Magnesium 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:

Zinc

(Zn)

6 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the CDCA7 (Mouse) Binds Non-B-Form Dna Oligo 36-Mer (Sg C2-Form 2), PDB code: 8tlf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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 X:Mg103 b:14.7 occ:1.00 OP2 X:DG25 2.0 15.6 1.0 O X:HOH248 2.1 14.1 1.0 O X:HOH250 2.1 14.4 1.0 O X:HOH271 2.1 15.0 1.0 P X:DG25 3.5 16.4 1.0 O X:HOH246 4.1 13.4 1.0 O5' X:DG25 4.2 16.1 1.0 C3' X:DC24 4.2 17.1 1.0 O3' X:DC24 4.2 15.5 1.0 O5' X:DC24 4.4 14.1 1.0 OP1 X:DG25 4.4 18.9 1.0 O4 X:DT27 4.6 14.2 1.0 O X:HOH264 4.7 15.5 1.0 C8 X:DG25 4.7 16.3 1.0 N7 X:DG25 5.0 15.0 1.0

Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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 X:Mg104 b:17.5 occ:1.00 OP2 X:DG31 2.1 16.9 1.0 N7 X:DG31 2.3 17.7 1.0 C8 X:DG31 3.0 22.1 1.0 P X:DG31 3.4 17.3 1.0 C5 X:DG31 3.4 19.6 1.0 O5' X:DG31 3.7 17.9 1.0 O X:HOH247 3.8 19.8 1.0 O6 X:DG31 4.1 19.9 1.0 C6 X:DG31 4.1 16.8 1.0 OP1 X:DG31 4.2 17.8 1.0 N9 X:DG31 4.2 22.1 1.0 C4 X:DG31 4.4 23.1 1.0 O3' X:DC30 4.5 16.7 1.0 O X:HOH268 4.6 19.0 1.0 C3' X:DC30 4.6 20.0 1.0

Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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 X:Mg105 b:37.5 occ:1.00 O X:HOH286 2.0 38.1 1.0 O X:HOH219 2.1 34.8 1.0 O X:HOH210 2.1 28.4 1.0 O X:HOH267 2.1 34.6 1.0 O X:HOH284 2.2 38.8 1.0 O A:HOH618 4.1 28.8 1.0 N7 X:DA19 4.1 25.7 1.0 O X:HOH232 4.3 30.4 1.0 O A:HOH651 4.3 29.7 1.0 O6 X:DG20 4.3 25.2 1.0 OP2 X:DA19 4.4 31.9 1.0 O X:HOH226 4.6 38.5 1.0 C8 X:DA19 4.6 23.2 1.0 O X:HOH236 4.7 38.0 1.0 C2' X:DG18 4.8 28.0 1.0

Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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 Y:Mg101 b:39.3 occ:1.00 O Y:HOH204 2.1 29.0 1.0 O Y:HOH266 2.1 40.4 1.0 O Y:HOH208 2.1 39.0 1.0 O Y:HOH264 2.1 37.5 1.0 O Y:HOH246 2.1 34.1 1.0 O B:HOH524 4.0 34.4 1.0 O Y:HOH232 4.1 30.4 1.0 N7 Y:DA19 4.1 25.8 1.0 O B:HOH542 4.2 33.9 1.0 O6 Y:DG20 4.3 31.5 1.0 OP2 Y:DA19 4.4 36.3 1.0 C8 Y:DA19 4.6 31.2 1.0 C2' Y:DG18 4.8 33.4 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