Zinc in PDB 8ssq: Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4

The structure of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4, PDB code: 8ssq 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)	41.86 / 3.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	352.07, 67.768, 61.194, 90, 92.59, 90
R / Rfree (%)	24 / 27.1

The structure of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Zinc atom in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4 (pdb code 8ssq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4, PDB code: 8ssq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


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 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:216.4 occ:1.00 NE2 A:HIS345 2.0 237.8 1.0 NE2 A:HIS340 2.0 204.8 1.0 CD2 A:HIS345 2.2 238.1 1.0 SG A:CYS327 2.3 200.6 1.0 SG A:CYS324 2.3 232.1 1.0 CD2 A:HIS340 2.9 198.5 1.0 CE1 A:HIS340 3.0 208.3 1.0 CB A:CYS324 3.1 231.2 1.0 CE1 A:HIS345 3.3 238.4 1.0 CG A:HIS345 3.5 232.7 1.0 CB A:CYS327 3.6 217.1 1.0 N A:CYS327 3.9 226.1 1.0 ND1 A:HIS345 4.0 234.7 1.0 CG A:HIS340 4.0 193.0 1.0 ND1 A:HIS340 4.1 199.2 1.0 CA A:CYS327 4.3 220.8 1.0 CB A:ASP326 4.5 224.5 1.0 CA A:CYS324 4.5 231.4 1.0 CB A:MET329 4.6 228.8 1.0 C A:ASP326 4.7 224.0 1.0 CB A:HIS345 4.7 231.0 1.0 C A:CYS327 4.7 218.8 1.0 N A:ASP326 4.9 234.8 1.0 C A:CYS324 4.9 229.2 1.0 CA A:ASP326 4.9 229.2 1.0 CG A:ARG341 5.0 206.7 1.0 O A:CYS324 5.0 230.3 1.0 CG A:MET329 5.0 216.1 1.0 N A:MET329 5.0 226.4 1.0

Zinc binding site 2 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


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 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:242.7 occ:1.00 CD2 A:HIS369 1.8 213.8 1.0 NE2 A:HIS369 2.0 220.7 1.0 NE2 A:HIS373 2.1 215.7 1.0 SG A:CYS356 2.3 216.7 1.0 SG A:CYS353 2.3 247.1 1.0 CB A:CYS353 2.9 234.8 1.0 CE1 A:HIS373 3.0 212.5 1.0 CG A:HIS369 3.1 208.5 1.0 CD2 A:HIS373 3.1 210.1 1.0 CE1 A:HIS369 3.2 214.2 1.0 ND1 A:HIS369 3.7 210.0 1.0 CB A:TYR358 3.9 215.4 1.0 CB A:CYS356 3.9 204.7 1.0 N A:CYS356 4.0 222.8 1.0 ND1 A:HIS373 4.1 209.9 1.0 CG A:HIS373 4.2 203.8 1.0 CB A:HIS369 4.2 190.8 1.0 CA A:CYS353 4.3 232.8 1.0 CA A:CYS356 4.4 221.2 1.0 CB A:MET355 4.5 212.3 1.0 CD1 A:TYR358 4.6 211.7 1.0 CG A:TYR358 4.6 215.0 1.0 N A:TYR358 4.7 221.4 1.0 C A:CYS356 4.8 230.9 1.0 CA A:TYR358 4.8 221.0 1.0 C A:CYS353 4.9 223.2 1.0 C A:MET355 4.9 223.1 1.0 O A:CYS356 4.9 232.6 1.0 N A:MET355 4.9 217.5 1.0 O A:TYR358 4.9 225.6 1.0 O A:HIS369 5.0 193.6 1.0

Zinc binding site 3 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


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 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:118.0 occ:1.00 NE2 A:HIS401 2.0 106.9 1.0 NE2 A:HIS397 2.0 106.7 1.0 SG A:CYS381 2.3 140.7 1.0 SG A:CYS384 2.3 126.3 1.0 CB A:CYS384 2.7 145.1 1.0 CE1 A:HIS397 2.8 117.1 1.0 CE1 A:HIS401 3.0 116.5 1.0 CD2 A:HIS401 3.0 121.2 1.0 CD2 A:HIS397 3.1 119.4 1.0 CB A:CYS381 3.3 117.5 1.0 N A:CYS384 3.4 124.6 1.0 CA A:CYS384 3.6 129.0 1.0 ND1 A:HIS397 3.9 104.8 1.0 CG A:HIS397 4.0 105.7 1.0 ND1 A:HIS401 4.1 117.7 1.0 CG A:HIS401 4.1 114.9 1.0 C A:LEU383 4.3 133.5 1.0 C A:CYS384 4.4 117.2 1.0 N A:LEU383 4.6 114.1 1.0 CB A:LEU383 4.6 135.1 1.0 CA A:CYS381 4.7 120.9 1.0 CA A:LEU383 4.7 131.5 1.0 O A:HIS397 4.9 121.0 1.0 SD A:MET398 4.9 118.8 1.0 O A:CYS384 4.9 123.1 1.0

Zinc binding site 4 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


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 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn704 b:121.4 occ:1.00 NE2 A:HIS430 2.0 163.8 1.0 NE2 A:HIS425 2.0 97.6 1.0 SG A:CYS412 2.3 101.7 1.0 SG A:CYS409 2.3 121.9 1.0 CD2 A:HIS425 2.7 103.3 1.0 CD2 A:HIS430 2.8 156.3 1.0 CE1 A:HIS430 2.9 160.6 1.0 CB A:CYS409 3.1 116.7 1.0 CE1 A:HIS425 3.2 126.4 1.0 CB A:CYS412 3.4 106.3 1.0 N A:CYS412 3.6 115.3 1.0 CG A:HIS430 3.8 150.8 1.0 ND1 A:HIS430 3.9 153.1 1.0 CG A:HIS425 4.0 106.2 1.0 CA A:CYS412 4.0 111.0 1.0 ND1 A:HIS425 4.2 105.6 1.0 CB A:ILE411 4.5 149.7 1.0 CA A:CYS409 4.6 109.8 1.0 C A:ILE411 4.7 147.4 1.0 CG1 A:ILE426 4.7 109.6 1.0 C A:CYS412 4.7 124.3 1.0 N A:HIS413 4.8 134.7 1.0 N A:ILE411 4.8 143.0 1.0 CA A:ILE411 4.9 139.9 1.0

Zinc binding site 5 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


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 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn705 b:140.5 occ:1.00 NE2 A:HIS455 2.0 95.9 1.0 NE2 A:HIS460 2.0 95.7 1.0 SG A:CYS442 2.2 97.8 1.0 SG A:CYS439 2.2 124.3 1.0 CE1 A:HIS460 2.6 128.5 1.0 CD2 A:HIS455 2.9 91.0 1.0 CB A:CYS442 3.1 101.3 1.0 CE1 A:HIS455 3.1 106.2 1.0 CD2 A:HIS460 3.1 115.8 1.0 CB A:CYS439 3.2 114.1 1.0 OG1 A:THR444 3.6 142.2 1.0 ND1 A:HIS460 3.7 97.9 1.0 N A:CYS442 3.8 104.3 1.0 CA A:CYS442 4.0 104.8 1.0 CG A:HIS460 4.0 113.0 1.0 CG A:HIS455 4.1 88.4 1.0 ND1 A:HIS455 4.1 89.1 1.0 C A:HIS441 4.5 107.4 1.0 C A:CYS442 4.6 128.4 1.0 CA A:CYS439 4.7 100.4 1.0 CB A:HIS441 4.9 130.8 1.0 CB A:GLN459 4.9 83.8 1.0 N A:HIS441 5.0 115.0 1.0

Zinc binding site 6 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


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 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn706 b:109.0 occ:1.00 NE2 A:HIS485 2.0 108.2 1.0 NE2 A:HIS489 2.0 93.0 1.0 SG A:CYS472 2.3 95.8 1.0 SG A:CYS469 2.4 84.0 1.0 CD2 A:HIS489 2.6 94.2 1.0 CD2 A:HIS485 2.7 125.3 1.0 CE1 A:HIS485 3.1 138.6 1.0 CE1 A:HIS489 3.1 123.8 1.0 CB A:CYS472 3.4 101.4 1.0 CB A:CYS469 3.6 95.5 1.0 CG A:HIS489 3.8 97.5 1.0 CG A:HIS485 3.8 81.7 1.0 N A:CYS472 3.8 103.2 1.0 ND1 A:HIS485 3.9 111.9 1.0 ND1 A:HIS489 3.9 120.2 1.0 CA A:CYS472 4.2 86.8 1.0 O A:HIS485 4.4 123.7 1.0 C A:TYR471 4.5 106.8 1.0 CB A:TYR471 4.6 107.2 1.0 N A:TYR471 4.7 120.7 1.0 C A:HIS485 4.8 97.9 1.0 CA A:TYR471 4.8 113.6 1.0 CA A:GLN486 4.8 91.8 1.0 CA A:CYS469 5.0 80.8 1.0 CD2 A:TYR471 5.0 96.9 1.0 C A:CYS472 5.0 85.8 1.0

Zinc binding site 7 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


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 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn707 b:144.5 occ:1.00 NE2 A:HIS513 2.0 130.5 1.0 NE2 A:HIS517 2.0 191.6 1.0 CD2 A:HIS517 2.2 167.3 1.0 SG A:CYS500 2.3 165.0 1.0 SG A:CYS497 2.3 194.8 1.0 CD2 A:HIS513 2.7 133.2 1.0 CB A:CYS497 3.1 156.4 1.0 CE1 A:HIS513 3.2 136.3 1.0 CE1 A:HIS517 3.3 176.5 1.0 CB A:CYS500 3.4 168.6 1.0 N A:CYS500 3.5 168.3 1.0 CG A:HIS517 3.5 152.3 1.0 C A:GLN499 3.9 166.6 1.0 CG A:HIS513 3.9 131.8 1.0 CA A:CYS500 4.0 165.1 1.0 ND1 A:HIS517 4.0 144.9 1.0 CB A:GLN499 4.0 168.4 1.0 ND1 A:HIS513 4.2 130.7 1.0 N A:GLN499 4.2 193.2 1.0 CA A:GLN499 4.3 165.0 1.0 CA A:CYS497 4.5 146.6 1.0 O A:GLN499 4.6 171.6 1.0 C A:CYS500 4.6 174.8 1.0 CB A:HIS517 4.7 140.1 1.0 C A:CYS497 4.8 151.5 1.0 O A:CYS500 4.8 155.6 1.0 CB A:TYR502 4.9 159.0 1.0

Zinc binding site 8 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


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 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn708 b:204.2 occ:1.00 NE2 A:HIS541 2.0 148.2 1.0 NE2 A:HIS546 2.0 172.0 1.0 SG A:CYS528 2.3 162.8 1.0 SG A:CYS525 2.3 215.0 1.0 CD2 A:HIS541 2.9 162.7 1.0 CE1 A:HIS546 3.0 180.4 1.0 CD2 A:HIS546 3.0 174.0 1.0 CE1 A:HIS541 3.0 166.6 1.0 CB A:CYS525 3.3 195.1 1.0 CB A:CYS528 3.4 176.7 1.0 CG A:HIS541 4.0 161.2 1.0 ND1 A:HIS546 4.0 188.8 1.0 ND1 A:HIS541 4.1 171.5 1.0 CG A:HIS546 4.1 175.2 1.0 N A:CYS528 4.3 191.9 1.0 CA A:CYS528 4.5 196.8 1.0 CD A:LYS530 4.7 164.8 1.0 CA A:CYS525 4.7 188.8 1.0 C A:HIS527 4.8 197.0 1.0 CB A:LYS530 5.0 159.8 1.0

Zinc binding site 9 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn709 b:290.3 occ:1.00 NE2 A:HIS573 2.0 274.6 1.0 SG A:CYS560 2.3 259.0 1.0 SG A:CYS577 2.3 284.2 1.0 SG A:CYS557 2.3 269.6 1.0 CD2 A:HIS573 2.5 280.1 1.0 CE1 A:HIS573 3.1 266.9 1.0 CB A:CYS577 3.1 295.9 1.0 CB A:CYS560 3.2 255.4 1.0 CB A:CYS557 3.5 268.1 1.0 N A:CYS560 3.6 274.9 1.0 CG A:HIS573 3.6 277.2 1.0 ND1 A:HIS573 3.8 274.3 1.0 CA A:CYS560 4.0 264.5 1.0 O A:HIS573 4.3 304.1 1.0 CA A:CYS577 4.4 302.1 1.0 C A:HIS573 4.7 299.4 1.0 CB A:LYS559 4.7 283.2 1.0 C A:LYS559 4.8 280.6 1.0 N A:GLY561 4.8 262.1 1.0 CA A:ALA574 4.8 307.6 1.0 N A:LYS559 4.9 282.7 1.0 C A:CYS560 4.9 260.7 1.0 CA A:CYS557 4.9 274.1 1.0 CB A:HIS573 4.9 275.4 1.0 N A:ALA574 4.9 301.1 1.0

Zinc binding site 10 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:255.9 occ:1.00 NE2 D:HIS369 2.0 234.9 1.0 NE2 D:HIS373 2.0 221.5 1.0 SG D:CYS353 2.3 249.8 1.0 SG D:CYS356 2.3 236.2 1.0 CD2 D:HIS369 2.6 230.1 1.0 CD2 D:HIS373 2.9 218.8 1.0 CE1 D:HIS373 3.0 222.6 1.0 CE1 D:HIS369 3.2 226.9 1.0 CB D:CYS353 3.6 248.1 1.0 CB D:CYS356 3.7 226.6 1.0 CG D:HIS369 3.8 228.6 1.0 N D:CYS356 3.8 240.5 1.0 CB D:MET355 3.8 235.8 1.0 ND1 D:HIS369 4.0 225.0 1.0 CG D:HIS373 4.1 219.9 1.0 ND1 D:HIS373 4.1 229.2 1.0 CA D:CYS356 4.3 237.8 1.0 C D:MET355 4.3 242.3 1.0 CA D:MET355 4.4 243.4 1.0 CB D:TYR358 4.4 249.5 1.0 N D:MET355 4.5 246.3 1.0 O D:HIS369 4.6 224.3 1.0 CG D:MET355 4.7 228.9 1.0 OG D:SER372 4.8 210.6 1.0 C D:HIS369 4.9 220.6 1.0 C D:CYS356 4.9 244.6 1.0 CA D:CYS353 5.0 251.7 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