Zinc in PDB 5ke7: Mouse KLF4 ZNF1-3 and Tpg/Mpa Sequence Dna Complex Structure

The structure of Mouse KLF4 ZNF1-3 and Tpg/Mpa Sequence Dna Complex Structure, PDB code: 5ke7 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)	34.60 / 2.06
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.750, 50.750, 130.390, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.6

The binding sites of Zinc atom in the Mouse KLF4 ZNF1-3 and Tpg/Mpa Sequence Dna Complex Structure (pdb code 5ke7). 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 and Tpg/Mpa Sequence Dna Complex Structure, PDB code: 5ke7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mouse KLF4 ZNF1-3 and Tpg/Mpa Sequence Dna Complex Structure


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 and Tpg/Mpa Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:35.2 occ:1.00 NE2 A:HIS482 2.1 43.3 1.0 NE2 A:HIS478 2.1 39.6 1.0 SG A:CYS465 2.3 37.6 1.0 SG A:CYS462 2.3 31.6 1.0 CD2 A:HIS478 3.0 36.1 1.0 CE1 A:HIS482 3.0 43.8 1.0 HD2 A:HIS478 3.0 43.2 1.0 CD2 A:HIS482 3.1 41.3 1.0 HB3 A:CYS465 3.2 47.7 1.0 HE1 A:HIS482 3.2 52.5 1.0 CE1 A:HIS478 3.2 41.8 1.0 HB3 A:CYS462 3.2 38.2 1.0 CB A:CYS462 3.3 31.8 1.0 CB A:CYS465 3.3 39.8 1.0 HD2 A:HIS482 3.3 49.6 1.0 HB2 A:CYS462 3.4 38.2 1.0 HE1 A:HIS478 3.5 50.0 1.0 H A:CYS465 3.5 44.6 1.0 N A:CYS465 3.7 37.3 1.0 HB2 A:LYS464 3.7 51.2 1.0 HB2 A:ARG467 4.0 51.7 1.0 H A:LYS464 4.0 46.0 1.0 CA A:CYS465 4.0 39.6 1.0 HB2 A:CYS465 4.1 47.7 1.0 ND1 A:HIS482 4.1 44.0 1.0 C A:LYS464 4.1 43.8 1.0 CG A:HIS478 4.2 36.3 1.0 CG A:HIS482 4.2 41.6 1.0 ND1 A:HIS478 4.2 40.0 1.0 H A:ARG467 4.4 48.0 1.0 CB A:LYS464 4.4 42.6 1.0 HB3 A:LYS464 4.6 51.2 1.0 C A:CYS465 4.6 39.8 1.0 CA A:LYS464 4.6 41.0 1.0 HG3 A:ARG467 4.7 54.6 1.0 CA A:CYS462 4.7 32.6 1.0 N A:LYS464 4.7 38.3 1.0 O A:LYS464 4.7 48.9 1.0 HA A:CYS465 4.9 47.4 1.0 HA A:MET479 4.9 38.1 1.0 HD1 A:HIS482 4.9 52.9 1.0 CB A:ARG467 4.9 43.1 1.0 HD3 A:ARG467 5.0 63.9 1.0 O A:CYS465 5.0 38.4 1.0 HE1 A:PHE469 5.0 39.7 1.0

Zinc binding site 2 out of 3 in the Mouse KLF4 ZNF1-3 and Tpg/Mpa Sequence Dna Complex Structure


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 and Tpg/Mpa Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:26.4 occ:1.00 NE2 A:HIS450 2.1 28.7 1.0 NE2 A:HIS454 2.1 31.4 1.0 SG A:CYS432 2.3 24.6 1.0 SG A:CYS437 2.3 28.0 1.0 CD2 A:HIS450 2.9 26.5 1.0 HD2 A:HIS450 2.9 31.8 1.0 CD2 A:HIS454 3.0 28.8 1.0 HB3 A:CYS437 3.0 34.3 1.0 HD2 A:HIS454 3.1 34.6 1.0 CB A:CYS437 3.1 28.6 1.0 HB3 A:CYS432 3.1 29.0 1.0 CB A:CYS432 3.2 24.3 1.0 CE1 A:HIS454 3.2 30.9 1.0 CE1 A:HIS450 3.2 29.6 1.0 HB3 A:TRP434 3.3 36.8 1.0 HB2 A:CYS432 3.3 29.0 1.0 HB2 A:CYS437 3.3 34.3 1.0 HE1 A:HIS454 3.4 37.2 1.0 HE1 A:HIS450 3.5 35.5 1.0 HB2 A:TRP439 3.5 33.6 1.0 HB2 A:TRP434 3.7 36.8 1.0 CB A:TRP434 3.9 30.6 1.0 CG A:HIS450 4.1 26.7 1.0 CG A:HIS454 4.2 33.4 1.0 H A:TRP434 4.2 34.3 1.0 ND1 A:HIS450 4.2 27.5 1.0 ND1 A:HIS454 4.2 32.5 1.0 H A:TRP439 4.3 30.1 1.0 HD1 A:TRP439 4.3 43.7 1.0 CB A:TRP439 4.5 28.0 1.0 CA A:CYS437 4.6 37.1 1.0 CA A:CYS432 4.6 25.4 1.0 CG A:TRP434 4.8 30.8 1.0 HB3 A:TRP439 4.8 33.6 1.0 N A:TRP434 4.9 28.6 1.0 CD1 A:TRP439 4.9 36.4 1.0 HA A:CYS437 4.9 44.5 1.0 C A:CYS437 4.9 40.0 1.0 HA A:CYS432 4.9 30.5 1.0 CA A:TRP434 5.0 33.1 1.0

Zinc binding site 3 out of 3 in the Mouse KLF4 ZNF1-3 and Tpg/Mpa Sequence Dna Complex Structure


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 and Tpg/Mpa Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:35.0 occ:1.00 NE2 A:HIS420 2.1 32.5 1.0 NE2 A:HIS424 2.1 35.2 1.0 SG A:CYS402 2.3 33.4 1.0 SG A:CYS407 2.4 34.2 1.0 HB3 A:CYS407 2.7 43.6 1.0 CB A:CYS407 2.9 36.5 1.0 HB2 A:CYS407 2.9 43.6 1.0 CD2 A:HIS424 2.9 32.7 1.0 HD2 A:HIS424 3.0 39.3 1.0 CD2 A:HIS420 3.0 28.9 1.0 CE1 A:HIS420 3.1 28.9 1.0 HB3 A:CYS402 3.1 49.2 1.0 HD2 A:HIS420 3.2 34.6 1.0 CB A:CYS402 3.2 41.0 1.0 CE1 A:HIS424 3.2 34.4 1.0 HE1 A:HIS420 3.3 34.6 1.0 HB2 A:CYS402 3.4 49.2 1.0 HE1 A:HIS424 3.5 41.3 1.0 HB2 A:LYS409 3.7 50.1 1.0 HB3 A:TYR404 3.8 46.4 1.0 CG A:HIS424 4.1 31.9 1.0 ND1 A:HIS420 4.2 27.7 1.0 CG A:HIS420 4.2 29.6 1.0 ND1 A:HIS424 4.2 34.0 1.0 HD2 A:LYS409 4.2 61.2 1.0 HD23 A:LEU421 4.3 40.9 1.0 H A:LYS409 4.4 60.4 1.0 CA A:CYS407 4.4 42.2 1.0 H A:TYR404 4.4 49.0 1.0 CA A:CYS402 4.6 44.4 1.0 CB A:LYS409 4.6 41.7 1.0 CB A:TYR404 4.7 38.6 1.0 HA A:CYS407 4.8 50.7 1.0 O A:TYR404 4.8 56.4 1.0 HA A:LEU421 4.8 36.3 1.0 HB2 A:TYR404 4.8 46.4 1.0 H A:GLY408 4.9 65.1 1.0 HD3 A:LYS409 4.9 61.2 1.0 H A:CYS407 4.9 54.2 1.0 CD A:LYS409 4.9 51.0 1.0 HD1 A:HIS420 5.0 33.1 1.0 HB3 A:LYS409 5.0 50.1 1.0 C A:CYS407 5.0 47.9 1.0 HG1 A:THR423 5.0 36.8 1.0 HA A:CYS402 5.0 53.3 1.0 C A:CYS402 5.0 49.5 1.0

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