Zinc in PDB 4m9e: Structure of KLF4 Zinc Finger Dna Binding Domain in Complex with Methylated Dna

The structure of Structure of KLF4 Zinc Finger Dna Binding Domain in Complex with Methylated Dna, PDB code: 4m9e was solved by Y.Liu, Y.O.Olanrewaju, R.M.Blumenthal, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.44 / 1.85
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	48.705, 48.705, 131.015, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.4

The binding sites of Zinc atom in the Structure of KLF4 Zinc Finger Dna Binding Domain in Complex with Methylated Dna (pdb code 4m9e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of KLF4 Zinc Finger Dna Binding Domain in Complex with Methylated Dna, PDB code: 4m9e:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of KLF4 Zinc Finger Dna Binding Domain in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of KLF4 Zinc Finger Dna Binding Domain in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:19.6 occ:1.00 NE2 A:HIS482 2.0 20.8 1.0 NE2 A:HIS478 2.0 16.5 1.0 SG A:CYS465 2.3 20.3 1.0 SG A:CYS462 2.3 16.8 1.0 CE1 A:HIS482 3.0 23.0 1.0 CD2 A:HIS478 3.0 15.6 1.0 CE1 A:HIS478 3.0 19.1 1.0 CD2 A:HIS482 3.0 21.6 1.0 CB A:CYS462 3.2 16.4 1.0 CB A:CYS465 3.4 20.0 1.0 N A:CYS465 3.6 19.6 1.0 CA A:CYS465 4.0 21.8 1.0 ND1 A:HIS482 4.1 23.0 1.0 ND1 A:HIS478 4.1 16.5 1.0 CG A:HIS478 4.1 15.3 1.0 C A:LYS464 4.1 28.7 1.0 CG A:HIS482 4.2 22.2 1.0 CB A:LYS464 4.5 22.8 1.0 C A:CYS465 4.5 25.4 1.0 CA A:CYS462 4.7 16.3 1.0 CA A:LYS464 4.7 21.3 1.0 N A:LYS464 4.7 19.9 1.0 O A:LYS464 4.7 27.8 1.0 O A:CYS465 4.8 24.0 1.0 SD A:MET479 4.9 46.8 1.0 CB A:ARG467 4.9 24.4 1.0

Zinc binding site 2 out of 3 in the Structure of KLF4 Zinc Finger Dna Binding Domain in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of KLF4 Zinc Finger Dna Binding Domain in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:13.3 occ:1.00 NE2 A:HIS450 2.0 12.3 1.0 NE2 A:HIS454 2.0 14.0 1.0 SG A:CYS432 2.3 13.2 1.0 SG A:CYS437 2.3 14.5 1.0 CD2 A:HIS454 2.9 13.8 1.0 CD2 A:HIS450 3.0 11.7 1.0 CE1 A:HIS450 3.1 12.2 1.0 CB A:CYS437 3.1 15.0 1.0 CE1 A:HIS454 3.1 20.1 1.0 CB A:CYS432 3.2 12.6 1.0 CB A:TRP434 3.9 15.5 1.0 CG A:HIS454 4.1 15.4 1.0 CG A:HIS450 4.1 11.3 1.0 ND1 A:HIS450 4.1 11.7 1.0 ND1 A:HIS454 4.2 15.1 1.0 CB A:TRP439 4.4 12.2 1.0 CA A:CYS437 4.6 16.4 1.0 CA A:CYS432 4.6 12.7 1.0 CG A:TRP434 4.7 16.3 1.0 CD1 A:TRP439 4.8 30.4 1.0 CG A:TRP439 4.9 20.9 1.0 N A:TRP439 4.9 14.3 1.0 N A:TRP434 4.9 15.4 1.0

Zinc binding site 3 out of 3 in the Structure of KLF4 Zinc Finger Dna Binding Domain in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of KLF4 Zinc Finger Dna Binding Domain in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:20.8 occ:1.00 NE2 A:HIS420 2.0 19.7 1.0 NE2 A:HIS424 2.1 26.0 1.0 SG A:CYS402 2.2 21.0 1.0 SG A:CYS407 2.3 24.0 1.0 CD2 A:HIS424 3.0 23.1 1.0 CE1 A:HIS420 3.0 21.9 1.0 CD2 A:HIS420 3.0 18.2 1.0 CB A:CYS407 3.1 29.5 1.0 CB A:CYS402 3.1 23.6 1.0 CE1 A:HIS424 3.1 24.1 1.0 ND1 A:HIS420 4.1 17.7 1.0 CG A:HIS420 4.1 17.6 1.0 CG A:HIS424 4.1 25.0 1.0 ND1 A:HIS424 4.2 24.9 1.0 CA A:CYS402 4.5 22.8 1.0 CA A:CYS407 4.5 34.5 1.0 CB A:LYS409 4.7 33.8 1.0 CB A:TYR404 4.7 22.6 1.0 CG A:LYS409 4.8 37.5 1.0 O A:TYR404 4.9 33.9 1.0 N A:LYS409 5.0 38.6 1.0

Y.Liu, Y.O.Olanrewaju, Y.Zheng, H.Hashimoto, R.M.Blumenthal, X.Zhang, X.Cheng. Structural Basis For KLF4 Recognition of Methylated Dna. Nucleic Acids Res. V. 42 4859 2014.
ISSN: ISSN 0305-1048
PubMed: 24520114
DOI: 10.1093/NAR/GKU134