Zinc in PDB 8tlg: CDCA7 (Mouse) Binds Non-B-Form 34-Mer Dna Oligo

The structure of CDCA7 (Mouse) Binds Non-B-Form 34-Mer Dna Oligo, PDB code: 8tlg 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)	30.28 / 2.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.491, 60.562, 53.229, 90, 123.1, 90
R / Rfree (%)	18.6 / 22.3

The structure of CDCA7 (Mouse) Binds Non-B-Form 34-Mer Dna Oligo also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the CDCA7 (Mouse) Binds Non-B-Form 34-Mer Dna Oligo (pdb code 8tlg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the CDCA7 (Mouse) Binds Non-B-Form 34-Mer Dna Oligo, PDB code: 8tlg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the CDCA7 (Mouse) Binds Non-B-Form 34-Mer Dna Oligo


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 34-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:33.1 occ:1.00 SG A:CYS284 2.2 33.2 1.0 SG A:CYS308 2.3 37.7 1.0 SG A:CYS281 2.3 31.1 1.0 SG A:CYS311 2.3 35.9 1.0 CB A:CYS311 3.1 33.3 1.0 CB A:CYS281 3.1 23.7 1.0 CB A:CYS284 3.2 35.8 1.0 CB A:CYS308 3.5 34.5 1.0 N A:CYS284 3.6 27.9 1.0 NZ A:LYS271 3.6 38.1 1.0 CA A:CYS284 4.0 32.2 1.0 N A:CYS308 4.1 31.4 1.0 CA A:CYS311 4.3 34.9 1.0 CA A:CYS308 4.4 34.8 1.0 CB A:GLN283 4.4 29.7 1.0 N A:CYS311 4.4 36.0 1.0 CA A:CYS281 4.6 24.3 1.0 O A:HOH507 4.6 28.8 1.0 C A:GLN283 4.7 34.9 1.0 C A:CYS284 4.9 34.6 1.0 N A:GLN283 4.9 27.0 1.0 CA A:GLN283 4.9 31.7 1.0 CE A:LYS271 4.9 43.6 1.0 C A:CYS281 5.0 25.7 1.0

Zinc binding site 2 out of 3 in the CDCA7 (Mouse) Binds Non-B-Form 34-Mer Dna Oligo


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 34-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:34.9 occ:1.00 NE2 A:HIS282 2.1 29.1 1.0 SG A:CYS338 2.3 39.4 1.0 SG A:CYS343 2.3 45.1 1.0 SG A:CYS340 2.3 38.3 1.0 CD2 A:HIS282 3.0 34.1 1.0 CB A:CYS343 3.1 36.8 1.0 CE1 A:HIS282 3.1 40.4 1.0 CB A:CYS340 3.4 27.7 1.0 CB A:CYS338 3.4 41.2 1.0 N A:CYS343 4.1 39.8 1.0 CG A:HIS282 4.1 30.2 1.0 ND1 A:HIS282 4.1 30.9 1.0 CA A:CYS343 4.2 39.5 1.0 N A:CYS340 4.2 35.0 1.0 CA A:CYS340 4.4 29.9 1.0 CG A:PRO333 4.4 33.0 1.0 CA A:CYS338 4.7 38.2 1.0 O A:HOH513 4.7 34.1 1.0 C A:CYS338 4.8 41.6 1.0 C A:CYS340 5.0 37.4 1.0 O A:CYS338 5.0 39.4 1.0

Zinc binding site 3 out of 3 in the CDCA7 (Mouse) Binds Non-B-Form 34-Mer Dna Oligo


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 34-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:40.2 occ:1.00 SG A:CYS331 2.3 42.2 1.0 SG A:CYS295 2.3 37.5 1.0 SG A:CYS300 2.3 44.0 1.0 SG A:CYS334 2.3 43.1 1.0 CB A:CYS300 3.1 48.9 1.0 CB A:CYS295 3.2 36.9 1.0 CB A:CYS334 3.4 46.4 1.0 CB A:CYS331 3.4 36.8 1.0 N A:CYS331 3.8 34.7 1.0 NH1 A:ARG304 4.0 45.0 1.0 CA A:CYS331 4.1 42.1 1.0 N A:CYS334 4.3 44.5 1.0 CA A:CYS300 4.3 36.7 1.0 CA A:CYS334 4.4 40.1 1.0 CA A:GLY305 4.5 31.2 1.0 CB A:ASN297 4.5 44.3 1.0 CG A:ARG304 4.6 34.1 1.0 CA A:CYS295 4.7 39.2 1.0 O A:CYS331 4.7 37.6 1.0 O A:HOH520 4.7 36.8 1.0 C A:CYS331 4.8 41.6 1.0 N A:GLY305 4.9 35.4 1.0 ND2 A:ASN297 4.9 49.3 1.0 C A:HIS330 4.9 43.1 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