Zinc in PDB 5ke8: Mouse KLF4 E446P ZNF1-3 and Mpg/Mpg Sequence Dna Complex Structure

The structure of Mouse KLF4 E446P ZNF1-3 and Mpg/Mpg Sequence Dna Complex Structure, PDB code: 5ke8 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)	35.67 / 2.45
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.450, 50.450, 130.490, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 27

The binding sites of Zinc atom in the Mouse KLF4 E446P ZNF1-3 and Mpg/Mpg Sequence Dna Complex Structure (pdb code 5ke8). 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 Mpg/Mpg Sequence Dna Complex Structure, PDB code: 5ke8:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mouse KLF4 E446P ZNF1-3 and Mpg/Mpg 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 Mpg/Mpg Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:64.8 occ:1.00 NE2 A:HIS478 2.0 59.0 1.0 NE2 A:HIS482 2.0 81.8 1.0 SG A:CYS465 2.3 52.6 1.0 SG A:CYS462 2.3 62.3 1.0 H A:CYS465 2.8 79.1 1.0 CD2 A:HIS478 2.8 55.6 1.0 CD2 A:HIS482 2.9 81.5 1.0 HD2 A:HIS478 2.9 66.9 1.0 HD2 A:HIS482 3.0 98.0 1.0 CE1 A:HIS482 3.1 83.2 1.0 CE1 A:HIS478 3.1 56.9 1.0 HE1 A:HIS482 3.4 0.0 1.0 CB A:CYS462 3.4 58.7 1.0 HB3 A:CYS462 3.4 70.6 1.0 HB3 A:LYS464 3.4 95.9 1.0 HE1 A:HIS478 3.4 68.4 1.0 CB A:CYS465 3.5 61.7 1.0 HB2 A:CYS462 3.5 70.6 1.0 N A:CYS465 3.6 65.8 1.0 HB3 A:CYS465 3.6 74.2 1.0 CA A:CYS465 4.0 64.2 1.0 CG A:HIS478 4.1 53.8 1.0 CG A:HIS482 4.1 83.5 1.0 HB2 A:ARG467 4.1 81.7 1.0 ND1 A:HIS482 4.2 86.0 1.0 ND1 A:HIS478 4.2 56.4 1.0 H A:LYS464 4.2 91.5 1.0 HB2 A:CYS465 4.3 74.2 1.0 CB A:LYS464 4.4 79.7 1.0 O A:CYS465 4.4 56.4 1.0 C A:CYS465 4.5 60.4 1.0 H A:ARG467 4.5 85.2 1.0 HD3 A:LYS464 4.6 98.8 1.0 C A:LYS464 4.6 81.4 1.0 CA A:CYS462 4.8 57.7 1.0 HB2 A:LYS464 4.8 95.9 1.0 N A:LYS464 4.8 76.1 1.0 CA A:LYS464 4.9 80.0 1.0 HA A:CYS465 4.9 77.2 1.0 HD1 A:HIS482 5.0 0.4 1.0 HD1 A:HIS478 5.0 67.9 1.0

Zinc binding site 2 out of 3 in the Mouse KLF4 E446P ZNF1-3 and Mpg/Mpg 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 Mpg/Mpg Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:39.4 occ:1.00 NE2 A:HIS450 2.0 31.0 1.0 NE2 A:HIS454 2.0 45.4 1.0 SG A:CYS432 2.2 32.8 1.0 SG A:CYS437 2.2 49.1 1.0 CD2 A:HIS450 2.7 28.8 1.0 HD2 A:HIS450 2.7 33.6 1.0 CD2 A:HIS454 2.8 43.3 1.0 HB2 A:CYS437 2.9 62.4 1.0 HD2 A:HIS454 2.9 52.1 1.0 CB A:CYS437 2.9 51.9 1.0 HB3 A:CYS437 3.0 62.4 1.0 CE1 A:HIS454 3.2 45.1 1.0 CE1 A:HIS450 3.2 31.1 1.0 CB A:CYS432 3.3 32.3 1.0 HB3 A:CYS432 3.3 38.8 1.0 HB2 A:CYS432 3.4 38.8 1.0 HE1 A:HIS454 3.5 54.3 1.0 HE1 A:HIS450 3.6 36.3 1.0 HB2 A:TRP434 3.6 67.1 1.0 HB2 A:TRP439 3.6 44.4 1.0 HB3 A:TRP434 3.8 67.1 1.0 CG A:HIS450 3.9 27.5 1.0 CG A:HIS454 4.1 45.6 1.0 ND1 A:HIS450 4.1 28.9 1.0 ND1 A:HIS454 4.2 46.9 1.0 CB A:TRP434 4.2 55.8 1.0 H A:TRP439 4.3 50.3 1.0 HD1 A:TRP439 4.4 44.8 1.0 CA A:CYS437 4.4 53.0 1.0 H A:TRP434 4.5 56.2 1.0 CB A:TRP439 4.6 36.8 1.0 HA A:TYR451 4.6 35.1 1.0 HA A:CYS437 4.7 63.8 1.0 HD1 A:TYR451 4.7 37.1 1.0 CA A:CYS432 4.7 34.3 1.0 HB3 A:TRP439 4.9 44.4 1.0 HD1 A:HIS450 5.0 33.8 1.0 CG A:TRP434 5.0 54.3 1.0 HD1 A:HIS454 5.0 56.4 1.0 HA A:CYS432 5.0 41.3 1.0

Zinc binding site 3 out of 3 in the Mouse KLF4 E446P ZNF1-3 and Mpg/Mpg 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 Mpg/Mpg Sequence Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:62.2 occ:1.00 NE2 A:HIS424 2.0 61.8 1.0 NE2 A:HIS420 2.1 58.4 1.0 SG A:CYS407 2.3 65.2 1.0 SG A:CYS402 2.3 51.1 1.0 HB3 A:CYS407 2.7 83.6 1.0 CD2 A:HIS424 2.8 58.6 1.0 CB A:CYS407 2.8 69.5 1.0 HB2 A:CYS407 2.8 83.6 1.0 HD2 A:HIS424 2.9 70.5 1.0 CE1 A:HIS420 2.9 54.1 1.0 HB2 A:CYS402 3.0 66.9 1.0 HB3 A:CYS402 3.0 66.9 1.0 CB A:CYS402 3.0 55.6 1.0 CD2 A:HIS420 3.0 54.5 1.0 CE1 A:HIS424 3.1 60.7 1.0 HE1 A:HIS420 3.1 65.2 1.0 HD2 A:HIS420 3.3 65.6 1.0 HE1 A:HIS424 3.4 73.1 1.0 HB2 A:TYR404 3.6 91.0 1.0 CG A:HIS424 4.0 57.6 1.0 ND1 A:HIS420 4.0 51.9 1.0 ND1 A:HIS424 4.1 59.2 1.0 CG A:HIS420 4.1 51.5 1.0 HB2 A:LYS409 4.2 85.0 1.0 HD23 A:LEU421 4.2 51.7 1.0 CA A:CYS407 4.3 75.6 1.0 HD2 A:LYS409 4.3 86.6 1.0 CA A:CYS402 4.5 58.9 1.0 CB A:TYR404 4.5 75.6 1.0 HD2 A:TYR404 4.5 88.8 1.0 H A:TYR404 4.6 93.5 1.0 HA A:CYS407 4.7 90.9 1.0 H A:LYS409 4.7 91.2 1.0 HD1 A:HIS420 4.8 62.4 1.0 HA A:CYS402 4.8 70.8 1.0 HA A:LEU421 4.8 54.0 1.0 C A:CYS407 4.9 78.7 1.0 HD1 A:HIS424 4.9 71.3 1.0 HB3 A:TYR404 4.9 91.0 1.0 CD2 A:TYR404 4.9 73.8 1.0 CG A:TYR404 4.9 74.5 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