Zinc in PDB 5ke6: Mouse KLF4 ZNF1-3 and Tpg/Cpa Sequence Dna Complex Structure

The structure of Mouse KLF4 ZNF1-3 and Tpg/Cpa Sequence Dna Complex Structure, PDB code: 5ke6 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)	34.68 / 1.99
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.870, 50.870, 130.540, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.4

The binding sites of Zinc atom in the Mouse KLF4 ZNF1-3 and Tpg/Cpa Sequence Dna Complex Structure (pdb code 5ke6). 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/Cpa Sequence Dna Complex Structure, PDB code: 5ke6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mouse KLF4 ZNF1-3 and Tpg/Cpa 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/Cpa Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:46.4 occ:1.00 NE2 A:HIS482 2.0 69.2 1.0 NE2 A:HIS478 2.1 78.7 1.0 SG A:CYS462 2.3 46.4 1.0 SG A:CYS465 2.3 46.8 1.0 CD2 A:HIS478 2.8 76.0 1.0 HD2 A:HIS478 2.9 91.2 1.0 CE1 A:HIS482 2.9 72.7 1.0 CD2 A:HIS482 3.0 68.7 1.0 HB3 A:CYS465 3.1 59.3 1.0 HE1 A:HIS482 3.1 87.2 1.0 CE1 A:HIS478 3.2 80.1 1.0 HB3 A:CYS462 3.2 55.5 1.0 CB A:CYS462 3.2 46.2 1.0 HD2 A:HIS482 3.2 82.4 1.0 CB A:CYS465 3.3 49.5 1.0 HB2 A:CYS462 3.4 55.5 1.0 HE1 A:HIS478 3.5 96.1 1.0 H A:CYS465 3.7 61.3 1.0 N A:CYS465 3.8 51.1 1.0 HB2 A:LYS464 3.9 68.5 1.0 HB2 A:ARG467 3.9 70.7 1.0 CA A:CYS465 4.0 51.9 1.0 ND1 A:HIS482 4.0 72.2 1.0 H A:LYS464 4.0 65.0 1.0 CG A:HIS478 4.1 72.8 1.0 HB2 A:CYS465 4.1 59.3 1.0 CG A:HIS482 4.1 67.8 1.0 C A:LYS464 4.2 59.6 1.0 ND1 A:HIS478 4.2 77.7 1.0 H A:ARG467 4.4 68.7 1.0 CB A:LYS464 4.6 57.0 1.0 C A:CYS465 4.6 52.6 1.0 HG3 A:ARG467 4.6 78.3 1.0 HB3 A:LYS464 4.6 68.5 1.0 CA A:CYS462 4.7 44.6 1.0 O A:LYS464 4.7 62.7 1.0 HA A:MET479 4.7 53.5 1.0 CA A:LYS464 4.7 57.5 1.0 N A:LYS464 4.7 54.1 1.0 HE1 A:MET479 4.8 63.8 1.0 HE1 A:PHE469 4.8 53.2 1.0 HD1 A:HIS482 4.8 86.7 1.0 CB A:ARG467 4.8 58.9 1.0 O A:CYS465 4.8 51.1 1.0 HE2 A:MET479 4.8 63.8 1.0 HD3 A:ARG467 4.9 82.5 1.0 HA A:CYS465 4.9 62.3 1.0 HA A:CYS462 5.0 53.5 1.0

Zinc binding site 2 out of 3 in the Mouse KLF4 ZNF1-3 and Tpg/Cpa 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/Cpa Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:33.4 occ:1.00 NE2 A:HIS450 2.0 43.2 1.0 NE2 A:HIS454 2.1 48.2 1.0 SG A:CYS432 2.3 33.2 1.0 SG A:CYS437 2.3 40.7 1.0 CD2 A:HIS450 2.8 39.2 1.0 HD2 A:HIS450 2.9 47.1 1.0 HB3 A:CYS437 2.9 51.8 1.0 CD2 A:HIS454 3.0 47.0 1.0 CB A:CYS437 3.1 43.2 1.0 HB3 A:CYS432 3.1 38.9 1.0 CE1 A:HIS454 3.1 50.4 1.0 CB A:CYS432 3.1 32.4 1.0 CE1 A:HIS450 3.2 42.6 1.0 HD2 A:HIS454 3.2 56.4 1.0 HB2 A:CYS432 3.2 38.9 1.0 HB2 A:CYS437 3.3 51.8 1.0 HB3 A:TRP434 3.3 44.6 1.0 HE1 A:HIS454 3.3 60.5 1.0 HE1 A:HIS450 3.5 51.2 1.0 HB2 A:TRP439 3.6 42.8 1.0 HB2 A:TRP434 3.7 44.6 1.0 CB A:TRP434 3.9 37.2 1.0 CG A:HIS450 4.0 37.6 1.0 ND1 A:HIS450 4.2 40.7 1.0 H A:TRP434 4.2 45.7 1.0 CG A:HIS454 4.2 47.9 1.0 ND1 A:HIS454 4.2 50.4 1.0 H A:TRP439 4.3 40.4 1.0 HD1 A:TRP439 4.5 53.9 1.0 CA A:CYS437 4.5 45.6 1.0 CB A:TRP439 4.6 35.6 1.0 CA A:CYS432 4.6 29.5 1.0 CG A:TRP434 4.8 39.6 1.0 HA A:CYS432 4.9 35.5 1.0 N A:TRP434 4.9 38.1 1.0 HA A:CYS437 4.9 54.8 1.0 C A:CYS437 4.9 45.3 1.0 HB3 A:TRP439 4.9 42.8 1.0 HD1 A:HIS450 5.0 48.8 1.0 HD1 A:HIS454 5.0 60.5 1.0

Zinc binding site 3 out of 3 in the Mouse KLF4 ZNF1-3 and Tpg/Cpa 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/Cpa Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:36.0 occ:1.00 NE2 A:HIS424 2.0 50.9 1.0 NE2 A:HIS420 2.1 46.4 1.0 SG A:CYS402 2.3 35.9 1.0 SG A:CYS407 2.4 39.2 1.0 HB3 A:CYS407 2.8 49.9 1.0 CD2 A:HIS424 2.9 47.2 1.0 HB2 A:CYS407 2.9 49.9 1.0 CB A:CYS407 2.9 41.7 1.0 CD2 A:HIS420 3.0 42.3 1.0 HD2 A:HIS424 3.0 56.7 1.0 HD2 A:HIS420 3.1 50.8 1.0 CE1 A:HIS420 3.1 43.1 1.0 CE1 A:HIS424 3.1 50.0 1.0 HB3 A:CYS402 3.1 45.2 1.0 CB A:CYS402 3.2 37.8 1.0 HE1 A:HIS420 3.4 51.8 1.0 HB2 A:CYS402 3.4 45.2 1.0 HE1 A:HIS424 3.4 60.0 1.0 HB2 A:LYS409 3.8 61.3 1.0 HB3 A:TYR404 3.8 55.8 1.0 CG A:HIS424 4.1 45.2 1.0 ND1 A:HIS424 4.2 48.0 1.0 CG A:HIS420 4.2 39.2 1.0 ND1 A:HIS420 4.2 40.4 1.0 HD23 A:LEU421 4.3 43.6 1.0 H A:TYR404 4.4 54.7 1.0 H A:LYS409 4.4 70.9 1.0 CA A:CYS407 4.4 55.8 1.0 HD2 A:LYS409 4.5 64.4 1.0 CA A:CYS402 4.6 40.2 1.0 H A:GLY408 4.7 72.9 1.0 CB A:TYR404 4.7 46.5 1.0 CB A:LYS409 4.8 51.0 1.0 O A:TYR404 4.8 55.1 1.0 HA A:CYS407 4.8 67.0 1.0 HA A:LEU421 4.8 37.0 1.0 HB2 A:TYR404 4.8 55.8 1.0 H A:CYS407 5.0 71.0 1.0 HD1 A:HIS424 5.0 57.6 1.0 HG1 A:THR423 5.0 47.6 1.0 HG3 A:LYS409 5.0 64.5 1.0 HA A:CYS402 5.0 48.1 1.0 HD1 A:HIS420 5.0 48.5 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