Zinc in PDB 8ssu: Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna

The structure of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna, PDB code: 8ssu was solved by J.R.Horton, J.Yang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.34 / 2.89
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.464, 80.464, 187.598, 90, 90, 120
R / Rfree (%)	20 / 24

The binding sites of Zinc atom in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna (pdb code 8ssu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna, PDB code: 8ssu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:97.7 occ:1.00 NE2 A:HIS340 2.0 91.7 1.0 NE2 A:HIS345 2.0 113.2 1.0 SG A:CYS327 2.2 95.7 1.0 SG A:CYS324 2.3 109.5 1.0 CE1 A:HIS345 2.8 112.1 1.0 CD2 A:HIS340 2.8 85.7 1.0 CD2 A:HIS345 2.9 112.4 1.0 CE1 A:HIS340 3.1 87.8 1.0 CB A:CYS324 3.4 113.8 1.0 CB A:CYS327 3.7 111.1 1.0 ND1 A:HIS345 3.7 108.1 1.0 CG A:HIS345 3.8 109.2 1.0 CG A:HIS340 4.0 82.7 1.0 ND1 A:HIS340 4.1 78.8 1.0 N A:CYS327 4.3 119.9 1.0 CG A:MET329 4.5 106.1 1.0 CA A:CYS327 4.6 106.5 1.0 CB A:MET329 4.6 99.2 1.0 CA A:CYS324 4.8 98.2 1.0 C A:ASP326 4.8 122.0 1.0 CB A:ASP326 5.0 117.3 1.0 CG A:ARG341 5.0 95.9 1.0

Zinc binding site 2 out of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:70.4 occ:1.00 NE2 A:HIS373 2.0 80.4 1.0 NE2 A:HIS369 2.0 59.3 1.0 SG A:CYS356 2.2 61.8 1.0 SG A:CYS353 2.3 96.3 1.0 CD2 A:HIS373 2.5 69.1 1.0 CD2 A:HIS369 2.9 80.0 1.0 CE1 A:HIS369 3.1 76.2 1.0 CE1 A:HIS373 3.3 85.2 1.0 CB A:CYS353 3.3 83.5 1.0 CB A:CYS356 3.3 63.1 1.0 N A:CYS356 3.6 88.0 1.0 CG A:HIS373 3.8 72.1 1.0 CA A:CYS356 4.0 66.3 1.0 CG A:HIS369 4.1 68.0 1.0 ND1 A:HIS373 4.1 75.1 1.0 ND1 A:HIS369 4.1 67.6 1.0 CB A:MET355 4.3 77.2 1.0 C A:MET355 4.3 76.0 1.0 CB A:TYR358 4.5 62.1 1.0 N A:MET355 4.6 78.7 1.0 CA A:MET355 4.6 82.0 1.0 C A:CYS356 4.6 90.0 1.0 CA A:CYS353 4.7 79.3 1.0 O A:CYS356 5.0 94.6 1.0

Zinc binding site 3 out of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn704 b:81.5 occ:1.00 NE2 A:HIS401 2.0 94.9 1.0 NE2 A:HIS397 2.0 69.9 1.0 SG A:CYS384 2.2 73.4 1.0 SG A:CYS381 2.3 104.6 1.0 CD2 A:HIS401 2.9 86.5 1.0 CD2 A:HIS397 2.9 81.4 1.0 CE1 A:HIS401 3.0 96.4 1.0 CE1 A:HIS397 3.1 76.1 1.0 CB A:CYS381 3.3 87.8 1.0 CB A:CYS384 3.4 79.5 1.0 N A:CYS384 3.6 107.8 1.0 CG A:HIS401 4.0 90.1 1.0 ND1 A:HIS401 4.0 92.6 1.0 CA A:CYS384 4.0 86.3 1.0 CB A:LEU383 4.1 98.4 1.0 CG A:HIS397 4.1 74.8 1.0 ND1 A:HIS397 4.1 77.5 1.0 CB A:TYR386 4.4 72.0 1.0 C A:LEU383 4.5 109.4 1.0 C A:CYS384 4.6 102.4 1.0 CA A:LEU383 4.6 106.2 1.0 N A:LEU383 4.7 95.4 1.0 CA A:CYS381 4.8 92.1 1.0 O A:CYS384 4.9 107.4 1.0 CD2 A:LEU383 4.9 106.7 1.0

Zinc binding site 4 out of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn705 b:114.0 occ:1.00 NE2 A:HIS430 2.0 101.9 1.0 NE2 A:HIS425 2.0 108.5 1.0 SG A:CYS412 2.3 109.7 1.0 SG A:CYS409 2.4 134.4 1.0 CD2 A:HIS425 2.8 105.5 1.0 CD2 A:HIS430 3.0 104.9 1.0 CE1 A:HIS430 3.0 111.0 1.0 CE1 A:HIS425 3.2 113.0 1.0 CB A:CYS412 3.4 111.5 1.0 CB A:CYS409 3.5 120.6 1.0 N A:CYS412 3.7 124.6 1.0 CG A:HIS425 4.0 88.8 1.0 ND1 A:HIS430 4.1 108.7 1.0 CG A:HIS430 4.1 108.2 1.0 CA A:CYS412 4.1 121.5 1.0 ND1 A:HIS425 4.2 108.1 1.0 CB A:ILE411 4.3 122.3 1.0 C A:ILE411 4.7 125.3 1.0 CG2 A:ILE426 4.7 98.6 1.0 CA A:CYS409 4.9 117.3 1.0 C A:CYS412 4.9 128.3 1.0 N A:ILE411 4.9 113.7 1.0 CA A:ILE411 4.9 122.5 1.0 CG2 A:ILE411 5.0 113.3 1.0

Zinc binding site 5 out of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn706 b:76.3 occ:1.00 NE2 A:HIS455 2.0 69.8 1.0 NE2 A:HIS460 2.0 72.2 1.0 SG A:CYS442 2.3 103.8 1.0 SG A:CYS439 2.3 88.0 1.0 CD2 A:HIS455 2.8 80.9 1.0 CE1 A:HIS460 2.9 85.9 1.0 CD2 A:HIS460 3.0 81.8 1.0 CE1 A:HIS455 3.2 83.5 1.0 CB A:CYS439 3.2 90.4 1.0 CB A:CYS442 3.4 95.5 1.0 N A:CYS442 3.8 94.3 1.0 ND1 A:HIS460 4.0 81.3 1.0 CG A:HIS455 4.0 77.8 1.0 CG A:HIS460 4.1 81.5 1.0 CA A:CYS442 4.1 87.2 1.0 ND1 A:HIS455 4.1 90.8 1.0 CG2 A:THR444 4.3 97.5 1.0 CB A:HIS441 4.7 103.2 1.0 O A:CYS442 4.7 96.4 1.0 C A:CYS442 4.7 83.5 1.0 CA A:CYS439 4.7 93.7 1.0 C A:HIS441 4.7 88.9 1.0 CD2 A:LEU456 4.8 79.8 1.0 N A:HIS441 5.0 97.4 1.0

Zinc binding site 6 out of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn707 b:135.5 occ:1.00 NE2 A:HIS485 2.0 114.6 1.0 NE2 A:HIS489 2.0 146.1 1.0 SG A:CYS472 2.1 124.4 1.0 SG A:CYS469 2.4 103.2 1.0 CD2 A:HIS485 2.5 113.3 1.0 CD2 A:HIS489 2.9 144.3 1.0 CE1 A:HIS489 3.1 142.5 1.0 CE1 A:HIS485 3.2 116.0 1.0 CB A:CYS472 3.5 106.3 1.0 CB A:CYS469 3.5 121.9 1.0 CG A:HIS485 3.7 107.7 1.0 N A:CYS472 3.9 115.5 1.0 ND1 A:HIS485 4.0 110.9 1.0 CG A:HIS489 4.1 139.7 1.0 ND1 A:HIS489 4.2 138.7 1.0 CA A:CYS472 4.3 112.5 1.0 O A:HIS485 4.5 114.9 1.0 CB A:TYR471 4.5 104.7 1.0 C A:TYR471 4.6 116.4 1.0 C A:HIS485 4.8 101.6 1.0 N A:TYR471 4.9 115.1 1.0 CA A:GLN486 4.9 91.5 1.0 CA A:TYR471 4.9 112.0 1.0 CA A:CYS469 4.9 117.1 1.0 CB A:HIS485 5.0 102.7 1.0 N A:GLN486 5.0 90.4 1.0

Zinc binding site 7 out of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn708 b:117.6 occ:1.00 NE2 A:HIS513 2.0 87.5 1.0 NE2 A:HIS517 2.0 134.1 1.0 SG A:CYS500 2.3 92.5 1.0 SG A:CYS497 2.3 190.5 1.0 CD2 A:HIS517 2.8 126.0 1.0 CD2 A:HIS513 2.8 88.6 1.0 CE1 A:HIS517 3.0 123.7 1.0 CE1 A:HIS513 3.1 89.0 1.0 CB A:CYS500 3.4 103.2 1.0 N A:CYS500 3.5 122.3 1.0 CB A:GLN499 3.9 122.2 1.0 CG A:HIS517 3.9 119.3 1.0 CB A:CYS497 3.9 115.3 1.0 CA A:CYS500 4.0 110.6 1.0 ND1 A:HIS517 4.0 123.4 1.0 O A:CYS497 4.0 137.1 1.0 C A:GLN499 4.0 120.0 1.0 CG A:HIS513 4.1 88.4 1.0 ND1 A:HIS513 4.2 86.8 1.0 CA A:GLN499 4.3 117.1 1.0 N A:GLN499 4.5 125.0 1.0 CB A:TYR502 4.5 97.5 1.0 C A:CYS497 4.6 130.4 1.0 C A:CYS500 4.6 115.2 1.0 O A:GLN499 4.8 114.8 1.0 CA A:CYS497 4.8 136.8 1.0 CG A:GLN499 4.9 112.9 1.0 O A:HIS513 4.9 105.2 1.0 O A:CYS500 5.0 129.9 1.0

Zinc binding site 8 out of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn709 b:73.5 occ:1.00 NE2 A:HIS546 2.0 90.6 1.0 NE2 A:HIS541 2.0 70.6 1.0 SG A:CYS528 2.2 73.0 1.0 SG A:CYS525 2.3 97.6 1.0 CD2 A:HIS546 2.7 78.0 1.0 CD2 A:HIS541 2.9 69.5 1.0 CE1 A:HIS541 3.1 70.5 1.0 CB A:CYS525 3.2 93.2 1.0 CE1 A:HIS546 3.2 97.5 1.0 CB A:CYS528 3.3 76.1 1.0 N A:CYS528 3.6 91.5 1.0 CG A:HIS546 3.9 81.7 1.0 CA A:CYS528 3.9 91.5 1.0 CG A:HIS541 4.1 70.1 1.0 ND1 A:HIS541 4.2 70.7 1.0 ND1 A:HIS546 4.2 93.1 1.0 C A:HIS527 4.4 94.7 1.0 C A:CYS528 4.5 90.9 1.0 O A:CYS528 4.5 91.5 1.0 CA A:CYS525 4.6 93.7 1.0 CB A:HIS527 4.7 94.2 1.0 N A:HIS527 4.8 98.8 1.0 CA A:HIS527 4.9 99.6 1.0

J.Yang, J.R.Horton, B.Liu, V.G.Corces, R.M.Blumenthal, X.Zhang, X.Cheng. Structures of Ctcf-Dna Complexes Including All 11 Zinc Fingers. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37439339
DOI: 10.1093/NAR/GKAD594