Zinc in PDB 8tle: CDCA7 (Mouse) Binds Non-B-Form 36-Mer Dna Oligo (Sg C2-Form 1)

The structure of CDCA7 (Mouse) Binds Non-B-Form 36-Mer Dna Oligo (Sg C2-Form 1), PDB code: 8tle 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)	30.38 / 2.08
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.666, 60.768, 49.09, 90, 117.51, 90
R / Rfree (%)	23.2 / 26.2

The structure of CDCA7 (Mouse) Binds Non-B-Form 36-Mer Dna Oligo (Sg C2-Form 1) also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the CDCA7 (Mouse) Binds Non-B-Form 36-Mer Dna Oligo (Sg C2-Form 1) (pdb code 8tle). 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 36-Mer Dna Oligo (Sg C2-Form 1), PDB code: 8tle:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the CDCA7 (Mouse) Binds Non-B-Form 36-Mer Dna Oligo (Sg C2-Form 1)


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 36-Mer Dna Oligo (Sg C2-Form 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:75.2 occ:1.00 SG A:CYS311 2.3 65.2 1.0 SG A:CYS308 2.3 79.3 1.0 SG A:CYS284 2.3 80.0 1.0 SG A:CYS281 2.3 64.2 1.0 CB A:CYS311 3.0 56.4 1.0 CB A:CYS281 3.1 52.4 1.0 CB A:CYS284 3.1 71.1 1.0 N A:CYS284 3.5 73.5 1.0 CB A:CYS308 3.5 65.0 1.0 NZ A:LYS271 3.8 57.1 1.0 CA A:CYS284 3.9 70.4 1.0 N A:CYS308 4.0 52.8 1.0 CA A:CYS311 4.3 84.0 1.0 CB A:GLN283 4.3 61.5 1.0 CA A:CYS308 4.3 67.9 1.0 N A:CYS311 4.4 90.4 1.0 CA A:CYS281 4.5 63.7 1.0 C A:GLN283 4.6 73.9 1.0 C A:CYS284 4.8 66.8 1.0 CA A:GLN283 4.8 69.1 1.0 N A:GLN283 4.8 51.0 1.0 C A:CYS281 4.9 56.8 1.0 C A:CYS308 5.0 88.5 1.0

Zinc binding site 2 out of 3 in the CDCA7 (Mouse) Binds Non-B-Form 36-Mer Dna Oligo (Sg C2-Form 1)


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 36-Mer Dna Oligo (Sg C2-Form 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:51.6 occ:1.00 NE2 A:HIS282 2.0 61.5 1.0 SG A:CYS343 2.3 62.2 1.0 SG A:CYS340 2.3 46.0 1.0 SG A:CYS338 2.3 51.3 1.0 CE1 A:HIS282 2.9 64.8 1.0 CD2 A:HIS282 3.0 47.8 1.0 CB A:CYS343 3.1 76.0 1.0 CB A:CYS340 3.3 51.8 1.0 CB A:CYS338 3.5 56.9 1.0 ND1 A:HIS282 4.0 49.1 1.0 CG A:HIS282 4.1 66.5 1.0 N A:CYS343 4.2 66.6 1.0 N A:CYS340 4.3 71.3 1.0 CA A:CYS343 4.3 82.6 1.0 CG A:PRO333 4.3 53.7 1.0 CA A:CYS340 4.4 47.8 1.0 CA A:CYS338 4.8 47.9 1.0 C A:CYS338 4.9 61.2 1.0 C A:CYS340 5.0 69.9 1.0

Zinc binding site 3 out of 3 in the CDCA7 (Mouse) Binds Non-B-Form 36-Mer Dna Oligo (Sg C2-Form 1)


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 36-Mer Dna Oligo (Sg C2-Form 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:60.1 occ:1.00 SG A:CYS331 2.3 62.3 1.0 SG A:CYS334 2.3 79.0 1.0 SG A:CYS295 2.3 74.0 1.0 SG A:CYS300 2.3 57.1 1.0 CB A:CYS300 2.9 70.5 1.0 CB A:CYS295 3.3 77.2 1.0 CB A:CYS334 3.5 71.3 1.0 CB A:CYS331 3.5 47.8 1.0 N A:CYS331 3.9 64.2 1.0 CA A:CYS300 4.2 65.8 1.0 CA A:CYS331 4.3 62.3 1.0 CB A:ASN297 4.3 81.3 1.0 N A:CYS334 4.4 67.7 1.0 NE A:ARG304 4.4 74.4 1.0 CA A:CYS334 4.5 73.2 1.0 CA A:GLY305 4.5 63.3 1.0 ND2 A:ASN297 4.6 77.0 1.0 CA A:CYS295 4.7 79.0 1.0 NH2 A:ARG304 4.8 78.9 1.0 O A:CYS331 4.8 74.2 1.0 N A:GLY305 4.9 65.0 1.0 CG A:ARG304 4.9 64.4 1.0 C A:CYS331 4.9 74.1 1.0 N A:CYS300 5.0 69.6 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