Zinc in PDB 5k5h: Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and Dna Complex Structure

The structure of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and Dna Complex Structure, PDB code: 5k5h 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)	50.32 / 3.11
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	52.800, 52.800, 166.170, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 26.4

The binding sites of Zinc atom in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and Dna Complex Structure (pdb code 5k5h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and Dna Complex Structure, PDB code: 5k5h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and 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 Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:72.4 occ:1.00 NE2 A:HIS369 2.0 77.1 1.0 NE2 A:HIS373 2.0 0.4 1.0 SG A:CYS356 2.3 98.7 1.0 SG A:CYS353 2.3 0.4 1.0 CE1 A:HIS373 2.9 0.9 1.0 CD2 A:HIS369 2.9 73.5 1.0 CD2 A:HIS373 2.9 0.8 1.0 CE1 A:HIS369 3.1 71.2 1.0 N A:CYS356 3.1 0.5 1.0 CB A:CYS356 3.2 0.9 1.0 CB A:MET355 3.5 0.8 1.0 CA A:CYS356 3.7 0.6 1.0 CB A:CYS353 3.8 0.9 1.0 ND1 A:HIS373 3.9 0.5 1.0 CG A:HIS373 4.0 0.0 1.0 C A:MET355 4.0 0.5 1.0 CG A:HIS369 4.1 69.2 1.0 ND1 A:HIS369 4.2 68.3 1.0 CA A:MET355 4.2 0.9 1.0 CG A:MET355 4.4 0.3 1.0 N A:MET355 4.4 0.3 1.0 C A:CYS356 4.4 81.3 1.0 CB A:TYR358 4.6 88.3 1.0 N A:ASP357 4.7 97.2 1.0 N A:TYR358 5.0 98.1 1.0

Zinc binding site 2 out of 4 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and 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 Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:76.9 occ:1.00 NE2 A:HIS401 2.0 98.6 1.0 NE2 A:HIS397 2.1 99.3 1.0 SG A:CYS381 2.3 0.3 1.0 SG A:CYS384 2.3 0.6 1.0 CE1 A:HIS401 2.6 94.5 1.0 CE1 A:HIS397 2.8 90.5 1.0 CD2 A:HIS397 3.0 90.4 1.0 CD2 A:HIS401 3.2 90.0 1.0 CB A:CYS384 3.5 0.5 1.0 CB A:CYS381 3.5 0.5 1.0 N A:CYS384 3.6 94.8 1.0 ND1 A:HIS401 3.8 91.8 1.0 ND1 A:HIS397 3.8 87.5 1.0 CG A:HIS397 4.0 82.5 1.0 CA A:CYS384 4.1 95.1 1.0 CG A:HIS401 4.1 87.1 1.0 CB A:LEU383 4.3 96.4 1.0 C A:LEU383 4.3 0.0 1.0 N A:LEU383 4.6 0.3 1.0 CA A:LEU383 4.6 99.8 1.0 O A:HIS397 4.6 61.6 1.0 CB A:TYR386 4.7 75.6 1.0 C A:CYS384 4.8 93.3 1.0 SD A:MET398 4.9 0.7 1.0 CA A:CYS381 4.9 0.3 1.0

Zinc binding site 3 out of 4 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and 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 Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:62.9 occ:1.00 NE2 A:HIS430 2.0 0.1 1.0 NE2 A:HIS425 2.0 69.2 1.0 SG A:CYS409 2.3 73.0 1.0 SG A:CYS412 2.3 67.5 1.0 CD2 A:HIS430 2.7 0.6 1.0 CE1 A:HIS425 2.7 66.0 1.0 CD2 A:HIS425 3.1 62.0 1.0 CE1 A:HIS430 3.2 0.2 1.0 CB A:CYS412 3.3 71.2 1.0 CB A:CYS409 3.5 74.6 1.0 N A:CYS412 3.6 64.0 1.0 ND1 A:HIS425 3.8 62.8 1.0 CG A:HIS430 3.9 0.1 1.0 CG A:HIS425 4.1 52.4 1.0 CA A:CYS412 4.1 67.2 1.0 ND1 A:HIS430 4.1 0.4 1.0 CB A:ILE411 4.3 61.8 1.0 CD1 A:ILE426 4.4 40.8 1.0 C A:ILE411 4.7 57.3 1.0 CG2 A:ILE411 4.8 68.3 1.0 CA A:ILE411 4.9 57.9 1.0 C A:CYS412 4.9 65.7 1.0 CA A:CYS409 4.9 73.3 1.0 CB A:ALA414 5.0 40.9 1.0 N A:ILE411 5.0 61.1 1.0

Zinc binding site 4 out of 4 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF4-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:82.6 occ:1.00 NE2 A:HIS460 2.0 0.2 1.0 NE2 A:HIS455 2.0 0.4 1.0 SG A:CYS439 2.3 0.4 1.0 SG A:CYS442 2.3 0.4 1.0 CD2 A:HIS455 2.8 0.2 1.0 CD2 A:HIS460 2.9 0.8 1.0 CB A:CYS442 3.1 0.3 1.0 CE1 A:HIS460 3.1 0.4 1.0 CE1 A:HIS455 3.2 0.2 1.0 CB A:CYS439 3.7 0.5 1.0 CG A:HIS455 4.1 0.2 1.0 CG A:HIS460 4.1 0.6 1.0 N A:CYS442 4.1 0.2 1.0 CG A:GLN459 4.1 96.8 1.0 ND1 A:HIS460 4.2 0.6 1.0 ND1 A:HIS455 4.2 0.1 1.0 CA A:CYS442 4.2 0.3 1.0 CD2 A:LEU456 4.3 0.0 1.0 C A:HIS441 4.4 0.2 1.0 CB A:GLN459 4.6 93.0 1.0 O A:HIS441 4.7 0.6 1.0 CG2 A:THR444 4.9 0.7 1.0 N A:HIS441 4.9 0.7 1.0

H.Hashimoto, D.Wang, J.R.Horton, X.Zhang, V.G.Corces, X.Cheng. Structural Basis For the Versatile and Methylation-Dependent Binding of Ctcf to Dna. Mol. Cell V. 66 711 2017.
ISSN: ISSN 1097-4164
PubMed: 28529057
DOI: 10.1016/J.MOLCEL.2017.05.004