Zinc in PDB 5und: Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna

The structure of Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna, PDB code: 5und was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.61 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.072, 73.825, 93.289, 90.00, 91.38, 90.00
R / Rfree (%)	21.1 / 23.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna (pdb code 5und). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna, PDB code: 5und:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna


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(Znf 4-10) with 28-Mer Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.3 occ:1.00 NE2 A:HIS369 2.0 0.1 1.0 NE2 A:HIS373 2.0 0.3 1.0 SG A:CYS356 2.3 93.9 1.0 SG A:CYS353 2.3 0.5 1.0 CD2 A:HIS373 2.4 0.2 1.0 CD2 A:HIS369 2.6 0.5 1.0 CE1 A:HIS369 3.1 0.8 1.0 CE1 A:HIS373 3.2 0.2 1.0 CB A:CYS356 3.3 95.0 1.0 N A:CYS356 3.6 0.9 1.0 CB A:CYS353 3.6 0.4 1.0 CG A:HIS373 3.7 0.4 1.0 CG A:HIS369 3.8 0.8 1.0 ND1 A:HIS369 3.9 0.3 1.0 C A:MET355 4.0 0.4 1.0 CA A:CYS356 4.0 0.8 1.0 ND1 A:HIS373 4.0 0.5 1.0 CB A:MET355 4.1 1.0 1.0 CA A:MET355 4.4 0.7 1.0 N A:MET355 4.4 0.7 1.0 O A:MET355 4.6 0.6 1.0 O A:HIS369 4.6 0.1 1.0 C A:CYS356 4.7 0.7 1.0 CB A:TYR358 4.8 97.8 1.0 CG A:MET355 4.9 0.2 1.0 C A:HIS369 4.9 0.2 1.0 CB A:HIS373 4.9 0.2 1.0 CA A:CYS353 5.0 0.5 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna


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(Znf 4-10) with 28-Mer Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:98.5 occ:1.00 NE2 A:HIS397 2.0 0.7 1.0 NE2 A:HIS401 2.0 0.6 1.0 SG A:CYS384 2.3 1.0 1.0 SG A:CYS381 2.3 80.2 1.0 CD2 A:HIS397 2.9 0.0 1.0 CE1 A:HIS401 2.9 0.0 1.0 CD2 A:HIS401 3.1 0.7 1.0 CE1 A:HIS397 3.1 0.1 1.0 CB A:CYS381 3.2 80.8 1.0 N A:CYS384 3.3 93.5 1.0 CB A:CYS384 3.5 0.7 1.0 CA A:CYS384 3.9 0.1 1.0 CB A:LEU383 4.0 93.8 1.0 ND1 A:HIS401 4.0 0.0 1.0 CG A:HIS397 4.1 0.7 1.0 CG A:HIS401 4.1 0.7 1.0 ND1 A:HIS397 4.1 0.7 1.0 CB A:TYR386 4.3 0.5 1.0 C A:CYS384 4.3 0.4 1.0 C A:LEU383 4.4 99.1 1.0 O A:CYS384 4.4 1.0 1.0 CA A:LEU383 4.6 95.6 1.0 N A:LEU383 4.6 0.8 1.0 CA A:CYS381 4.6 92.0 1.0 N A:TYR386 4.8 0.2 1.0 CD2 A:TYR386 5.0 89.8 1.0 SD A:MET398 5.0 1.0 1.0 C A:CYS381 5.0 0.5 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna


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(Znf 4-10) with 28-Mer Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:41.0 occ:1.00 NE2 A:HIS425 2.0 47.6 1.0 NE2 A:HIS430 2.1 32.9 1.0 SG A:CYS412 2.3 39.0 1.0 SG A:CYS409 2.3 39.9 1.0 CD2 A:HIS430 2.8 32.5 1.0 CD2 A:HIS425 3.0 49.8 1.0 CE1 A:HIS425 3.0 40.6 1.0 CB A:CYS409 3.2 25.4 1.0 CE1 A:HIS430 3.2 33.0 1.0 CB A:CYS412 3.2 38.6 1.0 N A:CYS412 3.6 45.0 1.0 CA A:CYS412 3.9 39.4 1.0 CG A:HIS430 4.1 42.2 1.0 ND1 A:HIS425 4.1 49.0 1.0 CG A:HIS425 4.1 50.0 1.0 ND1 A:HIS430 4.2 29.3 1.0 CB A:ILE411 4.4 45.9 1.0 C A:CYS412 4.5 31.4 1.0 N A:HIS413 4.6 36.9 1.0 CA A:CYS409 4.6 52.0 1.0 C A:ILE411 4.6 49.0 1.0 CG2 A:ILE411 4.9 28.3 1.0 CA A:ILE411 4.9 37.4 1.0 N A:ILE411 4.9 44.7 1.0 N A:ALA414 5.0 55.8 1.0 C A:CYS409 5.0 45.3 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna


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(Znf 4-10) with 28-Mer Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:59.7 occ:1.00 NE2 A:HIS460 2.0 91.6 1.0 NE2 A:HIS455 2.0 69.4 1.0 SG A:CYS442 2.2 57.0 1.0 SG A:CYS439 2.3 76.5 1.0 CD2 A:HIS460 2.9 80.6 1.0 CD2 A:HIS455 2.9 60.8 1.0 CE1 A:HIS460 3.1 65.8 1.0 CB A:CYS439 3.1 76.6 1.0 CE1 A:HIS455 3.1 69.9 1.0 CB A:CYS442 3.5 70.5 1.0 N A:CYS442 3.8 84.0 1.0 CG A:HIS460 4.1 73.2 1.0 CG A:HIS455 4.1 62.4 1.0 ND1 A:HIS460 4.1 78.2 1.0 OG1 A:THR444 4.1 92.3 1.0 ND1 A:HIS455 4.2 57.1 1.0 CA A:CYS442 4.2 75.7 1.0 CB A:HIS441 4.5 57.6 1.0 C A:HIS441 4.5 92.2 1.0 CA A:CYS439 4.6 73.6 1.0 N A:HIS441 4.8 71.4 1.0 CA A:HIS441 4.8 75.7 1.0 C A:CYS442 4.9 87.0 1.0 CB A:GLN459 4.9 58.5 1.0 C A:CYS439 5.0 65.4 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna


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(Znf 4-10) with 28-Mer Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:53.0 occ:1.00 NE2 A:HIS489 2.0 70.0 1.0 NE2 A:HIS485 2.0 63.4 1.0 SG A:CYS472 2.3 52.3 1.0 SG A:CYS469 2.3 60.6 1.0 CD2 A:HIS485 2.6 55.5 1.0 CD2 A:HIS489 2.9 63.7 1.0 CE1 A:HIS489 3.1 55.2 1.0 CB A:CYS469 3.1 44.8 1.0 CE1 A:HIS485 3.2 67.9 1.0 CB A:CYS472 3.5 62.2 1.0 N A:CYS472 3.6 53.2 1.0 CG A:HIS485 3.9 58.2 1.0 CA A:CYS472 4.1 43.6 1.0 CG A:HIS489 4.1 70.1 1.0 ND1 A:HIS489 4.1 64.0 1.0 ND1 A:HIS485 4.1 54.3 1.0 C A:TYR471 4.2 65.2 1.0 CB A:TYR471 4.3 68.5 1.0 CB A:ALA474 4.4 39.9 1.0 CA A:CYS469 4.6 45.2 1.0 C A:CYS472 4.6 49.5 1.0 CA A:TYR471 4.6 53.0 1.0 N A:TYR471 4.6 57.4 1.0 O A:CYS472 4.7 49.0 1.0 C A:CYS469 5.0 61.2 1.0 O A:HIS485 5.0 59.3 1.0 O A:TYR471 5.0 60.9 1.0 N A:ALA474 5.0 60.6 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna


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(Znf 4-10) with 28-Mer Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:0.6 occ:1.00 NE2 A:HIS513 2.0 0.7 1.0 NE2 A:HIS517 2.0 0.5 1.0 SG A:CYS500 2.3 0.9 1.0 CD2 A:HIS513 2.7 0.5 1.0 CE1 A:HIS517 2.9 0.1 1.0 CE1 A:HIS513 3.1 0.9 1.0 CD2 A:HIS517 3.2 0.6 1.0 CB A:CYS500 3.8 0.4 1.0 CG A:HIS513 3.9 0.8 1.0 ND1 A:HIS513 4.0 0.7 1.0 ND1 A:HIS517 4.0 0.3 1.0 CG A:HIS517 4.2 0.8 1.0 O A:HIS513 4.4 0.3 1.0 CB A:TYR502 4.6 1.0 1.0 N A:CYS500 4.6 0.8 1.0 CA A:CYS500 4.8 0.6 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna


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(Znf 4-10) with 28-Mer Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn607 b:0.4 occ:1.00 O A:HOH736 3.2 67.5 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna


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(Znf 4-10) with 28-Mer Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:0.1 occ:1.00 NE2 B:HIS369 2.0 0.8 1.0 NE2 B:HIS373 2.0 0.4 1.0 SG B:CYS353 2.3 0.7 1.0 SG B:CYS356 2.4 0.3 1.0 CD2 B:HIS373 2.8 0.6 1.0 CD2 B:HIS369 3.0 0.2 1.0 CE1 B:HIS369 3.0 0.5 1.0 CE1 B:HIS373 3.1 0.8 1.0 N B:CYS356 3.4 0.3 1.0 CB B:CYS353 3.6 0.8 1.0 CB B:CYS356 3.6 0.9 1.0 CB B:MET355 3.7 0.1 1.0 CG B:HIS373 4.0 0.1 1.0 C B:MET355 4.0 0.8 1.0 CA B:CYS356 4.0 0.5 1.0 ND1 B:HIS373 4.1 0.1 1.0 ND1 B:HIS369 4.1 0.1 1.0 CG B:HIS369 4.1 0.9 1.0 N B:MET355 4.2 1.0 1.0 CA B:MET355 4.2 0.9 1.0 CB B:TYR358 4.3 0.5 1.0 C B:CYS356 4.6 0.6 1.0 O B:CYS356 4.7 0.9 1.0 CG B:MET355 4.8 0.1 1.0 O B:MET355 4.9 0.9 1.0 CA B:CYS353 4.9 0.1 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna


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(Znf 4-10) with 28-Mer Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:0.5 occ:1.00 NE2 B:HIS397 2.0 0.6 1.0 NE2 B:HIS401 2.0 0.4 1.0 SG B:CYS384 2.3 1.0 1.0 SG B:CYS381 2.3 0.7 1.0 CD2 B:HIS401 2.7 0.1 1.0 CE1 B:HIS397 2.9 0.9 1.0 CD2 B:HIS397 3.0 0.5 1.0 CE1 B:HIS401 3.2 0.7 1.0 N B:CYS384 3.4 0.9 1.0 CB B:CYS384 3.4 0.8 1.0 CB B:CYS381 3.7 0.1 1.0 CB B:LEU383 3.8 0.7 1.0 CG B:HIS401 3.9 0.4 1.0 ND1 B:HIS397 3.9 0.1 1.0 CA B:CYS384 4.0 0.6 1.0 CG B:HIS397 4.0 0.3 1.0 ND1 B:HIS401 4.2 0.2 1.0 C B:LEU383 4.3 0.1 1.0 CA B:LEU383 4.5 0.8 1.0 CB B:TYR386 4.6 0.4 1.0 C B:CYS384 4.6 0.5 1.0 N B:LEU383 4.6 0.2 1.0 SD B:MET398 4.7 0.4 1.0 O B:CYS384 4.9 0.3 1.0 O B:HIS397 4.9 87.6 1.0 CA B:CYS381 5.0 0.9 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Ctcf(Znf 4-10) with 28-Mer Dna


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(Znf 4-10) with 28-Mer Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:40.3 occ:1.00 NE2 B:HIS430 2.1 45.4 1.0 NE2 B:HIS425 2.1 46.0 1.0 SG B:CYS412 2.2 36.2 1.0 SG B:CYS409 2.3 43.6 1.0 CD2 B:HIS430 2.8 33.0 1.0 CD2 B:HIS425 3.0 46.2 1.0 CE1 B:HIS425 3.1 26.2 1.0 CE1 B:HIS430 3.2 37.3 1.0 CB B:CYS409 3.2 49.4 1.0 CB B:CYS412 3.3 25.2 1.0 N B:CYS412 3.7 36.0 1.0 CA B:CYS412 4.0 37.0 1.0 CG B:HIS430 4.0 43.5 1.0 ND1 B:HIS425 4.2 42.0 1.0 ND1 B:HIS430 4.2 30.9 1.0 C2 B:EDO606 4.2 82.9 1.0 CG B:HIS425 4.2 57.8 1.0 CB B:ILE411 4.6 43.4 1.0 C B:CYS412 4.6 28.8 1.0 CA B:CYS409 4.7 33.0 1.0 C B:ILE411 4.7 34.4 1.0 N B:HIS413 4.8 40.7 1.0 CB B:ALA414 4.9 27.5 1.0 O2 B:EDO606 4.9 77.9 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