Zinc in PDB 5kkq: Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure

The structure of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure, PDB code: 5kkq was solved by H.Hashimoto, D.Wang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.94 / 1.74
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.994, 44.911, 86.797, 98.33, 92.40, 94.80
R / Rfree (%)	17 / 19.9

The binding sites of Zinc atom in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure (pdb code 5kkq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure, PDB code: 5kkq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 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) ZNF3-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:55.7 occ:1.00 NE2 A:HIS345 2.0 68.3 1.0 NE2 A:HIS340 2.1 53.7 1.0 SG A:CYS324 2.2 51.4 1.0 SG A:CYS327 2.4 54.4 1.0 CD2 A:HIS345 2.9 65.6 1.0 CE1 A:HIS340 3.1 47.4 1.0 HD2 A:HIS345 3.1 78.7 1.0 CE1 A:HIS345 3.1 66.9 1.0 HB3 A:CYS324 3.1 59.4 1.0 CD2 A:HIS340 3.1 48.5 1.0 CB A:CYS324 3.1 49.5 1.0 HB2 A:CYS324 3.2 59.4 1.0 HE1 A:HIS340 3.2 56.9 1.0 HD2 A:HIS340 3.3 58.2 1.0 HE1 A:HIS345 3.3 80.3 1.0 HB3 A:CYS327 3.3 70.9 1.0 CB A:CYS327 3.4 59.1 1.0 HB2 A:ASP326 3.6 87.6 1.0 H A:CYS327 3.8 77.0 1.0 N A:CYS327 3.8 64.2 1.0 HB2 A:MET329 4.0 67.8 1.0 H A:ASP326 4.0 81.3 1.0 CG A:HIS345 4.1 65.4 1.0 CA A:CYS327 4.1 62.5 1.0 ND1 A:HIS345 4.2 67.0 1.0 C A:ASP326 4.2 69.4 1.0 ND1 A:HIS340 4.2 44.7 1.0 CG A:HIS340 4.2 44.6 1.0 HB2 A:CYS327 4.3 70.9 1.0 HG2 A:ARG341 4.3 61.3 1.0 H A:MET329 4.4 73.8 1.0 CB A:ASP326 4.5 73.0 1.0 HB2 A:LYS344 4.5 60.5 1.0 CA A:CYS324 4.6 50.9 1.0 O A:ASP326 4.6 69.5 1.0 CA A:ASP326 4.7 70.6 1.0 C A:CYS327 4.7 63.3 1.0 N A:ASP326 4.7 67.8 1.0 HA A:CYS324 4.9 61.1 1.0 HB3 A:ASP326 4.9 87.6 1.0 HB3 A:LYS344 4.9 60.5 1.0 HA A:ARG341 4.9 53.8 1.0 HE2 A:PHE331 4.9 46.6 1.0 O A:CYS327 4.9 61.7 1.0 HG3 A:MET329 4.9 71.0 1.0 CB A:MET329 4.9 56.5 1.0 HD1 A:HIS345 5.0 80.5 1.0 HD1 A:HIS340 5.0 53.6 1.0 C A:CYS324 5.0 55.7 1.0 HA A:CYS327 5.0 75.0 1.0

Zinc binding site 2 out of 10 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 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) ZNF3-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:37.5 occ:1.00 NE2 A:HIS373 2.0 40.9 1.0 NE2 A:HIS369 2.1 34.9 1.0 SG A:CYS356 2.2 37.8 1.0 SG A:CYS353 2.3 39.2 1.0 CD2 A:HIS373 3.0 39.2 1.0 CE1 A:HIS373 3.0 40.7 1.0 CD2 A:HIS369 3.0 33.7 1.0 CE1 A:HIS369 3.1 34.1 1.0 HD2 A:HIS373 3.1 47.1 1.0 HB3 A:CYS353 3.2 48.8 1.0 HD2 A:HIS369 3.2 40.4 1.0 HE1 A:HIS373 3.2 48.9 1.0 CB A:CYS353 3.2 40.7 1.0 HE1 A:HIS369 3.3 40.9 1.0 HB2 A:CYS353 3.3 48.8 1.0 HB3 A:CYS356 3.3 49.0 1.0 CB A:CYS356 3.4 40.8 1.0 HB3 A:TYR358 3.4 40.8 1.0 H A:CYS356 3.5 56.2 1.0 HB2 A:MET355 3.6 63.6 1.0 N A:CYS356 3.7 46.9 1.0 HB2 A:TYR358 4.0 40.8 1.0 CA A:CYS356 4.0 44.5 1.0 H A:MET355 4.0 62.5 1.0 H A:TYR358 4.1 45.1 1.0 ND1 A:HIS373 4.1 38.4 1.0 CG A:HIS373 4.1 38.3 1.0 CB A:TYR358 4.1 34.0 1.0 HB2 A:CYS356 4.1 49.0 1.0 ND1 A:HIS369 4.2 31.0 1.0 CG A:HIS369 4.2 30.7 1.0 C A:MET355 4.2 50.2 1.0 CB A:MET355 4.5 53.0 1.0 C A:CYS356 4.5 44.8 1.0 CA A:CYS353 4.7 43.8 1.0 N A:MET355 4.7 52.1 1.0 CA A:MET355 4.7 52.0 1.0 O A:CYS356 4.8 45.2 1.0 N A:TYR358 4.8 37.6 1.0 O A:MET355 4.9 52.1 1.0 HD1 A:HIS373 4.9 46.0 1.0 HA A:CYS356 4.9 53.3 1.0 HD2 A:TYR358 4.9 37.5 1.0 HB3 A:MET355 4.9 63.6 1.0 HD1 A:HIS369 5.0 37.2 1.0 HA A:CYS353 5.0 52.6 1.0

Zinc binding site 3 out of 10 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 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) ZNF3-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:37.3 occ:1.00 NE2 A:HIS397 2.1 36.5 1.0 NE2 A:HIS401 2.1 43.6 1.0 SG A:CYS384 2.2 38.3 1.0 SG A:CYS381 2.3 37.7 1.0 CD2 A:HIS397 3.0 32.2 1.0 CE1 A:HIS401 3.1 43.3 1.0 CD2 A:HIS401 3.1 41.2 1.0 HD2 A:HIS397 3.1 38.7 1.0 CE1 A:HIS397 3.1 34.8 1.0 HB3 A:CYS381 3.2 44.5 1.0 HD2 A:HIS401 3.2 49.5 1.0 CB A:CYS381 3.3 37.1 1.0 HE1 A:HIS401 3.3 52.0 1.0 HB3 A:CYS384 3.3 48.7 1.0 CB A:CYS384 3.3 40.6 1.0 HE1 A:HIS397 3.4 41.7 1.0 HB2 A:CYS381 3.4 44.5 1.0 HB3 A:TYR386 3.4 39.2 1.0 HB2 A:LEU383 3.5 48.1 1.0 H A:CYS384 3.6 52.7 1.0 N A:CYS384 3.7 43.9 1.0 H A:LEU383 4.0 50.1 1.0 CA A:CYS384 4.0 43.1 1.0 HB2 A:CYS384 4.1 48.7 1.0 ND1 A:HIS401 4.2 44.7 1.0 CG A:HIS397 4.2 29.8 1.0 CG A:HIS401 4.2 42.7 1.0 ND1 A:HIS397 4.2 30.6 1.0 C A:LEU383 4.2 43.9 1.0 H A:TYR386 4.2 44.2 1.0 CB A:TYR386 4.3 32.7 1.0 HB2 A:TYR386 4.3 39.2 1.0 CB A:LEU383 4.4 40.1 1.0 C A:CYS384 4.5 41.9 1.0 HD2 A:TYR386 4.6 35.1 1.0 HE1 A:MET398 4.6 52.0 1.0 CA A:LEU383 4.7 43.7 1.0 N A:LEU383 4.7 41.8 1.0 CA A:CYS381 4.7 37.1 1.0 O A:CYS384 4.7 41.9 1.0 HB3 A:LEU383 4.8 48.1 1.0 O A:LEU383 4.8 46.8 1.0 SD A:MET398 4.8 44.4 1.0 HG1 A:THR400 4.8 36.6 1.0 HA A:CYS384 4.9 51.7 1.0 N A:TYR386 4.9 36.9 1.0 HD1 A:HIS401 4.9 53.6 1.0 HA A:CYS381 5.0 44.5 1.0

Zinc binding site 4 out of 10 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 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) ZNF3-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:33.0 occ:1.00 NE2 A:HIS425 2.1 29.8 1.0 NE2 A:HIS430 2.1 36.4 1.0 SG A:CYS409 2.2 28.6 1.0 SG A:CYS412 2.2 35.0 1.0 CD2 A:HIS425 3.0 28.4 1.0 CD2 A:HIS430 3.0 31.7 1.0 H A:CYS412 3.0 47.1 1.0 CE1 A:HIS425 3.1 28.2 1.0 HB3 A:CYS412 3.1 47.6 1.0 HD2 A:HIS430 3.1 38.1 1.0 HD2 A:HIS425 3.1 34.1 1.0 HB3 A:CYS409 3.1 36.7 1.0 CE1 A:HIS430 3.2 34.9 1.0 CB A:CYS409 3.2 30.6 1.0 CB A:CYS412 3.3 39.7 1.0 HB2 A:CYS409 3.3 36.7 1.0 HE1 A:HIS425 3.3 33.9 1.0 HE1 A:HIS430 3.4 41.8 1.0 N A:CYS412 3.6 39.2 1.0 HB A:ILE411 3.7 45.1 1.0 CA A:CYS412 4.0 39.2 1.0 HB3 A:ALA414 4.0 43.4 1.0 HB2 A:CYS412 4.1 47.6 1.0 CG A:HIS425 4.2 24.9 1.0 ND1 A:HIS425 4.2 26.7 1.0 CG A:HIS430 4.2 32.2 1.0 H A:ALA414 4.2 44.9 1.0 ND1 A:HIS430 4.2 33.1 1.0 H A:ILE411 4.4 45.8 1.0 HG22 A:ILE411 4.4 47.2 1.0 H A:HIS413 4.5 44.4 1.0 HG12 A:ILE426 4.5 32.3 1.0 HB2 A:LYS429 4.5 40.2 1.0 C A:CYS412 4.6 40.3 1.0 CB A:ILE411 4.6 37.6 1.0 HZ A:PHE416 4.6 31.3 1.0 C A:ILE411 4.6 41.4 1.0 CA A:CYS409 4.6 30.6 1.0 HB2 A:ALA414 4.6 43.4 1.0 N A:HIS413 4.7 37.0 1.0 CB A:ALA414 4.8 36.2 1.0 HA A:CYS412 4.8 47.1 1.0 HA A:ILE426 4.9 26.0 1.0 HE2 A:PHE416 4.9 30.3 1.0 CG2 A:ILE411 4.9 39.3 1.0 N A:ALA414 5.0 37.4 1.0 CA A:ILE411 5.0 39.2 1.0 HD1 A:HIS425 5.0 32.1 1.0 HA A:CYS409 5.0 36.8 1.0 N A:ILE411 5.0 38.2 1.0

Zinc binding site 5 out of 10 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:33.5 occ:1.00 NE2 A:HIS460 2.0 37.8 1.0 NE2 A:HIS455 2.0 29.6 1.0 SG A:CYS442 2.1 33.7 1.0 SG A:CYS439 2.3 30.8 1.0 CD2 A:HIS455 2.9 26.7 1.0 CD2 A:HIS460 3.0 35.9 1.0 CE1 A:HIS460 3.0 40.6 1.0 CE1 A:HIS455 3.1 30.0 1.0 HB3 A:CYS442 3.1 49.1 1.0 HD2 A:HIS455 3.1 32.0 1.0 HB3 A:CYS439 3.1 33.4 1.0 HD2 A:HIS460 3.1 43.1 1.0 H A:CYS442 3.2 47.2 1.0 CB A:CYS442 3.2 40.9 1.0 CB A:CYS439 3.2 27.9 1.0 HE1 A:HIS460 3.2 48.7 1.0 HE1 A:HIS455 3.3 36.0 1.0 HB2 A:CYS439 3.4 33.4 1.0 N A:CYS442 3.6 39.4 1.0 HB2 A:HIS441 3.6 51.8 1.0 CA A:CYS442 3.9 39.0 1.0 HB2 A:CYS442 4.0 49.1 1.0 ND1 A:HIS460 4.1 38.9 1.0 CG A:HIS460 4.1 36.9 1.0 CG A:HIS455 4.1 25.0 1.0 ND1 A:HIS455 4.1 24.6 1.0 HB A:THR444 4.2 39.3 1.0 H A:HIS441 4.2 50.4 1.0 HG1 A:THR444 4.3 43.8 1.0 HB2 A:GLN459 4.3 44.7 1.0 C A:HIS441 4.4 42.2 1.0 CB A:HIS441 4.6 43.1 1.0 HD23 A:LEU456 4.6 38.0 1.0 CA A:CYS439 4.6 28.1 1.0 H A:THR444 4.6 39.6 1.0 OG1 A:THR444 4.6 36.5 1.0 C A:CYS442 4.7 38.1 1.0 N A:HIS441 4.7 42.0 1.0 HA A:CYS442 4.8 46.8 1.0 CA A:HIS441 4.8 42.7 1.0 H A:ASP443 4.8 47.0 1.0 HD2 A:HIS441 4.9 49.1 1.0 CB A:THR444 4.9 32.8 1.0 HD1 A:HIS460 4.9 46.7 1.0 HD1 A:HIS455 4.9 29.5 1.0 HA A:CYS439 4.9 33.7 1.0 C A:CYS439 5.0 36.7 1.0

Zinc binding site 6 out of 10 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:46.1 occ:1.00 NE2 D:HIS345 2.0 63.7 1.0 NE2 D:HIS340 2.1 53.2 1.0 SG D:CYS324 2.2 49.7 1.0 SG D:CYS327 2.3 45.6 1.0 CD2 D:HIS345 2.9 60.1 1.0 CE1 D:HIS345 3.0 60.3 1.0 CE1 D:HIS340 3.1 47.7 1.0 HD2 D:HIS345 3.1 72.1 1.0 HB3 D:CYS324 3.1 62.1 1.0 CD2 D:HIS340 3.1 49.0 1.0 CB D:CYS324 3.2 51.7 1.0 HE1 D:HIS345 3.2 72.3 1.0 HB3 D:CYS327 3.2 58.2 1.0 HE1 D:HIS340 3.2 57.3 1.0 HB2 D:CYS324 3.3 62.1 1.0 HD2 D:HIS340 3.3 58.8 1.0 CB D:CYS327 3.4 48.5 1.0 HB2 D:ASP326 3.5 77.0 1.0 HB2 D:MET329 3.7 62.8 0.5 N D:CYS327 3.8 57.1 1.0 H D:CYS327 3.8 68.6 1.0 HB2 D:MET329 3.8 62.7 0.5 H D:ASP326 4.0 78.6 1.0 ND1 D:HIS345 4.1 59.9 1.0 CG D:HIS345 4.1 58.7 1.0 CA D:CYS327 4.1 53.9 1.0 HG2 D:ARG341 4.1 62.5 1.0 C D:ASP326 4.1 60.6 1.0 HB2 D:CYS327 4.2 58.2 1.0 HB2 D:LYS344 4.2 52.3 1.0 ND1 D:HIS340 4.2 44.3 1.0 CG D:HIS340 4.3 45.0 1.0 H D:MET329 4.4 66.9 0.5 H D:MET329 4.4 66.9 0.5 CB D:ASP326 4.4 64.2 1.0 HG3 D:MET329 4.4 60.3 0.5 HG3 D:MET329 4.5 60.0 0.5 CA D:CYS324 4.6 55.6 1.0 CA D:ASP326 4.6 63.8 1.0 O D:ASP326 4.6 59.5 1.0 N D:ASP326 4.7 65.5 1.0 CB D:MET329 4.7 52.3 0.5 C D:CYS327 4.7 56.2 1.0 HA D:ARG341 4.7 52.1 1.0 CB D:MET329 4.8 52.3 0.5 HB3 D:ASP326 4.8 77.0 1.0 HG2 D:MET329 4.8 60.0 0.5 HD1 D:HIS345 4.8 71.9 1.0 HB3 D:LYS344 4.8 52.3 1.0 CG D:MET329 4.9 50.0 0.5 HA D:CYS324 4.9 66.7 1.0 O D:CYS327 4.9 58.6 1.0 CB D:LYS344 4.9 43.6 1.0 HG3 D:LYS344 4.9 53.4 1.0 HD1 D:HIS340 5.0 53.2 1.0 HG3 D:ARG341 5.0 62.5 1.0 HA D:CYS327 5.0 64.6 1.0 CG D:ARG341 5.0 52.1 1.0 C D:CYS324 5.0 61.1 1.0 HE2 D:PHE331 5.0 56.8 1.0

Zinc binding site 7 out of 10 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:34.1 occ:1.00 NE2 D:HIS373 2.0 42.2 1.0 NE2 D:HIS369 2.1 37.6 1.0 SG D:CYS353 2.3 35.2 1.0 SG D:CYS356 2.3 36.7 1.0 CD2 D:HIS373 2.9 39.0 1.0 HD2 D:HIS373 3.0 46.9 1.0 CE1 D:HIS369 3.0 34.6 1.0 CD2 D:HIS369 3.1 33.4 1.0 CE1 D:HIS373 3.1 42.0 1.0 HB3 D:CYS353 3.1 41.7 1.0 CB D:CYS353 3.2 34.7 1.0 HE1 D:HIS369 3.2 41.5 1.0 HD2 D:HIS369 3.2 40.1 1.0 HB2 D:CYS353 3.3 41.7 1.0 HB3 D:CYS356 3.4 47.5 1.0 HE1 D:HIS373 3.4 50.4 1.0 CB D:CYS356 3.4 39.5 1.0 HB2 D:MET355 3.5 53.0 1.0 HB3 D:TYR358 3.5 39.7 1.0 H D:CYS356 3.6 51.0 1.0 N D:CYS356 3.7 42.5 1.0 H D:MET355 4.1 50.6 1.0 CG D:HIS373 4.1 38.6 1.0 CA D:CYS356 4.1 40.4 1.0 H D:TYR358 4.1 43.2 1.0 ND1 D:HIS369 4.1 31.9 1.0 ND1 D:HIS373 4.2 42.4 1.0 CG D:HIS369 4.2 31.2 1.0 HB2 D:CYS356 4.3 47.5 1.0 C D:MET355 4.3 44.4 1.0 HB2 D:TYR358 4.3 39.7 1.0 CB D:TYR358 4.4 33.1 1.0 CB D:MET355 4.4 44.2 1.0 C D:CYS356 4.6 39.7 1.0 CA D:CYS353 4.6 35.5 1.0 CA D:MET355 4.7 44.2 1.0 N D:MET355 4.7 42.2 1.0 HB3 D:MET355 4.8 53.0 1.0 O D:CYS356 4.8 39.2 1.0 HD2 D:TYR358 4.9 38.1 1.0 N D:TYR358 4.9 36.0 1.0 O D:MET355 4.9 45.8 1.0 HA D:CYS353 4.9 42.6 1.0 HD1 D:HIS369 4.9 38.3 1.0 HD1 D:HIS373 5.0 50.9 1.0 HA D:CYS356 5.0 48.5 1.0 HA D:ILE370 5.0 39.0 1.0

Zinc binding site 8 out of 10 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn503 b:32.6 occ:1.00 NE2 D:HIS401 2.1 38.8 1.0 NE2 D:HIS397 2.1 34.9 1.0 SG D:CYS384 2.2 33.1 1.0 SG D:CYS381 2.2 34.7 1.0 CD2 D:HIS401 3.0 35.4 1.0 CD2 D:HIS397 3.1 34.6 1.0 CE1 D:HIS397 3.1 34.4 1.0 CE1 D:HIS401 3.1 40.4 1.0 HD2 D:HIS401 3.2 42.4 1.0 HD2 D:HIS397 3.2 41.5 1.0 HE1 D:HIS397 3.2 41.3 1.0 HB3 D:CYS381 3.3 40.7 1.0 CB D:CYS381 3.3 34.0 1.0 HE1 D:HIS401 3.3 48.5 1.0 HB3 D:CYS384 3.4 46.4 1.0 CB D:CYS384 3.4 38.7 1.0 HB2 D:CYS381 3.4 40.7 1.0 H D:CYS384 3.4 45.7 1.0 HB3 D:TYR386 3.5 41.3 1.0 HB2 D:LEU383 3.6 47.1 1.0 N D:CYS384 3.6 38.1 1.0 CA D:CYS384 4.0 38.4 1.0 H D:LEU383 4.1 49.3 1.0 ND1 D:HIS397 4.2 31.4 1.0 CG D:HIS401 4.2 36.7 1.0 ND1 D:HIS401 4.2 36.9 1.0 HB2 D:CYS384 4.2 46.4 1.0 CG D:HIS397 4.2 29.8 1.0 C D:LEU383 4.2 39.8 1.0 H D:TYR386 4.2 43.1 1.0 CB D:TYR386 4.4 34.4 1.0 HD2 D:TYR386 4.4 35.8 1.0 CB D:LEU383 4.5 39.2 1.0 C D:CYS384 4.5 40.2 1.0 HE1 D:MET398 4.6 46.1 1.0 HB2 D:TYR386 4.6 41.3 1.0 O D:CYS384 4.7 37.9 1.0 N D:LEU383 4.7 41.1 1.0 CA D:LEU383 4.7 41.3 1.0 CA D:CYS381 4.7 34.3 1.0 SD D:MET398 4.7 39.3 1.0 HB3 D:LEU383 4.8 47.1 1.0 HG1 D:THR400 4.8 37.8 1.0 HA D:CYS384 4.9 46.0 1.0 O D:LEU383 4.9 41.0 1.0 HD1 D:HIS397 4.9 37.7 1.0 N D:TYR386 5.0 35.9 1.0 HD1 D:HIS401 5.0 44.3 1.0 HA D:CYS381 5.0 41.2 1.0

Zinc binding site 9 out of 10 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn504 b:34.5 occ:1.00 NE2 D:HIS430 2.1 38.5 1.0 NE2 D:HIS425 2.1 35.3 1.0 SG D:CYS412 2.2 37.1 1.0 SG D:CYS409 2.3 30.7 1.0 CD2 D:HIS430 3.0 35.8 1.0 H D:CYS412 3.0 44.7 1.0 CD2 D:HIS425 3.0 29.7 1.0 HB3 D:CYS412 3.1 49.1 1.0 HD2 D:HIS430 3.1 43.0 1.0 CE1 D:HIS430 3.1 40.4 1.0 HB3 D:CYS409 3.1 37.0 1.0 HD2 D:HIS425 3.1 35.6 1.0 CE1 D:HIS425 3.1 33.3 1.0 CB D:CYS409 3.2 30.9 1.0 HB2 D:CYS409 3.2 37.0 1.0 CB D:CYS412 3.2 40.9 1.0 HE1 D:HIS430 3.3 48.5 1.0 HE1 D:HIS425 3.4 40.0 1.0 N D:CYS412 3.7 37.2 1.0 HB D:ILE411 3.7 48.2 1.0 CA D:CYS412 4.0 40.8 1.0 HB2 D:CYS412 4.0 49.1 1.0 H D:ALA414 4.1 40.0 1.0 CG D:HIS430 4.2 36.5 1.0 CG D:HIS425 4.2 28.2 1.0 ND1 D:HIS430 4.2 40.4 1.0 HB3 D:ALA414 4.2 39.7 1.0 ND1 D:HIS425 4.2 30.0 1.0 H D:HIS413 4.2 48.5 1.0 H D:ILE411 4.4 42.3 1.0 C D:CYS412 4.6 41.7 1.0 CA D:CYS409 4.6 31.4 1.0 CB D:ILE411 4.6 40.2 1.0 HG12 D:ILE426 4.6 35.0 1.0 HB2 D:LYS429 4.6 50.7 1.0 N D:HIS413 4.6 40.4 1.0 HZ D:PHE416 4.7 34.2 1.0 HB2 D:ALA414 4.7 39.7 1.0 C D:ILE411 4.8 38.9 1.0 HA D:CYS412 4.8 48.9 1.0 CB D:ALA414 4.9 33.1 1.0 HA D:ILE426 4.9 36.4 1.0 HA D:CYS409 4.9 37.7 1.0 HG22 D:ILE411 4.9 52.5 1.0 N D:ALA414 5.0 33.4 1.0 HG13 D:ILE426 5.0 35.0 1.0 HD1 D:HIS430 5.0 48.4 1.0

Zinc binding site 10 out of 10 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF3-7 and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn505 b:30.5 occ:1.00 NE2 D:HIS460 2.0 34.3 1.0 NE2 D:HIS455 2.1 31.2 1.0 SG D:CYS439 2.3 25.1 1.0 SG D:CYS442 2.3 32.5 1.0 CE1 D:HIS460 3.0 36.6 1.0 CD2 D:HIS460 3.0 33.2 1.0 CD2 D:HIS455 3.1 24.7 1.0 CE1 D:HIS455 3.1 30.3 1.0 HB3 D:CYS439 3.2 30.6 1.0 CB D:CYS439 3.2 25.5 1.0 HD2 D:HIS455 3.2 29.7 1.0 HE1 D:HIS460 3.2 44.0 1.0 HD2 D:HIS460 3.2 39.8 1.0 HB2 D:CYS439 3.2 30.6 1.0 HB3 D:CYS442 3.3 38.5 1.0 H D:CYS442 3.3 37.6 1.0 HE1 D:HIS455 3.3 36.3 1.0 CB D:CYS442 3.3 32.1 1.0 HB2 D:HIS441 3.6 43.0 1.0 N D:CYS442 3.6 31.4 1.0 HB D:THR444 3.6 38.5 1.0 H D:HIS441 4.0 39.4 1.0 CA D:CYS442 4.0 34.0 1.0 ND1 D:HIS460 4.1 36.2 1.0 HB2 D:CYS442 4.2 38.5 1.0 CG D:HIS460 4.2 34.8 1.0 CG D:HIS455 4.2 25.7 1.0 ND1 D:HIS455 4.2 26.4 1.0 H D:THR444 4.3 41.6 1.0 C D:HIS441 4.3 35.8 1.0 HG1 D:THR444 4.4 48.5 1.0 HB2 D:GLN459 4.4 45.3 1.0 CB D:HIS441 4.5 35.8 1.0 C D:CYS442 4.5 33.0 1.0 CB D:THR444 4.5 32.1 1.0 OG1 D:THR444 4.6 40.4 1.0 CA D:CYS439 4.6 26.9 1.0 O D:CYS442 4.6 30.4 1.0 N D:HIS441 4.7 32.8 1.0 CA D:HIS441 4.7 35.3 1.0 HD23 D:LEU456 4.8 35.2 1.0 HA D:CYS442 4.9 40.9 1.0 HA D:CYS439 4.9 32.3 1.0 HD1 D:HIS460 4.9 43.4 1.0 HB3 D:HIS441 4.9 43.0 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