Zinc in PDB 8tll: CDCA7 (Mouse) Binds Non-B-Form 26-Mer Dna Oligo

The structure of CDCA7 (Mouse) Binds Non-B-Form 26-Mer Dna Oligo, PDB code: 8tll 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)	48.40 / 2.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.71, 60.724, 84.106, 90, 113.96, 90
R / Rfree (%)	23.5 / 28.2

The structure of CDCA7 (Mouse) Binds Non-B-Form 26-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 26-Mer Dna Oligo (pdb code 8tll). 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 26-Mer Dna Oligo, PDB code: 8tll:
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 26-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 26-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:37.0 occ:1.00 SG A:CYS284 2.2 42.9 1.0 SG A:CYS308 2.3 38.3 1.0 SG A:CYS281 2.3 36.5 1.0 SG A:CYS311 2.3 39.6 1.0 CB A:CYS284 2.9 33.8 1.0 CB A:CYS311 3.1 35.3 1.0 CB A:CYS281 3.1 37.1 1.0 N A:CYS284 3.4 35.2 1.0 CB A:CYS308 3.5 39.6 1.0 CA A:CYS284 3.7 34.0 1.0 NZ A:LYS271 3.8 45.0 1.0 N A:CYS308 4.1 36.3 1.0 CA A:CYS311 4.3 40.6 1.0 CA A:CYS308 4.4 37.4 1.0 O A:HOH502 4.4 33.7 1.0 N A:CYS311 4.5 38.3 1.0 CB A:GLN283 4.5 32.8 1.0 C A:GLN283 4.5 36.0 1.0 CA A:CYS281 4.6 30.5 1.0 C A:CYS284 4.7 35.6 1.0 CA A:GLN283 4.9 34.0 1.0 N A:GLN283 4.9 35.2 1.0 N A:ARG285 4.9 35.3 1.0 C A:CYS281 5.0 35.8 1.0 C A:CYS308 5.0 37.6 1.0

Zinc binding site 2 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 26-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 26-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:44.5 occ:1.00 NE2 A:HIS282 2.1 38.5 1.0 SG A:CYS340 2.3 40.4 1.0 SG A:CYS343 2.3 59.0 1.0 SG A:CYS338 2.3 37.9 1.0 CE1 A:HIS282 2.9 38.4 1.0 CB A:CYS343 2.9 47.9 1.0 CD2 A:HIS282 3.1 34.6 1.0 CB A:CYS340 3.3 41.6 1.0 CB A:CYS338 3.5 43.7 1.0 ND1 A:HIS282 4.0 37.5 1.0 N A:CYS343 4.0 48.6 1.0 CA A:CYS343 4.0 55.1 1.0 CG A:HIS282 4.1 39.7 1.0 N A:CYS340 4.2 41.6 1.0 CA A:CYS340 4.3 38.5 1.0 CG A:PRO333 4.6 42.1 1.0 CA A:CYS338 4.7 43.0 1.0 C A:CYS338 4.8 42.1 1.0 C A:CYS340 4.9 45.1 1.0

Zinc binding site 3 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 26-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 26-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:47.1 occ:1.00 SG A:CYS331 2.3 44.5 1.0 SG A:CYS295 2.3 46.5 1.0 SG A:CYS300 2.4 51.0 1.0 SG A:CYS334 2.4 59.2 1.0 CB A:CYS300 3.2 58.7 1.0 CB A:CYS295 3.3 47.4 1.0 CB A:CYS331 3.5 42.4 1.0 CB A:CYS334 3.6 52.3 1.0 N A:CYS331 3.9 42.5 1.0 NH2 A:ARG304 4.2 50.9 1.0 CA A:CYS331 4.3 41.9 1.0 N A:CYS334 4.3 48.3 1.0 NE A:ARG304 4.4 46.9 1.0 CB A:ASN297 4.5 66.9 1.0 CA A:CYS334 4.5 51.8 1.0 CA A:CYS300 4.5 63.9 1.0 CA A:GLY305 4.6 34.7 1.0 CA A:CYS295 4.8 49.9 1.0 CZ A:ARG304 4.8 48.2 1.0 O A:CYS331 4.8 49.1 1.0 ND2 A:ASN297 4.9 73.4 1.0 C A:CYS331 4.9 44.8 1.0 N A:GLY305 5.0 44.1 1.0 C A:HIS330 5.0 46.5 1.0

Zinc binding site 4 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 26-Mer Dna Oligo


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 26-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:33.4 occ:1.00 SG B:CYS308 2.2 39.5 1.0 SG B:CYS284 2.3 38.2 1.0 SG B:CYS281 2.3 36.3 1.0 SG B:CYS311 2.4 39.7 1.0 CB B:CYS281 3.1 36.2 1.0 CB B:CYS311 3.2 37.9 1.0 CB B:CYS284 3.3 32.9 1.0 CB B:CYS308 3.6 42.1 1.0 N B:CYS284 3.6 36.5 1.0 NZ B:LYS271 3.9 41.6 1.0 CA B:CYS284 4.1 32.9 1.0 N B:CYS308 4.1 42.3 1.0 CB B:GLN283 4.3 40.4 1.0 CA B:CYS308 4.4 43.4 1.0 CA B:CYS311 4.4 41.4 1.0 N B:CYS311 4.5 49.6 1.0 CA B:CYS281 4.6 33.8 1.0 C B:GLN283 4.6 39.1 1.0 CA B:GLN283 4.9 39.2 1.0 N B:GLN283 4.9 42.4 1.0 CG B:GLN283 4.9 43.2 1.0 C B:CYS284 5.0 34.4 1.0 C B:CYS281 5.0 34.5 1.0

Zinc binding site 5 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 26-Mer Dna Oligo


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 26-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:35.5 occ:1.00 NE2 B:HIS282 2.0 44.1 1.0 SG B:CYS343 2.3 45.0 1.0 SG B:CYS338 2.3 39.8 1.0 SG B:CYS340 2.3 31.3 1.0 CD2 B:HIS282 3.0 42.1 1.0 CE1 B:HIS282 3.0 42.3 1.0 CB B:CYS343 3.1 44.3 1.0 CB B:CYS340 3.2 39.9 1.0 CB B:CYS338 3.5 41.1 1.0 ND1 B:HIS282 4.0 40.4 1.0 N B:CYS343 4.0 43.8 1.0 CG B:HIS282 4.1 39.8 1.0 CA B:CYS343 4.1 48.2 1.0 N B:CYS340 4.3 41.4 1.0 CA B:CYS340 4.3 39.0 1.0 CG B:PRO333 4.4 42.6 1.0 CA B:CYS338 4.7 39.0 1.0 C B:CYS338 4.9 42.0 1.0 C B:CYS340 4.9 42.2 1.0 O B:CYS338 5.0 46.9 1.0

Zinc binding site 6 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 26-Mer Dna Oligo


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 26-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:49.8 occ:1.00 SG B:CYS334 2.3 58.7 1.0 SG B:CYS331 2.3 45.7 1.0 SG B:CYS295 2.3 52.8 1.0 SG B:CYS300 2.4 52.9 1.0 CB B:CYS300 3.1 57.7 1.0 CB B:CYS295 3.2 48.2 1.0 CB B:CYS334 3.5 53.1 1.0 CB B:CYS331 3.6 45.1 1.0 N B:CYS331 3.9 43.0 1.0 CA B:CYS331 4.3 45.8 1.0 CA B:CYS300 4.3 55.0 1.0 N B:CYS334 4.5 51.2 1.0 CB B:ASN297 4.5 59.6 1.0 CA B:CYS334 4.5 53.7 1.0 CA B:GLY305 4.7 49.4 1.0 CA B:CYS295 4.7 51.4 1.0 NH2 B:ARG304 4.7 57.2 1.0 ND2 B:ASN297 4.9 69.1 1.0 O B:CYS331 4.9 47.5 1.0 C B:HIS330 5.0 46.4 1.0 NE B:ARG304 5.0 52.7 1.0 C B:CYS331 5.0 45.8 1.0 CZ B:ARG304 5.0 54.0 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