Zinc in PDB 5k5i: Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P65

The structure of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P65, PDB code: 5k5i 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)	23.25 / 2.19
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	45.075, 45.075, 260.450, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 24.5

The binding sites of Zinc atom in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P65 (pdb code 5k5i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P65, PDB code: 5k5i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P65


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 P65 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:74.2 occ:1.00 NE2 A:HIS401 2.0 48.4 1.0 NE2 A:HIS397 2.0 75.7 1.0 SG A:CYS384 2.3 61.2 1.0 SG A:CYS381 2.3 67.7 1.0 CD2 A:HIS401 2.8 53.1 1.0 CD2 A:HIS397 2.9 79.2 1.0 CE1 A:HIS397 3.1 56.4 1.0 CE1 A:HIS401 3.2 58.7 1.0 CB A:CYS384 3.4 70.6 1.0 CB A:CYS381 3.5 69.8 1.0 N A:CYS384 3.9 61.8 1.0 CG A:HIS401 4.0 53.6 1.0 CG A:HIS397 4.0 62.1 1.0 ND1 A:HIS397 4.1 67.1 1.0 CA A:CYS384 4.1 62.9 1.0 ND1 A:HIS401 4.1 57.1 1.0 C A:LEU383 4.5 73.4 1.0 CB A:TYR386 4.5 63.0 1.0 C A:CYS384 4.7 67.7 1.0 SD A:MET398 4.8 82.2 1.0 N A:LEU383 4.8 81.3 1.0 CB A:LEU383 4.8 63.2 1.0 OG1 A:THR400 4.8 60.5 1.0 CA A:CYS381 4.9 81.8 1.0 CA A:LEU383 4.9 70.1 1.0 O A:HIS397 4.9 54.5 1.0 O A:CYS384 5.0 74.7 1.0

Zinc binding site 2 out of 5 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P65


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 P65 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:65.6 occ:1.00 NE2 A:HIS430 2.0 60.3 1.0 NE2 A:HIS425 2.0 61.3 1.0 SG A:CYS412 2.3 59.1 1.0 SG A:CYS409 2.3 57.2 1.0 CD2 A:HIS430 2.8 64.5 1.0 CD2 A:HIS425 2.8 46.1 1.0 CE1 A:HIS430 3.2 60.8 1.0 CE1 A:HIS425 3.2 45.5 1.0 CB A:CYS409 3.2 44.8 1.0 CB A:CYS412 3.7 70.1 1.0 N A:CYS412 3.8 71.6 1.0 CG A:HIS430 4.0 66.8 1.0 CG A:HIS425 4.1 47.7 1.0 ND1 A:HIS430 4.1 64.0 1.0 ND1 A:HIS425 4.2 52.6 1.0 CA A:CYS412 4.3 65.1 1.0 CB A:ILE411 4.5 56.7 1.0 CA A:CYS409 4.7 52.8 1.0 CB A:ALA414 4.7 51.7 1.0 C A:ILE411 4.8 65.7 1.0 N A:ILE411 4.9 64.9 1.0 C A:CYS412 5.0 62.7 1.0 CA A:ILE411 5.0 61.4 1.0

Zinc binding site 3 out of 5 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P65


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 P65 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:57.9 occ:1.00 NE2 A:HIS460 2.0 51.4 1.0 NE2 A:HIS455 2.0 59.9 1.0 SG A:CYS439 2.2 52.3 1.0 SG A:CYS442 2.3 54.2 1.0 CD2 A:HIS455 2.7 46.5 1.0 CD2 A:HIS460 2.9 55.9 1.0 CE1 A:HIS460 3.1 56.2 1.0 CB A:CYS439 3.2 44.8 1.0 CE1 A:HIS455 3.2 55.8 1.0 CB A:CYS442 3.4 51.9 1.0 N A:CYS442 3.8 57.7 1.0 CG A:HIS455 4.0 54.6 1.0 CG A:HIS460 4.1 47.4 1.0 ND1 A:HIS460 4.1 48.3 1.0 CA A:CYS442 4.1 44.2 1.0 ND1 A:HIS455 4.2 56.3 1.0 C A:HIS441 4.4 61.2 1.0 CA A:CYS439 4.6 53.7 1.0 CB A:THR444 4.7 51.3 1.0 OG1 A:THR444 4.7 71.8 1.0 C A:CYS442 4.7 61.9 1.0 CB A:HIS441 4.7 62.3 1.0 N A:HIS441 4.7 59.6 1.0 CA A:HIS441 4.9 56.4 1.0 CD2 A:LEU456 5.0 55.5 1.0

Zinc binding site 4 out of 5 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P65


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 P65 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:0.1 occ:1.00 NE2 A:HIS489 2.0 0.4 1.0 NE2 A:HIS485 2.0 84.4 1.0 SG A:CYS472 2.3 93.3 1.0 SG A:CYS469 2.3 82.4 1.0 CD2 A:HIS485 2.6 82.0 1.0 CD2 A:HIS489 2.9 0.2 1.0 CE1 A:HIS489 3.0 0.1 1.0 CE1 A:HIS485 3.1 89.1 1.0 CB A:CYS469 3.4 85.9 1.0 CB A:CYS472 3.7 90.0 1.0 CG A:HIS485 3.8 73.3 1.0 N A:CYS472 3.8 0.1 1.0 ND1 A:HIS485 4.0 80.8 1.0 CG A:HIS489 4.1 0.9 1.0 ND1 A:HIS489 4.1 0.1 1.0 CA A:CYS472 4.3 90.8 1.0 O A:HIS485 4.5 78.2 1.0 CB A:TYR471 4.6 0.0 1.0 CB A:ALA474 4.6 74.3 1.0 CA A:CYS469 4.8 83.5 1.0 C A:CYS472 4.9 98.3 1.0 C A:TYR471 4.9 0.8 1.0 C A:HIS485 4.9 70.6 1.0 N A:TYR471 4.9 0.4 1.0

Zinc binding site 5 out of 5 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P65


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF5-8 and Dna Complex Structure in Space Group P65 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:84.8 occ:1.00 OE2 A:GLU478 2.0 84.4 1.0 OE1 A:GLU478 2.0 87.2 1.0 NE2 A:HIS441 2.1 75.2 1.0 CD A:GLU478 2.1 55.3 1.0 CE1 A:HIS441 2.9 69.2 1.0 CD2 A:HIS441 3.2 73.5 1.0 CG A:GLU478 3.5 60.3 1.0 ND1 A:HIS441 4.1 63.1 1.0 CG A:HIS441 4.2 67.6 1.0 CB A:GLU478 4.3 60.1 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