Zinc in PDB 8tlf: CDCA7 (Mouse) Binds Non-B-Form Dna Oligo 36-Mer (Sg C2-Form 2)

The structure of CDCA7 (Mouse) Binds Non-B-Form Dna Oligo 36-Mer (Sg C2-Form 2), PDB code: 8tlf 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)	29.90 / 1.64
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.4, 31.492, 133.324, 90, 95.75, 90
R / Rfree (%)	19.2 / 21.8

The structure of CDCA7 (Mouse) Binds Non-B-Form Dna Oligo 36-Mer (Sg C2-Form 2) also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the CDCA7 (Mouse) Binds Non-B-Form Dna Oligo 36-Mer (Sg C2-Form 2) (pdb code 8tlf). 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 Dna Oligo 36-Mer (Sg C2-Form 2), PDB code: 8tlf:
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 Dna Oligo 36-Mer (Sg C2-Form 2)


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 Dna Oligo 36-Mer (Sg C2-Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:14.3 occ:1.00 SG A:CYS311 2.3 14.6 1.0 SG A:CYS284 2.3 13.9 1.0 SG A:CYS281 2.4 14.4 1.0 SG A:CYS308 2.4 17.2 1.0 CB A:CYS311 3.1 16.2 1.0 CB A:CYS281 3.2 8.7 1.0 CB A:CYS284 3.2 16.9 1.0 N A:CYS284 3.6 11.8 1.0 CB A:CYS308 3.6 16.5 1.0 NZ A:LYS271 3.6 17.2 1.0 CA A:CYS284 4.0 13.4 1.0 N A:CYS308 4.1 13.3 1.0 CB A:GLN283 4.3 12.9 1.0 CA A:CYS311 4.3 13.7 1.0 CA A:CYS308 4.4 16.2 1.0 N A:CYS311 4.4 15.9 1.0 O A:HOH607 4.5 18.4 1.0 C A:GLN283 4.6 14.2 1.0 CA A:CYS281 4.7 9.0 1.0 CA A:GLN283 4.8 15.2 1.0 N A:GLN283 4.8 15.6 1.0 C A:CYS284 4.9 11.8 1.0 CE A:LYS271 4.9 16.3 1.0 C A:CYS281 5.0 14.2 1.0

Zinc binding site 2 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form Dna Oligo 36-Mer (Sg C2-Form 2)


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 Dna Oligo 36-Mer (Sg C2-Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:15.4 occ:1.00 NE2 A:HIS282 2.0 13.4 1.0 SG A:CYS338 2.3 17.4 1.0 SG A:CYS343 2.3 21.1 1.0 SG A:CYS340 2.3 16.5 1.0 CD2 A:HIS282 2.9 17.8 1.0 CE1 A:HIS282 3.1 16.5 1.0 CB A:CYS343 3.1 23.9 1.0 CB A:CYS340 3.4 12.9 1.0 CB A:CYS338 3.5 14.9 1.0 CG A:HIS282 4.1 11.6 1.0 ND1 A:HIS282 4.1 13.6 1.0 N A:CYS343 4.2 22.0 1.0 CA A:CYS343 4.3 23.2 1.0 N A:CYS340 4.3 15.2 1.0 CA A:CYS340 4.4 13.8 1.0 O A:HOH608 4.5 15.6 1.0 CG A:PRO333 4.6 17.7 1.0 CA A:CYS338 4.7 16.9 1.0 C A:CYS338 4.9 16.6 1.0 C A:CYS340 5.0 16.3 1.0

Zinc binding site 3 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form Dna Oligo 36-Mer (Sg C2-Form 2)


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 Dna Oligo 36-Mer (Sg C2-Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:20.3 occ:1.00 SG A:CYS331 2.3 19.2 1.0 SG A:CYS334 2.3 20.8 1.0 SG A:CYS295 2.3 20.5 1.0 SG A:CYS300 2.3 20.2 1.0 CB A:CYS300 3.1 24.0 1.0 CB A:CYS295 3.2 20.6 1.0 CB A:CYS334 3.3 27.8 1.0 CB A:CYS331 3.5 17.2 1.0 N A:CYS331 3.9 20.7 1.0 NH1 A:ARG304 4.0 29.6 1.0 CA A:CYS331 4.2 18.2 1.0 N A:CYS334 4.3 17.1 1.0 CA A:CYS300 4.3 25.5 1.0 CA A:CYS334 4.3 19.0 1.0 CA A:GLY305 4.5 17.2 1.0 CB A:ASN297 4.6 26.3 1.0 CA A:CYS295 4.7 20.6 1.0 CG A:ARG304 4.7 26.1 1.0 O A:CYS331 4.7 20.3 1.0 C A:CYS331 4.9 21.8 1.0 N A:GLY305 4.9 16.9 1.0 O A:HOH613 4.9 20.2 1.0 CZ A:ARG304 5.0 27.8 1.0 C A:HIS330 5.0 25.5 1.0 ND2 A:ASN297 5.0 31.4 1.0

Zinc binding site 4 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form Dna Oligo 36-Mer (Sg C2-Form 2)


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 Dna Oligo 36-Mer (Sg C2-Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:17.0 occ:1.00 SG B:CYS311 2.3 16.7 1.0 SG B:CYS284 2.3 16.1 1.0 SG B:CYS308 2.3 20.0 1.0 SG B:CYS281 2.3 16.6 1.0 CB B:CYS311 3.0 19.6 1.0 CB B:CYS281 3.2 14.4 1.0 CB B:CYS284 3.2 17.0 1.0 CB B:CYS308 3.6 18.0 1.0 N B:CYS284 3.6 15.8 1.0 NZ B:LYS271 3.7 22.5 1.0 CA B:CYS284 4.0 17.7 1.0 N B:CYS308 4.1 18.5 1.0 CB B:GLN283 4.3 15.8 1.0 CA B:CYS311 4.3 16.8 1.0 CA B:CYS308 4.4 18.5 1.0 N B:CYS311 4.4 18.6 1.0 O B:HOH510 4.6 21.9 1.0 CA B:CYS281 4.6 14.6 1.0 C B:GLN283 4.6 16.6 1.0 CA B:GLN283 4.8 19.0 1.0 N B:GLN283 4.8 16.4 1.0 C B:CYS284 4.9 15.8 1.0 C B:CYS281 5.0 16.1 1.0

Zinc binding site 5 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form Dna Oligo 36-Mer (Sg C2-Form 2)


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 Dna Oligo 36-Mer (Sg C2-Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:18.5 occ:1.00 NE2 B:HIS282 2.0 17.5 1.0 SG B:CYS338 2.3 22.1 1.0 SG B:CYS340 2.3 23.6 1.0 SG B:CYS343 2.3 29.9 1.0 CD2 B:HIS282 3.0 19.7 1.0 CE1 B:HIS282 3.1 16.9 1.0 CB B:CYS343 3.3 31.7 1.0 CB B:CYS340 3.4 16.0 1.0 CB B:CYS338 3.5 21.8 1.0 CG B:HIS282 4.1 15.1 1.0 ND1 B:HIS282 4.1 18.6 1.0 N B:CYS340 4.3 17.5 1.0 N B:CYS343 4.3 32.5 1.0 CA B:CYS340 4.4 18.4 1.0 CA B:CYS343 4.4 35.9 1.0 CG B:PRO333 4.6 22.1 1.0 O B:HOH511 4.6 20.2 1.0 O B:HOH539 4.7 40.1 1.0 CA B:CYS338 4.7 20.0 1.0 C B:CYS338 4.8 25.8 1.0 C B:CYS340 5.0 23.7 1.0

Zinc binding site 6 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form Dna Oligo 36-Mer (Sg C2-Form 2)


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 Dna Oligo 36-Mer (Sg C2-Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:24.9 occ:1.00 SG B:CYS331 2.3 23.1 1.0 SG B:CYS334 2.3 31.1 1.0 SG B:CYS295 2.3 26.8 1.0 SG B:CYS300 2.3 25.1 1.0 CB B:CYS300 3.1 27.0 1.0 CB B:CYS295 3.2 26.0 1.0 CB B:CYS334 3.4 31.9 1.0 CB B:CYS331 3.5 24.4 1.0 N B:CYS331 3.9 25.5 1.0 NH1 B:ARG304 4.0 33.1 1.0 CA B:CYS331 4.2 25.5 1.0 CA B:CYS300 4.3 30.8 1.0 N B:CYS334 4.3 26.2 1.0 CA B:CYS334 4.4 27.3 1.0 CA B:GLY305 4.5 21.8 1.0 CB B:ASN297 4.6 34.8 1.0 CA B:CYS295 4.7 31.6 1.0 CG B:ARG304 4.7 27.9 1.0 O B:CYS331 4.7 24.1 1.0 C B:CYS331 4.9 25.6 1.0 O B:HOH518 4.9 22.9 1.0 N B:GLY305 4.9 20.9 1.0 CZ B:ARG304 4.9 28.6 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