Zinc in PDB 8ssr: Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20

The structure of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20, PDB code: 8ssr 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)	37.59 / 3.14
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	362.211, 68.09, 61.988, 90, 94.87, 90
R / Rfree (%)	24.9 / 28.4

The structure of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20 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- 20 (pdb code 8ssr). 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- 20, PDB code: 8ssr:
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- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:305.8 occ:1.00 NE2 A:HIS345 2.0 256.6 1.0 NE2 A:HIS340 2.0 293.9 1.0 SG A:CYS327 2.3 301.3 1.0 SG A:CYS324 2.3 305.5 1.0 CE1 A:HIS340 2.4 293.2 1.0 CD2 A:HIS345 2.7 246.7 1.0 CD2 A:HIS340 3.1 292.8 1.0 CE1 A:HIS345 3.2 258.3 1.0 CB A:CYS324 3.3 309.9 1.0 ND1 A:HIS340 3.5 294.5 1.0 CB A:CYS327 3.6 271.9 1.0 CG A:HIS340 3.9 293.1 1.0 CG A:HIS345 4.0 245.4 1.0 ND1 A:HIS345 4.2 256.0 1.0 N A:CYS327 4.6 280.8 1.0 CB A:LYS344 4.6 227.7 1.0 O A:HIS340 4.7 290.3 1.0 CA A:CYS327 4.7 275.3 1.0 CA A:CYS324 4.7 305.5 1.0 CD A:LYS344 4.8 218.1 1.0 CB A:MET329 4.8 282.8 1.0 CA A:ARG341 4.9 248.4 1.0 C A:HIS340 5.0 284.2 1.0

Zinc binding site 2 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:265.7 occ:1.00 NE2 A:HIS369 2.0 232.0 1.0 NE2 A:HIS373 2.0 216.2 1.0 SG A:CYS356 2.3 240.7 1.0 SG A:CYS353 2.3 316.9 1.0 CB A:CYS353 2.8 292.8 1.0 CD2 A:HIS373 2.9 200.6 1.0 CD2 A:HIS369 3.0 217.2 1.0 CE1 A:HIS369 3.0 229.5 1.0 CE1 A:HIS373 3.1 217.8 1.0 N A:CYS356 3.4 238.8 1.0 CB A:CYS356 3.6 226.1 1.0 CB A:MET355 3.6 217.7 1.0 CA A:CYS356 4.0 237.6 1.0 C A:MET355 4.1 233.2 1.0 ND1 A:HIS369 4.1 225.6 1.0 CG A:HIS373 4.1 204.4 1.0 CG A:HIS369 4.1 212.9 1.0 ND1 A:HIS373 4.1 218.2 1.0 CA A:MET355 4.2 233.5 1.0 CA A:CYS353 4.2 295.3 1.0 N A:MET355 4.2 237.9 1.0 C A:CYS356 4.5 251.9 1.0 CG A:MET355 4.5 213.4 1.0 C A:CYS353 4.7 290.8 1.0 O A:CYS356 4.7 251.3 1.0 CB A:TYR358 4.7 272.3 1.0 N A:CYS353 5.0 295.7 1.0

Zinc binding site 3 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:120.3 occ:1.00 NE2 A:HIS397 2.0 110.3 1.0 NE2 A:HIS401 2.0 142.4 1.0 SG A:CYS381 2.3 151.9 1.0 SG A:CYS384 2.3 120.2 1.0 CD2 A:HIS401 2.5 117.9 1.0 CE1 A:HIS397 2.8 143.9 1.0 CD2 A:HIS397 2.9 119.9 1.0 CB A:CYS384 3.0 154.9 1.0 CE1 A:HIS401 3.3 163.9 1.0 CB A:CYS381 3.6 138.9 1.0 N A:CYS384 3.7 133.0 1.0 CG A:HIS401 3.8 111.5 1.0 ND1 A:HIS397 3.9 116.0 1.0 CG A:HIS397 3.9 110.9 1.0 CA A:CYS384 3.9 126.8 1.0 ND1 A:HIS401 4.1 156.1 1.0 C A:LEU383 4.5 138.3 1.0 SD A:MET398 4.7 132.7 1.0 CB A:LEU383 4.7 126.8 1.0 O A:HIS397 4.7 132.8 1.0 N A:LEU383 4.8 118.3 1.0 C A:CYS384 4.9 111.2 1.0 CA A:LEU383 4.9 134.2 1.0 CA A:CYS381 4.9 142.1 1.0

Zinc binding site 4 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn704 b:156.9 occ:1.00 NE2 A:HIS425 2.0 95.0 1.0 NE2 A:HIS430 2.0 172.2 1.0 SG A:CYS412 2.3 83.3 1.0 SG A:CYS409 2.3 106.6 1.0 CD2 A:HIS430 2.6 171.8 1.0 CD2 A:HIS425 2.7 101.8 1.0 CE1 A:HIS430 3.1 169.9 1.0 CE1 A:HIS425 3.2 112.8 1.0 CB A:CYS409 3.3 128.4 1.0 CB A:CYS412 3.6 85.7 1.0 N A:CYS412 3.8 132.5 1.0 CG A:HIS430 3.8 175.1 1.0 CG A:HIS425 3.9 104.1 1.0 ND1 A:HIS430 4.0 174.3 1.0 ND1 A:HIS425 4.1 109.8 1.0 CA A:CYS412 4.3 94.5 1.0 CG1 A:ILE426 4.4 91.3 1.0 CB A:ILE411 4.6 183.6 1.0 CA A:CYS409 4.7 104.0 1.0 CA A:ILE426 4.8 136.6 1.0 C A:ILE411 4.9 165.5 1.0 C A:CYS412 5.0 137.2 1.0 O A:HIS425 5.0 123.8 1.0 N A:ILE426 5.0 112.5 1.0 N A:ILE411 5.0 176.5 1.0

Zinc binding site 5 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn705 b:233.0 occ:1.00 NE2 A:HIS460 2.0 106.1 1.0 NE2 A:HIS455 2.0 92.8 1.0 CD2 A:HIS455 2.3 99.5 1.0 SG A:CYS439 2.3 145.0 1.0 SG A:CYS442 2.3 94.3 1.0 CD2 A:HIS460 2.7 129.9 1.0 CE1 A:HIS460 2.7 156.1 1.0 CE1 A:HIS455 3.3 151.9 1.0 CB A:CYS439 3.5 105.7 1.0 ND1 A:HIS460 3.5 133.2 1.0 CG A:HIS460 3.6 134.8 1.0 CG A:HIS455 3.6 94.4 1.0 CB A:CYS442 3.7 92.8 1.0 OG1 A:THR444 3.9 138.2 1.0 ND1 A:HIS455 4.1 133.0 1.0 N A:CYS442 4.3 106.5 1.0 CD2 A:LEU456 4.6 109.8 1.0 CA A:CYS442 4.6 97.3 1.0 O A:HIS455 4.6 125.1 1.0 CB A:GLN459 4.7 77.8 1.0 CA A:CYS439 4.8 97.3 1.0 CB A:HIS455 4.8 82.8 1.0 C A:HIS455 4.9 79.1 1.0 CB A:HIS460 4.9 80.3 1.0

Zinc binding site 6 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn706 b:230.5 occ:1.00 NE2 A:HIS489 2.0 131.3 1.0 NE2 A:HIS485 2.0 121.2 1.0 SG A:CYS469 2.3 88.3 1.0 SG A:CYS472 2.3 113.3 1.0 CD2 A:HIS489 2.6 94.0 1.0 CD2 A:HIS485 2.7 148.8 1.0 CE1 A:HIS485 3.1 153.0 1.0 CE1 A:HIS489 3.2 150.2 1.0 CB A:CYS472 3.4 96.7 1.0 CB A:CYS469 3.6 85.3 1.0 CG A:HIS489 3.8 112.0 1.0 CG A:HIS485 3.8 91.2 1.0 N A:CYS472 3.9 92.5 1.0 ND1 A:HIS485 4.0 102.4 1.0 ND1 A:HIS489 4.0 152.5 1.0 C A:TYR471 4.2 95.3 1.0 CA A:CYS472 4.2 93.5 1.0 CB A:TYR471 4.6 129.2 1.0 N A:TYR471 4.6 145.1 1.0 O A:TYR471 4.6 125.3 1.0 O A:HIS485 4.6 106.3 1.0 CA A:TYR471 4.7 104.7 1.0 CA A:CYS469 5.0 89.6 1.0 C A:HIS485 5.0 88.0 1.0

Zinc binding site 7 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn707 b:146.8 occ:1.00 NE2 A:HIS517 2.0 224.2 1.0 NE2 A:HIS513 2.0 149.2 1.0 CD2 A:HIS517 2.3 215.1 1.0 SG A:CYS500 2.3 139.6 1.0 SG A:CYS497 2.3 205.2 1.0 CD2 A:HIS513 2.6 147.2 1.0 CB A:CYS497 3.2 180.1 1.0 CE1 A:HIS517 3.2 226.0 1.0 CE1 A:HIS513 3.2 145.2 1.0 CG A:HIS517 3.4 208.6 1.0 CB A:CYS500 3.5 150.0 1.0 N A:CYS500 3.8 161.8 1.0 CG A:HIS513 3.8 151.1 1.0 ND1 A:HIS517 3.8 217.9 1.0 ND1 A:HIS513 4.1 141.1 1.0 CB A:GLN499 4.2 211.3 1.0 CA A:CYS500 4.2 142.2 1.0 C A:GLN499 4.2 198.2 1.0 N A:GLN499 4.5 207.4 1.0 CA A:GLN499 4.5 205.2 1.0 CA A:CYS497 4.6 175.5 1.0 CB A:HIS517 4.6 192.3 1.0 CB A:TYR502 4.9 137.8 1.0 O A:HIS513 4.9 188.2 1.0 C A:CYS500 4.9 157.2 1.0 O A:GLN499 4.9 215.6 1.0 C A:CYS497 5.0 181.6 1.0

Zinc binding site 8 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn708 b:234.2 occ:1.00 NE2 A:HIS546 2.0 195.6 1.0 NE2 A:HIS541 2.0 224.9 1.0 SG A:CYS528 2.3 174.3 1.0 SG A:CYS525 2.4 216.9 1.0 CD2 A:HIS541 2.5 216.0 1.0 CD2 A:HIS546 3.0 196.5 1.0 CE1 A:HIS546 3.0 185.9 1.0 CE1 A:HIS541 3.3 223.3 1.0 CB A:CYS525 3.6 207.8 1.0 CB A:CYS528 3.7 175.0 1.0 CG A:HIS541 3.8 210.0 1.0 ND1 A:HIS541 4.1 216.9 1.0 ND1 A:HIS546 4.1 194.8 1.0 CG A:HIS546 4.1 198.2 1.0 N A:CYS528 4.7 203.4 1.0 CA A:CYS528 4.8 196.0 1.0 O A:HIS541 4.8 200.6 1.0 CA A:CYS525 5.0 214.2 1.0

Zinc binding site 9 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn709 b:318.2 occ:1.00 NE2 A:HIS573 2.0 324.8 1.0 SG A:CYS560 2.3 256.3 1.0 SG A:CYS557 2.3 286.1 1.0 SG A:CYS577 2.3 306.4 1.0 CD2 A:HIS573 2.4 328.2 1.0 CB A:CYS577 3.0 313.1 1.0 CB A:CYS560 3.1 263.6 1.0 CE1 A:HIS573 3.1 326.1 1.0 CB A:CYS557 3.4 278.8 1.0 CG A:HIS573 3.5 332.2 1.0 N A:CYS560 3.5 273.0 1.0 ND1 A:HIS573 3.8 332.6 1.0 CA A:CYS560 3.9 261.0 1.0 O A:HIS573 4.2 347.6 1.0 CA A:CYS577 4.3 316.3 1.0 C A:LYS559 4.3 277.8 1.0 CB A:LYS559 4.3 255.0 1.0 C A:HIS573 4.6 340.0 1.0 CA A:LYS559 4.7 270.2 1.0 CA A:ALA574 4.7 307.3 1.0 N A:LYS559 4.7 271.4 1.0 CB A:HIS573 4.8 328.5 1.0 N A:GLY561 4.8 263.1 1.0 C A:CYS560 4.8 251.8 1.0 CA A:CYS557 4.8 279.1 1.0 N A:ALA574 4.8 313.7 1.0

Zinc binding site 10 out of 17 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:401.5 occ:1.00 NE2 D:HIS369 2.0 311.6 1.0 NE2 D:HIS373 2.0 301.8 1.0 CD2 D:HIS369 2.3 314.6 1.0 SG D:CYS356 2.3 316.3 1.0 SG D:CYS353 2.4 493.9 1.0 CD2 D:HIS373 2.9 302.8 1.0 CE1 D:HIS373 3.0 300.5 1.0 CE1 D:HIS369 3.3 301.5 1.0 CG D:HIS369 3.6 302.8 1.0 CB D:CYS353 3.7 468.7 1.0 CB D:CYS356 3.7 328.4 1.0 N D:CYS356 3.9 375.9 1.0 CG D:HIS373 4.0 301.5 1.0 ND1 D:HIS373 4.0 297.7 1.0 ND1 D:HIS369 4.0 299.2 1.0 CB D:MET355 4.2 375.7 1.0 CB D:TYR358 4.3 321.7 1.0 O D:HIS369 4.3 302.4 1.0 CA D:CYS356 4.3 359.7 1.0 C D:MET355 4.5 377.8 1.0 CA D:MET355 4.7 386.1 1.0 C D:HIS369 4.7 310.4 1.0 N D:MET355 4.8 396.7 1.0 CB D:HIS369 4.8 301.4 1.0 OG D:SER372 4.9 297.2 1.0 C D:CYS356 4.9 365.1 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