Zinc in PDB 5k5j: Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P41212

The structure of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P41212, PDB code: 5k5j 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)	27.87 / 2.29
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.903, 58.903, 172.264, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.4

The binding sites of Zinc atom in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P41212 (pdb code 5k5j). 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) ZNF5-8 and Dna Complex Structure in Space Group P41212, PDB code: 5k5j:
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) ZNF5-8 and Dna Complex Structure in Space Group P41212


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) ZNF5-8 and Dna Complex Structure in Space Group P41212 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:48.9 occ:1.00 NE2 A:HIS401 2.0 51.9 1.0 NE2 A:HIS397 2.1 60.7 1.0 SG A:CYS384 2.3 44.5 1.0 SG A:CYS381 2.3 46.6 1.0 CE1 A:HIS401 2.9 51.1 1.0 CE1 A:HIS397 3.0 53.1 1.0 CD2 A:HIS401 3.0 53.4 1.0 CD2 A:HIS397 3.1 52.8 1.0 CB A:CYS384 3.2 38.9 1.0 CB A:CYS381 3.3 48.5 1.0 N A:CYS384 3.5 49.5 1.0 CA A:CYS384 3.9 43.4 1.0 ND1 A:HIS401 4.0 46.0 1.0 CG A:HIS401 4.1 52.1 1.0 ND1 A:HIS397 4.1 47.8 1.0 CG A:HIS397 4.2 51.4 1.0 CB A:TYR386 4.3 47.9 1.0 C A:CYS384 4.4 51.7 1.0 CB A:LEU383 4.5 47.0 1.0 C A:LEU383 4.5 52.2 1.0 O A:CYS384 4.7 55.6 1.0 CA A:CYS381 4.7 42.5 1.0 N A:TYR386 4.7 43.0 1.0 N A:LEU383 4.8 48.7 1.0 CA A:LEU383 4.8 52.3 1.0 SD A:MET398 5.0 66.6 1.0

Zinc binding site 2 out of 4 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P41212


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) ZNF5-8 and Dna Complex Structure in Space Group P41212 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:74.3 occ:1.00 NE2 A:HIS430 2.0 83.7 1.0 NE2 A:HIS425 2.0 85.6 1.0 SG A:CYS412 2.3 69.5 1.0 SG A:CYS409 2.3 72.2 1.0 CD2 A:HIS430 2.8 71.0 1.0 CD2 A:HIS425 2.9 70.9 1.0 CE1 A:HIS430 3.1 80.2 1.0 CE1 A:HIS425 3.1 70.3 1.0 CB A:CYS409 3.2 71.4 1.0 CB A:CYS412 3.4 72.5 1.0 N A:CYS412 3.7 82.5 1.0 CG A:HIS430 4.0 75.5 1.0 CA A:CYS412 4.1 82.6 1.0 CG A:HIS425 4.1 69.0 1.0 ND1 A:HIS430 4.1 83.2 1.0 ND1 A:HIS425 4.2 71.2 1.0 CB A:ILE411 4.6 83.9 1.0 CA A:CYS409 4.6 73.3 1.0 C A:CYS412 4.7 91.1 1.0 N A:HIS413 4.8 88.4 1.0 C A:ILE411 4.8 90.9 1.0 CB A:ALA414 4.9 67.0 1.0 CG1 A:ILE426 5.0 63.4 1.0 N A:ILE411 5.0 87.8 1.0

Zinc binding site 3 out of 4 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P41212


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) ZNF5-8 and Dna Complex Structure in Space Group P41212 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:55.0 occ:1.00 NE2 A:HIS460 2.0 60.2 1.0 NE2 A:HIS455 2.0 60.6 1.0 SG A:CYS442 2.2 56.6 1.0 SG A:CYS439 2.3 57.7 1.0 CD2 A:HIS455 2.9 48.5 1.0 CD2 A:HIS460 3.0 58.1 1.0 CE1 A:HIS460 3.0 59.2 1.0 CE1 A:HIS455 3.1 52.5 1.0 CB A:CYS439 3.2 62.1 1.0 CB A:CYS442 3.4 56.8 1.0 N A:CYS442 3.7 69.8 1.0 CA A:CYS442 4.1 63.1 1.0 ND1 A:HIS460 4.1 59.9 1.0 CG A:HIS460 4.1 58.2 1.0 CG A:HIS455 4.1 54.1 1.0 ND1 A:HIS455 4.2 47.1 1.0 C A:HIS441 4.3 74.9 1.0 CB A:HIS441 4.5 54.4 1.0 CA A:CYS439 4.6 63.9 1.0 C A:CYS442 4.7 71.4 1.0 N A:HIS441 4.7 72.7 1.0 CA A:HIS441 4.7 67.8 1.0 CB A:THR444 4.8 64.1 1.0 O A:CYS442 4.8 72.1 1.0 OG1 A:THR444 4.9 60.8 1.0 O A:HIS441 4.9 80.6 1.0

Zinc binding site 4 out of 4 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P41212


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) ZNF5-8 and Dna Complex Structure in Space Group P41212 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:50.0 occ:1.00 NE2 A:HIS489 2.0 62.0 1.0 NE2 A:HIS485 2.1 62.0 1.0 SG A:CYS472 2.2 48.7 1.0 SG A:CYS469 2.3 51.2 1.0 CD2 A:HIS485 2.9 52.5 1.0 CD2 A:HIS489 3.0 59.5 1.0 CE1 A:HIS489 3.0 53.5 1.0 CE1 A:HIS485 3.1 56.2 1.0 CB A:CYS469 3.1 44.2 1.0 CB A:CYS472 3.3 42.0 1.0 N A:CYS472 3.7 45.5 1.0 CA A:CYS472 4.0 44.8 1.0 CG A:HIS485 4.1 56.0 1.0 ND1 A:HIS489 4.1 60.2 1.0 ND1 A:HIS485 4.1 56.6 1.0 CG A:HIS489 4.1 61.3 1.0 C A:TYR471 4.3 52.4 1.0 CB A:TYR471 4.6 54.3 1.0 C A:CYS472 4.6 54.0 1.0 CA A:CYS469 4.6 52.8 1.0 CB A:ALA474 4.6 49.9 1.0 N A:TYR471 4.8 52.0 1.0 CA A:TYR471 4.8 53.1 1.0 O A:CYS472 4.8 50.2 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