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

The structure of CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC, PDB code: 8tlj 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)	45.03 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.874, 31.533, 91.823, 90, 110.75, 90
R / Rfree (%)	18.5 / 22.8

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC (pdb code 8tlj). 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 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC, PDB code: 8tlj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the CDCA7 (Mouse) 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 (Mouse) 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:37.8 occ:1.00 SG A:CYS284 2.3 35.7 1.0 SG A:CYS311 2.3 39.1 1.0 SG A:CYS308 2.3 39.6 1.0 SG A:CYS281 2.3 35.1 1.0 CB A:CYS311 3.1 34.8 1.0 CB A:CYS281 3.1 27.4 1.0 CB A:CYS284 3.2 38.7 1.0 CB A:CYS308 3.5 37.9 1.0 N A:CYS284 3.6 42.5 1.0 NZ A:LYS271 3.6 43.1 1.0 CA A:CYS284 4.0 38.3 1.0 N A:CYS308 4.1 38.0 1.0 CB A:GLN283 4.3 32.7 1.0 CA A:CYS311 4.3 45.7 1.0 CA A:CYS308 4.4 36.7 1.0 N A:CYS311 4.4 45.0 1.0 CA A:CYS281 4.5 30.9 1.0 C A:GLN283 4.6 33.1 1.0 O A:HOH501 4.8 35.7 1.0 CA A:GLN283 4.8 38.1 1.0 N A:GLN283 4.8 40.0 1.0 C A:CYS284 4.9 36.3 1.0 C A:CYS281 4.9 30.7 1.0 C A:CYS308 5.0 43.4 1.0 CE A:LYS271 5.0 38.5 1.0 O A:CYS308 5.0 35.8 1.0

Zinc binding site 2 out of 6 in the CDCA7 (Mouse) 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 (Mouse) 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:39.6 occ:1.00 NE2 A:HIS282 2.1 36.3 1.0 SG A:CYS338 2.3 39.5 1.0 SG A:CYS343 2.3 47.7 1.0 SG A:CYS340 2.3 34.7 1.0 CD2 A:HIS282 2.9 32.5 1.0 CB A:CYS343 3.1 47.4 1.0 CE1 A:HIS282 3.1 33.4 1.0 CB A:CYS338 3.4 41.6 1.0 CB A:CYS340 3.4 35.6 1.0 N A:CYS343 4.1 43.8 1.0 CG A:HIS282 4.1 35.8 1.0 ND1 A:HIS282 4.1 34.9 1.0 CA A:CYS343 4.2 55.6 1.0 N A:CYS340 4.2 42.6 1.0 CA A:CYS340 4.4 44.2 1.0 CG A:PRO333 4.4 37.7 1.0 O A:HOH516 4.5 36.5 1.0 CA A:CYS338 4.7 43.0 1.0 C A:CYS338 4.8 44.9 1.0 O1 A:GOL401 5.0 62.1 1.0 C A:CYS340 5.0 44.7 1.0

Zinc binding site 3 out of 6 in the CDCA7 (Mouse) 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 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:42.1 occ:1.00 SG A:CYS334 2.3 40.9 1.0 SG A:CYS331 2.3 39.8 1.0 SG A:CYS295 2.3 43.5 1.0 SG A:CYS300 2.4 40.6 1.0 CB A:CYS300 3.1 38.3 1.0 CB A:CYS334 3.2 43.0 1.0 CB A:CYS295 3.3 38.2 1.0 CB A:CYS331 3.5 37.8 1.0 NH1 A:ARG304 3.7 35.3 1.0 N A:CYS331 3.8 40.1 1.0 N A:CYS334 4.2 39.8 1.0 CA A:CYS334 4.2 43.9 1.0 CA A:CYS331 4.2 40.5 1.0 CA A:CYS300 4.3 43.4 1.0 CB A:ASN297 4.4 47.8 1.0 CA A:GLY305 4.5 36.3 1.0 CG A:ARG304 4.6 35.1 1.0 O A:CYS331 4.7 44.2 1.0 CA A:CYS295 4.7 43.1 1.0 O A:HOH519 4.8 37.9 1.0 C A:CYS331 4.8 42.4 1.0 CZ A:ARG304 4.9 40.1 1.0 ND2 A:ASN297 4.9 42.9 1.0 N A:GLY305 4.9 34.3 1.0 C A:HIS330 5.0 41.8 1.0

Zinc binding site 4 out of 6 in the CDCA7 (Mouse) 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 (Mouse) 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:48.2 occ:1.00 SG B:CYS308 2.3 44.1 1.0 SG B:CYS284 2.3 42.8 1.0 SG B:CYS311 2.3 49.0 1.0 SG B:CYS281 2.4 52.2 1.0 CB B:CYS311 3.0 47.8 1.0 CB B:CYS281 3.1 46.9 1.0 CB B:CYS284 3.3 53.0 1.0 N B:CYS284 3.5 48.5 1.0 CB B:CYS308 3.6 49.8 1.0 NZ B:LYS271 3.7 51.3 1.0 CA B:CYS284 4.0 45.1 1.0 N B:CYS308 4.1 49.1 1.0 CB B:GLN283 4.2 45.0 1.0 CA B:CYS311 4.3 52.2 1.0 N B:CYS311 4.4 54.2 1.0 CA B:CYS308 4.4 51.8 1.0 C B:GLN283 4.6 51.0 1.0 CA B:CYS281 4.6 49.5 1.0 CA B:GLN283 4.8 49.0 1.0 N B:GLN283 4.8 45.2 1.0 C B:CYS284 4.9 49.7 1.0 C B:CYS281 5.0 54.5 1.0 CE B:LYS271 5.0 48.3 1.0

Zinc binding site 5 out of 6 in the CDCA7 (Mouse) 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 (Mouse) 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:55.1 occ:1.00 NE2 B:HIS282 2.0 53.4 1.0 SG B:CYS343 2.2 63.2 1.0 SG B:CYS338 2.3 50.9 1.0 SG B:CYS340 2.3 49.6 1.0 CE1 B:HIS282 3.0 52.9 1.0 CD2 B:HIS282 3.0 53.5 1.0 CB B:CYS343 3.1 60.6 1.0 CB B:CYS340 3.4 47.5 1.0 CB B:CYS338 3.4 53.2 1.0 ND1 B:HIS282 4.1 49.5 1.0 N B:CYS343 4.1 67.4 1.0 CG B:HIS282 4.1 53.4 1.0 CA B:CYS343 4.2 65.1 1.0 N B:CYS340 4.3 51.5 1.0 CA B:CYS340 4.4 52.1 1.0 CG B:PRO333 4.5 58.9 1.0 CA B:CYS338 4.7 58.7 1.0 C B:CYS338 4.8 58.3 1.0 C B:CYS340 5.0 58.2 1.0

Zinc binding site 6 out of 6 in the CDCA7 (Mouse) 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 (Mouse) 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:60.8 occ:1.00 SG B:CYS334 2.2 56.4 1.0 SG B:CYS295 2.3 54.7 1.0 SG B:CYS331 2.3 60.0 1.0 SG B:CYS300 2.4 60.0 1.0 CB B:CYS300 3.1 62.3 1.0 CB B:CYS334 3.3 52.8 1.0 CB B:CYS295 3.3 58.9 1.0 CB B:CYS331 3.6 53.8 1.0 N B:CYS331 3.9 63.7 1.0 NH1 B:ARG304 4.1 59.9 1.0 N B:CYS334 4.2 58.2 1.0 CA B:CYS334 4.3 56.2 1.0 CA B:CYS331 4.3 61.4 1.0 CA B:CYS300 4.3 72.4 1.0 CG B:ARG304 4.5 58.5 1.0 CA B:GLY305 4.6 54.4 1.0 CB B:ASN297 4.7 69.5 1.0 O B:CYS331 4.7 59.1 1.0 CA B:CYS295 4.7 57.5 1.0 N B:GLY305 4.8 56.4 1.0 C B:CYS331 4.8 61.2 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