Zinc in PDB 8tlk: CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC

The structure of CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC, PDB code: 8tlk was solved by J.R.Horton, R.Ren, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.06 / 2.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	173.479, 31.538, 94.566, 90, 110.18, 90
R / Rfree (%)	24.3 / 30.2

The structure of CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC (pdb code 8tlk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC, PDB code: 8tlk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:26.7 occ:1.00 SG A:CYS300 2.2 20.8 1.0 SG A:CYS297 2.2 22.8 1.0 SG A:CYS273 2.3 33.5 1.0 SG A:CYS270 2.3 24.9 1.0 CB A:CYS300 3.0 22.1 1.0 CB A:CYS270 3.0 26.4 1.0 CB A:CYS297 3.4 24.9 1.0 CB A:CYS273 3.4 28.0 1.0 NZ A:LYS260 3.5 32.4 1.0 N A:CYS273 3.7 26.3 1.0 N A:CYS297 3.9 23.6 1.0 CA A:CYS273 4.2 27.1 1.0 CA A:CYS297 4.2 24.3 1.0 CA A:CYS300 4.3 23.1 1.0 N A:CYS300 4.4 24.3 1.0 CB A:GLN272 4.4 26.7 1.0 CA A:CYS270 4.5 26.1 1.0 CE A:LYS260 4.7 32.9 1.0 C A:GLN272 4.8 25.1 1.0 N A:GLN272 4.9 24.6 1.0 C A:CYS297 4.9 24.4 1.0 CA A:GLN272 5.0 24.7 1.0

Zinc binding site 2 out of 6 in the CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:22.4 occ:1.00 NE2 A:HIS271 2.0 23.1 1.0 SG A:CYS332 2.3 30.0 1.0 SG A:CYS327 2.3 26.8 1.0 SG A:CYS329 2.3 27.6 1.0 CD2 A:HIS271 2.9 24.6 1.0 CE1 A:HIS271 3.0 23.9 1.0 CB A:CYS332 3.1 34.4 1.0 CB A:CYS327 3.4 27.8 1.0 CB A:CYS329 3.5 26.8 1.0 CG A:HIS271 4.0 23.8 1.0 ND1 A:HIS271 4.1 23.9 1.0 N A:CYS332 4.2 37.6 1.0 CG A:PRO322 4.2 24.3 1.0 CA A:CYS332 4.3 38.4 1.0 N A:CYS329 4.3 27.6 1.0 CA A:CYS329 4.5 27.5 1.0 CA A:CYS327 4.7 28.3 1.0 C A:CYS327 4.8 28.8 1.0 CB A:PRO322 4.9 26.4 1.0 O A:CYS327 5.0 30.2 1.0

Zinc binding site 3 out of 6 in the CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:20.3 occ:1.00 SG A:CYS323 2.3 26.5 1.0 SG A:CYS284 2.3 28.6 1.0 SG A:CYS289 2.3 29.6 1.0 SG A:CYS320 2.3 25.1 1.0 CB A:CYS289 2.9 30.3 1.0 CB A:CYS284 3.3 28.2 1.0 CB A:CYS320 3.5 24.7 1.0 CB A:CYS323 3.5 26.2 1.0 NH1 A:ARG293 3.8 28.7 1.0 N A:CYS320 3.9 28.0 1.0 CA A:CYS289 4.1 31.4 1.0 CA A:CYS320 4.3 25.8 1.0 CA A:GLY294 4.4 25.6 1.0 N A:CYS323 4.4 28.6 1.0 CA A:CYS323 4.5 26.4 1.0 CG A:ARG293 4.5 26.9 1.0 CA A:CYS284 4.7 28.8 1.0 CB A:ASN286 4.7 32.1 1.0 N A:GLY294 4.7 25.7 1.0 CZ A:ARG293 4.8 28.2 1.0 O A:CYS320 4.9 27.5 1.0 C A:CYS320 5.0 27.3 1.0 CD A:ARG293 5.0 28.8 1.0

Zinc binding site 4 out of 6 in the CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:29.6 occ:1.00 SG B:CYS300 2.2 30.9 1.0 SG B:CYS273 2.3 34.6 1.0 SG B:CYS297 2.3 26.7 1.0 SG B:CYS270 2.3 33.7 1.0 CB B:CYS300 3.0 31.2 1.0 CB B:CYS270 3.1 32.5 1.0 CB B:CYS273 3.2 35.4 1.0 N B:CYS273 3.4 34.3 1.0 NZ B:LYS260 3.6 36.0 1.0 CB B:CYS297 3.6 30.3 1.0 CA B:CYS273 3.9 34.6 1.0 CB B:GLN272 4.1 35.4 1.0 N B:CYS297 4.2 32.3 1.0 CA B:CYS300 4.3 32.4 1.0 C B:GLN272 4.4 34.3 1.0 CA B:CYS297 4.5 34.2 1.0 CA B:CYS270 4.5 31.3 1.0 N B:CYS300 4.5 34.5 1.0 N B:GLN272 4.6 33.1 1.0 CA B:GLN272 4.6 34.2 1.0 C B:CYS270 4.8 31.1 1.0 C B:CYS273 4.9 33.4 1.0 CG B:GLN272 4.9 37.5 1.0

Zinc binding site 5 out of 6 in the CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:27.3 occ:1.00 NE2 B:HIS271 2.0 31.2 1.0 SG B:CYS329 2.3 44.4 1.0 SG B:CYS332 2.3 34.8 1.0 SG B:CYS327 2.3 38.6 1.0 CD2 B:HIS271 2.7 31.6 1.0 CE1 B:HIS271 2.9 30.3 1.0 CB B:CYS329 3.2 42.5 1.0 CB B:CYS332 3.4 44.8 1.0 CB B:CYS327 3.7 38.2 1.0 CG B:HIS271 3.8 30.9 1.0 ND1 B:HIS271 3.9 30.1 1.0 N B:CYS329 4.3 44.8 1.0 CA B:CYS329 4.3 46.5 1.0 N B:CYS332 4.4 46.9 1.0 CA B:CYS332 4.5 46.0 1.0 CG B:PRO322 4.5 28.6 1.0 O B:HIS271 4.7 31.9 1.0 CA B:CYS327 4.9 44.0 1.0 C B:CYS327 5.0 47.0 1.0

Zinc binding site 6 out of 6 in the CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of CDCA7 (Human) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:31.3 occ:1.00 SG B:CYS284 2.3 34.7 1.0 SG B:CYS323 2.3 35.0 1.0 SG B:CYS320 2.3 31.8 1.0 SG B:CYS289 2.3 36.1 1.0 CB B:CYS289 3.0 35.7 1.0 CB B:CYS284 3.1 34.0 1.0 CB B:CYS320 3.4 32.1 1.0 CB B:CYS323 3.4 35.6 1.0 N B:CYS320 3.7 36.1 1.0 NH1 B:ARG293 4.1 33.6 1.0 CA B:CYS320 4.1 34.4 1.0 CA B:CYS289 4.2 36.0 1.0 CB B:ASN286 4.4 40.2 1.0 N B:CYS323 4.4 35.8 1.0 CA B:CYS323 4.4 35.4 1.0 CA B:CYS284 4.6 32.6 1.0 CA B:GLY294 4.6 26.9 1.0 CG B:ARG293 4.7 29.6 1.0 ND2 B:ASN286 4.8 40.5 1.0 O B:CYS320 4.8 35.0 1.0 C B:HIS319 4.9 38.3 1.0 C B:CYS320 4.9 34.1 1.0 N B:GLY294 5.0 28.4 1.0

S.Hardikar, R.Ren, Z.Ying, J.R.Horton, M.D.Bramble, B.Liu, Y.Lu, J.Dan, X.Zhang, X.Cheng, T.Chen. The Icf Syndrome Protein CDCA7 Harbors A Unique Dna-Binding Domain That Recognizes A Cpg Dyad in the Context of A Non-B Dna Sci Adv 2024.
ISSN: ESSN 2375-2548