Magnesium 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:

Zinc

(Zn)

6 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo Containing A 5MC, PDB code: 8tlj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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 X:Mg101 b:72.5 occ:0.50 O X:HOH207 2.1 59.5 1.0 OP1 X:DG20 2.1 59.8 1.0 P X:DG20 3.6 53.5 1.0 N A:SER243 3.8 77.5 1.0 N A:MET244 3.9 78.5 1.0 CG A:MET244 4.3 80.7 1.0 CB A:MET244 4.3 75.2 1.0 O3' X:DA19 4.4 61.1 1.0 OP2 X:DG20 4.4 50.0 1.0 CB A:SER243 4.4 85.5 1.0 O5' X:DG20 4.5 52.2 1.0 CA A:SER243 4.5 97.1 1.0 C5' X:DG20 4.6 53.6 1.0 CA A:MET244 4.7 71.9 1.0 C A:SER243 4.7 91.0 1.0 OG1 A:THR245 4.9 51.6 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 X:Mg102 b:63.0 occ:1.00 O X:HOH248 2.0 55.9 1.0 O X:HOH243 2.1 61.9 1.0 O X:HOH205 2.1 50.3 1.0 O X:HOH246 2.3 55.4 1.0 O X:HOH210 2.3 54.2 1.0 O X:HOH228 2.3 52.0 1.0 OP2 X:DA19 4.1 57.8 1.0 N7 X:DA19 4.3 41.9 1.0 O X:HOH218 4.3 52.5 1.0 O A:HOH506 4.5 48.2 1.0 C2' X:DG18 4.5 46.2 1.0 O X:HOH221 4.5 46.8 1.0 O6 X:DG20 4.7 47.5 1.0 O A:HOH544 4.7 52.4 1.0 C8 X:DA19 4.7 45.0 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