Zinc in PDB 5yeh: Crystal Structure of Ctcf ZFS4-8-Ecbs

The structure of Crystal Structure of Ctcf ZFS4-8-Ecbs, PDB code: 5yeh was solved by M.Yin, J.Wang, M.Wang, X.Li, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.71 / 2.33
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.845, 54.876, 66.938, 81.17, 80.11, 79.72
R / Rfree (%)	22.2 / 27

The binding sites of Zinc atom in the Crystal Structure of Ctcf ZFS4-8-Ecbs (pdb code 5yeh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Ctcf ZFS4-8-Ecbs, PDB code: 5yeh:
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 Crystal Structure of Ctcf ZFS4-8-Ecbs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ctcf ZFS4-8-Ecbs within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:97.1 occ:1.00 NE2 A:HIS369 2.1 86.1 1.0 NE2 A:HIS373 2.1 74.1 1.0 CD2 A:HIS373 2.2 65.3 1.0 SG A:CYS353 2.3 93.6 1.0 SG A:CYS356 2.4 65.6 1.0 CD2 A:HIS369 2.9 78.0 1.0 CE1 A:HIS369 3.1 84.0 1.0 CE1 A:HIS373 3.4 71.5 1.0 CB A:CYS353 3.5 85.9 1.0 CB A:CYS356 3.5 77.6 1.0 CG A:HIS373 3.5 75.3 1.0 N A:CYS356 3.8 93.0 1.0 CG A:HIS369 4.0 78.6 1.0 ND1 A:HIS373 4.1 72.2 1.0 ND1 A:HIS369 4.1 84.5 1.0 CA A:CYS356 4.1 87.3 1.0 C A:CYS356 4.4 91.6 1.0 O A:CYS356 4.5 99.7 1.0 CB A:TYR358 4.6 80.1 1.0 CB A:MET355 4.6 76.4 1.0 CB A:HIS373 4.7 81.8 1.0 N A:MET355 4.9 86.1 1.0 C A:MET355 4.9 91.3 1.0 CA A:CYS353 4.9 86.7 1.0 O A:HIS369 5.0 63.8 1.0 N A:TYR358 5.0 89.7 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Ctcf ZFS4-8-Ecbs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ctcf ZFS4-8-Ecbs within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:46.3 occ:1.00 NE2 A:HIS401 2.1 47.7 1.0 SG A:CYS381 2.3 44.0 1.0 NE2 A:HIS397 2.3 34.6 1.0 SG A:CYS384 2.4 48.0 1.0 CD2 A:HIS401 2.9 38.1 1.0 CE1 A:HIS401 3.1 49.5 1.0 CD2 A:HIS397 3.2 36.3 1.0 CB A:CYS384 3.3 44.2 1.0 CB A:CYS381 3.3 58.4 1.0 CE1 A:HIS397 3.4 38.8 1.0 N A:CYS384 3.7 55.9 1.0 CA A:CYS384 4.0 50.8 1.0 CG A:HIS401 4.1 47.6 1.0 ND1 A:HIS401 4.2 47.1 1.0 CB A:LEU383 4.2 51.2 1.0 CB A:TYR386 4.3 64.3 1.0 C A:LEU383 4.4 59.5 1.0 CG A:HIS397 4.4 38.9 1.0 ND1 A:HIS397 4.5 51.2 1.0 C A:CYS384 4.5 65.8 1.0 CA A:LEU383 4.7 54.3 1.0 O A:CYS384 4.7 73.1 1.0 CA A:CYS381 4.8 65.6 1.0 N A:LEU383 4.8 62.6 1.0 N A:TYR386 4.9 66.9 1.0 SD A:MET398 5.0 51.9 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Ctcf ZFS4-8-Ecbs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ctcf ZFS4-8-Ecbs within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:43.0 occ:1.00 NE2 A:HIS430 2.1 46.5 1.0 SG A:CYS409 2.2 33.7 1.0 O A:HOH612 2.3 42.9 1.0 CE1 A:HIS425 2.4 37.4 1.0 SG A:CYS412 2.4 68.0 1.0 CD2 A:HIS430 3.0 56.9 1.0 CE1 A:HIS430 3.1 45.4 1.0 CB A:CYS409 3.2 32.0 1.0 CB A:CYS412 3.2 50.8 1.0 ND1 A:HIS425 3.3 42.0 1.0 NE2 A:HIS425 3.4 39.6 1.0 N A:CYS412 3.6 60.5 1.0 CA A:CYS412 3.9 54.2 1.0 CG A:HIS430 4.2 52.9 1.0 ND1 A:HIS430 4.2 46.3 1.0 CB A:ILE411 4.5 48.1 1.0 CG A:HIS425 4.5 47.4 1.0 CD2 A:HIS425 4.5 43.5 1.0 C A:CYS412 4.5 48.1 1.0 CA A:CYS409 4.6 39.5 1.0 C A:ILE411 4.6 56.5 1.0 N A:HIS413 4.7 63.2 1.0 CG2 A:ILE411 4.9 37.2 1.0 CA A:ILE411 4.9 55.0 1.0 N A:ILE411 4.9 60.8 1.0 N A:ALA414 5.0 36.6 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Ctcf ZFS4-8-Ecbs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ctcf ZFS4-8-Ecbs within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:38.1 occ:1.00 NE2 A:HIS460 2.0 52.3 1.0 NE2 A:HIS455 2.1 37.5 1.0 SG A:CYS442 2.2 46.5 1.0 SG A:CYS439 2.3 37.9 1.0 CE1 A:HIS460 2.9 46.5 1.0 CD2 A:HIS455 3.0 36.1 1.0 CD2 A:HIS460 3.1 48.6 1.0 CB A:CYS439 3.1 43.2 1.0 CE1 A:HIS455 3.2 43.0 1.0 CB A:CYS442 3.3 44.7 1.0 N A:CYS442 3.4 45.8 1.0 CA A:CYS442 3.9 54.7 1.0 ND1 A:HIS460 4.0 45.9 1.0 CG A:HIS460 4.1 35.2 1.0 CG A:HIS455 4.2 39.2 1.0 ND1 A:HIS455 4.3 36.4 1.0 C A:HIS441 4.3 59.0 1.0 OG1 A:THR444 4.4 53.8 1.0 CB A:HIS441 4.4 31.9 1.0 CA A:CYS439 4.6 42.1 1.0 C A:CYS442 4.6 59.3 1.0 CB A:THR444 4.7 49.0 1.0 N A:HIS441 4.7 30.1 1.0 CA A:HIS441 4.7 37.6 1.0 O A:CYS442 4.9 45.7 1.0 C A:CYS439 4.9 28.8 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Ctcf ZFS4-8-Ecbs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Ctcf ZFS4-8-Ecbs within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:86.4 occ:1.00 SG A:CYS472 2.0 0.6 1.0 CE1 A:HIS485 2.4 81.6 1.0 CE1 A:TYR471 2.6 95.6 1.0 SG A:CYS469 2.7 63.3 1.0 CB A:CYS472 2.8 82.3 1.0 CD1 A:TYR471 3.2 94.7 1.0 NE2 A:HIS485 3.2 78.9 1.0 ND1 A:HIS485 3.4 86.5 1.0 CZ A:TYR471 3.5 0.9 1.0 CB A:CYS469 3.5 70.3 1.0 OH A:TYR471 3.7 0.7 1.0 CA A:CYS472 3.8 83.8 1.0 N A:CYS472 3.8 87.0 1.0 CG A:TYR471 4.2 97.2 1.0 C A:CYS472 4.3 83.5 1.0 CD2 A:HIS485 4.4 82.7 1.0 CG A:HIS485 4.5 88.8 1.0 CE2 A:TYR471 4.5 0.7 1.0 O A:CYS472 4.6 89.1 1.0 C A:TYR471 4.7 88.7 1.0 CD2 A:TYR471 4.8 99.0 1.0 CB A:ALA474 5.0 73.0 1.0 CA A:CYS469 5.0 72.3 1.0 N A:ASP473 5.0 81.9 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Ctcf ZFS4-8-Ecbs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Ctcf ZFS4-8-Ecbs within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:88.9 occ:1.00 NE2 B:HIS373 1.8 0.0 1.0 CE1 B:HIS369 1.9 0.6 1.0 O B:HOH606 2.2 65.7 1.0 CD2 B:HIS373 2.5 99.9 1.0 SG B:CYS353 2.6 0.5 1.0 NE2 B:HIS369 2.6 0.5 1.0 CE1 B:HIS373 2.9 0.5 1.0 ND1 B:HIS369 3.1 0.6 1.0 SG B:CYS356 3.3 0.0 1.0 CB B:CYS356 3.5 0.3 1.0 CB B:CYS353 3.6 0.6 1.0 N B:CYS356 3.7 0.7 1.0 CG B:HIS373 3.7 0.4 1.0 CD2 B:HIS369 3.9 92.7 1.0 ND1 B:HIS373 3.9 0.2 1.0 CA B:CYS356 4.0 0.8 1.0 CG B:HIS369 4.1 89.7 1.0 C B:CYS356 4.2 0.3 1.0 O B:CYS356 4.3 0.8 1.0 CB B:TYR358 4.6 91.8 1.0 CB B:MET355 4.8 0.1 1.0 C B:MET355 4.8 0.5 1.0 N B:TYR358 4.9 93.2 1.0 N B:ASP357 5.0 99.2 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Ctcf ZFS4-8-Ecbs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Ctcf ZFS4-8-Ecbs within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:43.5 occ:1.00 NE2 B:HIS397 2.1 43.8 1.0 NE2 B:HIS401 2.2 46.5 1.0 SG B:CYS384 2.3 40.9 1.0 SG B:CYS381 2.3 35.3 1.0 CD2 B:HIS401 3.0 37.3 1.0 CD2 B:HIS397 3.0 31.8 1.0 CE1 B:HIS397 3.2 37.2 1.0 CB B:CYS384 3.3 36.9 1.0 CE1 B:HIS401 3.3 39.8 1.0 CB B:CYS381 3.3 34.6 1.0 N B:CYS384 3.7 35.5 1.0 CA B:CYS384 3.9 34.8 1.0 CG B:HIS397 4.2 32.6 1.0 CG B:HIS401 4.2 32.8 1.0 ND1 B:HIS397 4.2 41.0 1.0 CB B:TYR386 4.3 34.6 1.0 ND1 B:HIS401 4.3 29.3 1.0 CB B:LEU383 4.4 36.8 1.0 C B:LEU383 4.4 39.7 1.0 C B:CYS384 4.5 41.8 1.0 O B:CYS384 4.7 59.3 1.0 CA B:CYS381 4.7 39.6 1.0 CA B:LEU383 4.8 36.6 1.0 N B:LEU383 4.8 39.7 1.0 SD B:MET398 4.8 50.2 1.0 N B:TYR386 4.9 55.6 1.0 CD2 B:TYR386 4.9 35.4 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Ctcf ZFS4-8-Ecbs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Ctcf ZFS4-8-Ecbs within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:41.4 occ:1.00 NE2 B:HIS425 1.9 43.7 1.0 SG B:CYS409 2.1 31.1 1.0 SG B:CYS412 2.3 46.3 1.0 NE2 B:HIS430 2.3 40.2 1.0 CE1 B:HIS425 2.8 39.4 1.0 CD2 B:HIS430 2.9 39.4 1.0 CD2 B:HIS425 3.0 34.2 1.0 CB B:CYS409 3.2 24.9 1.0 CB B:CYS412 3.2 44.0 1.0 CE1 B:HIS430 3.5 53.6 1.0 N B:CYS412 3.7 50.9 1.0 ND1 B:HIS425 4.0 36.9 1.0 CA B:CYS412 4.0 40.6 1.0 CG B:HIS425 4.1 23.7 1.0 CG B:HIS430 4.2 49.7 1.0 ND1 B:HIS430 4.4 54.4 1.0 C B:CYS412 4.6 51.2 1.0 CA B:CYS409 4.7 34.7 1.0 CB B:ILE411 4.7 44.5 1.0 CB B:ALA414 4.8 40.5 1.0 C B:ILE411 4.8 47.3 1.0 N B:HIS413 4.8 47.8 1.0 N B:ALA414 5.0 32.9 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Ctcf ZFS4-8-Ecbs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Ctcf ZFS4-8-Ecbs within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:45.6 occ:1.00 NE2 B:HIS460 2.0 52.7 1.0 NE2 B:HIS455 2.1 53.8 1.0 SG B:CYS442 2.2 50.7 1.0 SG B:CYS439 2.4 46.5 1.0 CE1 B:HIS460 2.8 52.8 1.0 CD2 B:HIS460 3.0 50.9 1.0 CD2 B:HIS455 3.0 31.1 1.0 CE1 B:HIS455 3.1 42.8 1.0 CB B:CYS439 3.3 42.6 1.0 CB B:CYS442 3.4 47.5 1.0 N B:CYS442 3.6 51.7 1.0 ND1 B:HIS460 3.9 51.5 1.0 CG B:HIS460 4.0 51.0 1.0 CA B:CYS442 4.0 46.6 1.0 CG B:HIS455 4.2 34.4 1.0 ND1 B:HIS455 4.2 43.4 1.0 OG1 B:THR444 4.5 61.1 1.0 CB B:HIS441 4.5 42.3 1.0 C B:CYS442 4.6 50.8 1.0 C B:HIS441 4.6 50.5 1.0 CB B:THR444 4.7 55.9 1.0 CA B:CYS439 4.7 35.9 1.0 N B:HIS441 4.9 52.2 1.0 CA B:HIS441 4.9 48.4 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Ctcf ZFS4-8-Ecbs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Ctcf ZFS4-8-Ecbs within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:92.6 occ:1.00 NE2 B:HIS485 2.2 95.9 1.0 SG B:CYS472 2.2 80.4 1.0 SG B:CYS469 2.4 61.8 1.0 CD2 B:HIS485 2.9 90.2 1.0 CE1 B:TYR471 3.0 91.0 1.0 CE1 B:HIS485 3.1 92.0 1.0 CD1 B:TYR471 3.1 92.5 1.0 CB B:CYS469 3.2 71.7 1.0 CB B:CYS472 3.5 79.7 1.0 N B:CYS472 3.6 74.8 1.0 CZ B:TYR471 3.8 97.2 1.0 CG B:TYR471 3.8 95.8 1.0 CG B:HIS485 3.9 76.6 1.0 ND1 B:HIS485 4.0 79.0 1.0 C B:TYR471 4.0 83.0 1.0 O B:CYS472 4.0 0.7 1.0 CA B:CYS472 4.0 72.5 1.0 C B:CYS472 4.4 86.6 1.0 O B:TYR471 4.4 86.3 1.0 OH B:TYR471 4.4 97.9 1.0 CE2 B:TYR471 4.4 0.5 1.0 CD2 B:TYR471 4.5 0.0 1.0 CB B:ALA474 4.5 74.2 1.0 N B:TYR471 4.5 81.3 1.0 CA B:TYR471 4.6 81.4 1.0 CA B:CYS469 4.6 68.2 1.0 CB B:TYR471 4.7 83.2 1.0 C B:CYS469 5.0 74.7 1.0

M.Yin, J.Wang, M.Wang, X.Li, M.Zhang, Q.Wu, Y.Wang. Molecular Mechanism of Directional Ctcf Recognition of A Diverse Range of Genomic Sites Cell Res. V. 27 1365 2017.
ISSN: ISSN 1748-7838
PubMed: 29076501
DOI: 10.1038/CR.2017.131