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

The structure of Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form I, PDB code: 5kea 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)	47.41 / 2.46
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.850, 50.850, 131.050, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28.3

The binding sites of Zinc atom in the Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form I (pdb code 5kea). 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 I, PDB code: 5kea:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mouse KLF4 ZNF1-3 (E446D) and Cpg/Cpg Sequence Dna Complex Structure: Form I


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 I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:47.9 occ:1.00 NE2 A:HIS424 2.0 43.5 1.0 NE2 A:HIS420 2.0 35.1 1.0 SG A:CYS407 2.1 91.7 1.0 SG A:CYS402 2.2 66.4 1.0 HB2 A:CYS407 2.4 0.3 1.0 CB A:CYS407 2.5 93.7 1.0 HB3 A:CYS407 2.5 0.3 1.0 HB3 A:CYS402 2.8 80.3 1.0 CB A:CYS402 2.9 67.0 1.0 CE1 A:HIS420 2.9 34.4 1.0 HB2 A:CYS402 2.9 80.3 1.0 CE1 A:HIS424 2.9 39.8 1.0 HE1 A:HIS420 3.0 41.3 1.0 CD2 A:HIS424 3.1 42.7 1.0 HE1 A:HIS424 3.1 47.7 1.0 CD2 A:HIS420 3.1 35.3 1.0 HD2 A:HIS424 3.3 51.2 1.0 HD2 A:HIS420 3.4 42.3 1.0 HB2 A:TYR404 3.5 99.2 1.0 H A:GLY408 3.8 0.4 1.0 CA A:CYS407 4.0 94.4 1.0 ND1 A:HIS420 4.0 35.1 1.0 ND1 A:HIS424 4.1 45.8 1.0 CG A:HIS420 4.2 35.7 1.0 CG A:HIS424 4.2 45.8 1.0 HD23 A:LEU421 4.3 47.4 1.0 HA A:CYS407 4.3 0.2 1.0 H A:TYR404 4.3 91.6 1.0 CA A:CYS402 4.4 67.5 1.0 HD2 A:TYR404 4.4 98.8 1.0 N A:GLY408 4.5 92.0 1.0 CB A:TYR404 4.5 82.7 1.0 HG3 A:LYS409 4.6 79.2 1.0 H A:CYS407 4.7 0.9 1.0 HA A:CYS402 4.7 81.0 1.0 C A:CYS407 4.8 93.4 1.0 H A:LYS409 4.8 91.7 1.0 HD1 A:HIS420 4.8 42.1 1.0 HB2 A:LYS409 4.8 78.5 1.0 N A:CYS407 4.8 94.9 1.0 HD1 A:HIS424 4.9 54.9 1.0 HB3 A:TYR404 4.9 99.2 1.0 HD2 A:LYS409 4.9 63.4 1.0 C A:CYS402 4.9 68.7 1.0 CD2 A:TYR404 4.9 82.4 1.0

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


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 I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:40.6 occ:1.00 NE2 A:HIS454 2.0 49.7 1.0 NE2 A:HIS450 2.0 44.7 1.0 SG A:CYS432 2.2 41.4 1.0 SG A:CYS437 2.3 33.2 1.0 CD2 A:HIS454 2.8 45.8 1.0 HD2 A:HIS454 2.8 54.9 1.0 CE1 A:HIS450 3.0 43.2 1.0 CD2 A:HIS450 3.0 43.9 1.0 HB3 A:CYS437 3.0 52.6 1.0 CB A:CYS437 3.1 43.9 1.0 HB2 A:CYS437 3.1 52.6 1.0 HE1 A:HIS450 3.1 51.8 1.0 CE1 A:HIS454 3.2 45.8 1.0 HD2 A:HIS450 3.2 52.6 1.0 HB3 A:CYS432 3.3 50.0 1.0 CB A:CYS432 3.3 41.7 1.0 HB3 A:TRP434 3.4 60.3 1.0 HB2 A:CYS432 3.5 50.0 1.0 HE1 A:HIS454 3.5 54.9 1.0 HB2 A:TRP439 3.6 41.6 1.0 HB2 A:TRP434 3.7 60.3 1.0 CB A:TRP434 4.0 50.3 1.0 CG A:HIS454 4.0 46.3 1.0 ND1 A:HIS450 4.1 44.9 1.0 ND1 A:HIS454 4.1 47.4 1.0 CG A:HIS450 4.1 40.3 1.0 H A:TRP439 4.2 45.3 1.0 H A:TRP434 4.3 52.7 1.0 HD2 A:TYR451 4.4 45.8 1.0 CA A:CYS437 4.5 49.0 1.0 CB A:TRP439 4.5 34.8 1.0 HD1 A:TRP439 4.6 44.8 1.0 CA A:CYS432 4.7 41.8 1.0 HA A:TYR451 4.7 47.2 1.0 CG A:TRP434 4.8 52.4 1.0 HZ3 A:LYS453 4.8 66.7 1.0 HA A:CYS437 4.8 58.8 1.0 HD1 A:HIS450 4.8 53.8 1.0 HB3 A:TRP439 4.9 41.6 1.0 HE2 A:PHE441 4.9 48.6 1.0 H A:GLY438 4.9 35.5 1.0 HD1 A:HIS454 4.9 56.9 1.0 N A:TRP439 4.9 37.8 1.0

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


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 I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:70.4 occ:1.00 HB3 A:CYS465 1.5 0.1 1.0 NE2 A:HIS478 2.0 70.5 1.0 NE2 A:HIS482 2.0 86.0 1.0 CB A:CYS465 2.1 95.2 1.0 HB2 A:CYS465 2.1 0.1 1.0 SG A:CYS462 2.4 59.7 1.0 HG A:CYS465 2.7 0.1 1.0 SG A:CYS465 2.9 87.6 1.0 CD2 A:HIS478 3.0 64.4 1.0 CD2 A:HIS482 3.0 80.3 1.0 CE1 A:HIS482 3.0 88.0 1.0 CE1 A:HIS478 3.0 71.1 1.0 H A:CYS465 3.2 0.2 1.0 HD2 A:HIS478 3.2 77.2 1.0 HD2 A:HIS482 3.2 96.3 1.0 HB3 A:CYS462 3.2 0.3 1.0 HE1 A:HIS482 3.2 0.6 1.0 HE1 A:HIS478 3.2 85.3 1.0 CB A:CYS462 3.3 91.1 1.0 CA A:CYS465 3.4 80.4 1.0 HB2 A:ARG467 3.5 84.6 1.0 HB2 A:CYS462 3.5 0.3 1.0 N A:CYS465 3.6 91.0 1.0 H A:ARG467 3.7 86.7 1.0 HA A:CYS465 4.1 96.5 1.0 C A:CYS465 4.1 71.1 1.0 ND1 A:HIS482 4.1 86.2 1.0 ND1 A:HIS478 4.1 68.2 1.0 CG A:HIS482 4.1 80.2 1.0 CG A:HIS478 4.1 60.9 1.0 HB2 A:LYS464 4.3 0.8 1.0 H A:ASP466 4.4 0.2 1.0 N A:ASP466 4.5 87.7 1.0 CB A:ARG467 4.5 70.5 1.0 N A:ARG467 4.5 72.3 1.0 CA A:CYS462 4.8 92.8 1.0 HG3 A:ARG467 4.8 93.2 1.0 O A:CYS465 4.8 73.0 1.0 C A:LYS464 4.9 84.6 1.0 HD1 A:HIS482 4.9 0.3 1.0 HD1 A:HIS478 4.9 81.7 1.0 HB3 A:ARG467 4.9 84.6 1.0 O A:ARG467 4.9 59.1 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