 82.8 1.0
CA A:LYS464 4.8 78.3 1.0
HD3 A:ARG467 4.8 0.7 1.0
H A:ARG467 4.8 81.8 1.0
HB3 A:LYS464 4.8 99.3 1.0
HE2 A:PHE469 4.9 74.8 1.0
N A:LYS464 4.9 73.6 1.0
HD1 A:HIS482 4.9 0.1 1.0
C A:CYS465 4.9 89.2 1.0
HA A:CYS462 5.0 78.7 1.0
HD1 A:HIS478 5.0 71.9 1.0

Zinc binding site 2 out of 3 in 5keb

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Zinc binding site 2 out of 3 in the Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:70.7
occ:1.00
NE2 A:HIS450 2.0 92.1 1.0
NE2 A:HIS454 2.0 99.8 1.0
SG A:CYS437 2.2 66.7 1.0
SG A:CYS432 2.3 60.6 1.0
HD2 A:HIS450 2.4 0.0 1.0
CD2 A:HIS450 2.5 86.0 1.0
CD2 A:HIS454 2.8 93.5 1.0
HD2 A:HIS454 2.9 0.1 1.0
CE1 A:HIS454 3.2 99.2 1.0
CE1 A:HIS450 3.3 88.4 1.0
CB A:CYS437 3.3 72.9 1.0
HB2 A:CYS437 3.4 87.4 1.0
CB A:CYS432 3.4 58.9 1.0
HB2 A:CYS432 3.4 70.6 1.0
HB3 A:CYS437 3.4 87.4 1.0
HE1 A:HIS454 3.5 0.9 1.0
HB3 A:CYS432 3.5 70.6 1.0
HB3 A:TRP434 3.5 90.4 1.0
HB2 A:TRP439 3.6 87.3 1.0
HB2 A:TRP434 3.6 90.4 1.0
HE1 A:HIS450 3.7 1.0 1.0
CG A:HIS450 3.8 82.8 1.0
CG A:HIS454 4.0 94.5 1.0
CB A:TRP434 4.0 75.4 1.0
ND1 A:HIS450 4.1 85.2 1.0
ND1 A:HIS454 4.1 98.1 1.0
HD1 A:TRP439 4.4 91.2 1.0
H A:TRP439 4.4 89.7 1.0
H A:TRP434 4.5 91.5 1.0
CB A:TRP439 4.5 72.9 1.0
CA A:CYS437 4.7 80.3 1.0
CA A:CYS432 4.8 56.5 1.0
CG A:TRP434 4.8 78.2 1.0
HE1 A:PHE441 4.8 92.0 1.0
O A:HIS450 4.8 56.5 1.0
HB3 A:TRP439 4.8 87.3 1.0
CD1 A:TRP439 4.9 76.1 1.0
HA A:CYS437 4.9 96.3 1.0
HD1 A:HIS454 4.9 0.6 1.0
HD1 A:HIS450 5.0 0.1 1.0
HA A:CYS432 5.0 67.7 1.0
CG A:TRP439 5.0 73.5 1.0

Zinc binding site 3 out of 3 in 5keb

Go back to Zinc Binding Sites List in 5keb
Zinc binding site 3 out of 3 in the Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:63.6
occ:1.00
NE2 A:HIS420 2.0 75.4 1.0
NE2 A:HIS424 2.0 77.6 1.0
SG A:CYS407 2.3 86.1 1.0
SG A:CYS402 2.3 49.4 1.0
HB3 A:CYS407 2.8 0.2 1.0
CD2 A:HIS424 2.8 69.7 1.0
CB A:CYS407 2.9 88.6 1.0
CD2 A:HIS420 2.9 68.9 1.0
HD2 A:HIS424 2.9 83.5 1.0
HB2 A:CYS407 3.0 0.2 1.0
CE1 A:HIS420 3.0 71.1 1.0
CE1 A:HIS424 3.1 73.6 1.0
HD2 A:HIS420 3.1 82.5 1.0
HE1 A:HIS420 3.2 85.2 1.0
HE1 A:HIS424 3.4 88.2 1.0
CB A:CYS402 3.4 54.6 1.0
HB3 A:CYS402 3.5 65.4 1.0
HB2 A:CYS402 3.5 65.4 1.0
HB3 A:TYR404 3.9 98.3 1.0
HB2 A:TYR404 3.9 98.3 1.0
CG A:HIS424 4.0 68.6 1.0
CG A:HIS420 4.0 65.7 1.0
ND1 A:HIS420 4.0 67.5 1.0
ND1 A:HIS424 4.1 72.3 1.0
HD23 A:LEU421 4.1 67.3 1.0
HB2 A:LYS409 4.2 72.2 1.0
CB A:TYR404 4.4 82.0 1.0
CA A:CYS407 4.4 92.3 1.0
HD22 A:LEU421 4.6 67.3 1.0
H A:TYR404 4.6 0.2 1.0
HA A:LEU421 4.6 57.2 1.0
HD2 A:LYS409 4.7 82.0 1.0
CD2 A:LEU421 4.7 56.2 1.0
H A:LYS409 4.7 87.1 1.0
HA A:CYS407 4.8 0.6 1.0
CA A:CYS402 4.8 61.8 1.0
HD1 A:HIS420 4.8 80.9 1.0
HD1 A:HIS424 4.9 86.6 1.0
HG1 A:THR423 4.9 69.5 1.0
C A:CYS407 4.9 90.4 1.0
H A:CYS407 5.0 0.9 1.0
HG3 A:LYS409 5.0 80.5 1.0
HD2 A:TYR404 5.0 88.9 1.0
HD21 A:LEU421 5.0 67.3 1.0

Reference:

H.Hashimoto, D.Wang, A.N.Steves, P.Jin, R.M.Blumenthal, X.Zhang, X.Cheng. Distinctive KLF4 Mutants Determine Preference For Dna Methylation Status. Nucleic Acids Res. V. 44 10177 2016.
ISSN: ESSN 1362-4962
PubMed: 27596594
DOI: 10.1093/NAR/GKW774
Page generated: Wed Dec 16 06:27:15 2020

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