Zinc in PDB 5ke9: Mouse KLF4 E446P ZNF1-3 and Tpg/Cpa Sequence Dna Complex Structure

The structure of Mouse KLF4 E446P ZNF1-3 and Tpg/Cpa Sequence Dna Complex Structure, PDB code: 5ke9 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)	25.24 / 2.34
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	51.440, 51.440, 130.594, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 27.2

The binding sites of Zinc atom in the Mouse KLF4 E446P ZNF1-3 and Tpg/Cpa Sequence Dna Complex Structure (pdb code 5ke9). 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 E446P ZNF1-3 and Tpg/Cpa Sequence Dna Complex Structure, PDB code: 5ke9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mouse KLF4 E446P 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 E446P ZNF1-3 and Tpg/Cpa Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:61.2 occ:1.00 NE2 A:HIS482 2.0 81.1 1.0 NE2 A:HIS478 2.1 71.8 1.0 SG A:CYS465 2.3 63.8 1.0 SG A:CYS462 2.3 52.9 1.0 CD2 A:HIS482 3.0 74.8 1.0 CD2 A:HIS478 3.0 60.5 1.0 HB3 A:CYS465 3.0 80.9 1.0 H A:CYS465 3.0 81.4 1.0 CE1 A:HIS482 3.0 75.2 1.0 CE1 A:HIS478 3.1 65.3 1.0 HD2 A:HIS478 3.1 72.5 1.0 HB3 A:CYS462 3.1 78.6 1.0 HD2 A:HIS482 3.1 89.8 1.0 CB A:CYS462 3.2 65.5 1.0 CB A:CYS465 3.2 67.5 1.0 HE1 A:HIS482 3.3 90.3 1.0 HB2 A:CYS462 3.3 78.6 1.0 HE1 A:HIS478 3.3 78.4 1.0 N A:CYS465 3.7 67.8 1.0 HB3 A:LYS464 3.9 86.1 1.0 HB2 A:CYS465 4.0 80.9 1.0 CA A:CYS465 4.0 71.5 1.0 CG A:HIS482 4.1 72.3 1.0 ND1 A:HIS482 4.1 72.5 1.0 CG A:HIS478 4.1 56.1 1.0 ND1 A:HIS478 4.1 61.8 1.0 HG2 A:LYS464 4.1 98.5 1.0 HB2 A:ARG467 4.2 91.3 1.0 H A:LYS464 4.4 79.5 1.0 H A:ARG467 4.4 89.2 1.0 CA A:CYS462 4.6 70.0 1.0 H A:ASP466 4.6 84.2 1.0 CB A:LYS464 4.7 71.7 1.0 C A:CYS465 4.8 71.1 1.0 HA A:CYS465 4.8 85.8 1.0 C A:LYS464 4.8 71.6 1.0 HD3 A:ARG467 4.8 0.5 1.0 CG A:LYS464 4.8 82.1 1.0 HD1 A:HIS482 4.9 87.0 1.0 HA A:MET479 4.9 67.8 1.0 HD1 A:HIS478 4.9 74.2 1.0 HA A:CYS462 5.0 84.0 1.0 N A:ASP466 5.0 70.2 1.0 SD A:MET479 5.0 65.8 1.0

Zinc binding site 2 out of 3 in the Mouse KLF4 E446P 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 E446P ZNF1-3 and Tpg/Cpa Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:54.1 occ:1.00 NE2 A:HIS454 2.0 60.7 1.0 NE2 A:HIS450 2.0 68.9 1.0 SG A:CYS437 2.2 56.9 1.0 SG A:CYS432 2.3 55.3 1.0 HB2 A:CYS437 2.9 66.1 1.0 CD2 A:HIS454 2.9 55.0 1.0 CD2 A:HIS450 2.9 62.8 1.0 CB A:CYS437 3.0 55.1 1.0 CE1 A:HIS454 3.1 57.1 1.0 HB3 A:CYS437 3.1 66.1 1.0 CE1 A:HIS450 3.1 66.3 1.0 HD2 A:HIS450 3.1 75.3 1.0 HD2 A:HIS454 3.1 66.0 1.0 HB3 A:TRP434 3.3 90.9 1.0 HE1 A:HIS454 3.3 68.5 1.0 HE1 A:HIS450 3.3 79.6 1.0 HB3 A:CYS432 3.4 72.6 1.0 CB A:CYS432 3.4 60.5 1.0 HB2 A:CYS432 3.5 72.6 1.0 HB2 A:TRP439 3.7 78.0 1.0 HB2 A:TRP434 4.0 90.9 1.0 CB A:TRP434 4.1 75.8 1.0 CG A:HIS454 4.1 56.3 1.0 CG A:HIS450 4.1 55.6 1.0 ND1 A:HIS454 4.1 59.9 1.0 ND1 A:HIS450 4.1 64.8 1.0 H A:TRP439 4.4 74.8 1.0 CA A:CYS437 4.5 82.9 1.0 HD1 A:TRP439 4.5 67.5 1.0 H A:TRP434 4.6 0.7 1.0 HD1 A:TRP434 4.7 86.8 1.0 CB A:TRP439 4.7 65.0 1.0 HA A:CYS437 4.7 99.5 1.0 CG A:TRP434 4.7 69.6 1.0 HA A:TYR451 4.8 66.5 1.0 CA A:CYS432 4.8 71.1 1.0 HD1 A:HIS454 4.9 71.9 1.0 HD2 A:TYR451 4.9 88.5 1.0 CD1 A:TRP434 4.9 72.3 1.0 HD1 A:HIS450 4.9 77.7 1.0

Zinc binding site 3 out of 3 in the Mouse KLF4 E446P 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 E446P ZNF1-3 and Tpg/Cpa Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:88.8 occ:1.00 NE2 A:HIS420 2.0 0.7 1.0 NE2 A:HIS424 2.0 0.6 1.0 SG A:CYS402 2.3 83.2 1.0 SG A:CYS407 2.3 0.3 1.0 CD2 A:HIS420 2.7 0.2 1.0 CE1 A:HIS424 2.8 0.0 1.0 HB3 A:CYS407 2.8 0.7 1.0 HD2 A:HIS420 2.8 0.4 1.0 CD2 A:HIS424 2.9 0.5 1.0 HE1 A:HIS424 3.0 0.8 1.0 CB A:CYS407 3.0 0.7 1.0 CE1 A:HIS420 3.0 0.1 1.0 HB2 A:CYS407 3.2 0.7 1.0 HD2 A:HIS424 3.2 0.2 1.0 HE1 A:HIS420 3.4 0.1 1.0 CB A:CYS402 3.4 89.4 1.0 HB2 A:CYS402 3.4 0.3 1.0 HB3 A:CYS402 3.5 0.3 1.0 HB2 A:TYR404 3.6 0.9 1.0 ND1 A:HIS424 3.8 0.0 1.0 CG A:HIS420 3.8 96.0 1.0 CG A:HIS424 3.9 0.8 1.0 ND1 A:HIS420 4.0 0.1 1.0 HD2 A:TYR404 4.2 95.6 1.0 HD23 A:LEU421 4.3 76.7 1.0 HB3 A:LYS409 4.3 0.8 1.0 CA A:CYS407 4.5 0.4 1.0 HE2 A:LYS409 4.5 0.4 1.0 CB A:TYR404 4.5 88.2 1.0 HD1 A:HIS424 4.5 0.8 1.0 CD2 A:TYR404 4.6 79.6 1.0 HE3 A:LYS409 4.6 0.4 1.0 H A:TYR404 4.7 0.9 1.0 HD1 A:HIS420 4.7 0.3 1.0 HA A:LEU421 4.8 64.4 1.0 HB3 A:TYR404 4.8 0.9 1.0 CA A:CYS402 4.8 96.9 1.0 CG A:TYR404 4.8 85.7 1.0 H A:LYS409 4.9 0.5 1.0 O A:CYS407 4.9 0.3 1.0 HA A:CYS407 4.9 0.7 1.0 C A:CYS407 4.9 1.0 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