Magnesium 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:

Zinc

(Zn)

3 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg 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 X:Mg101 b:78.1 occ:0.50 O X:HOH203 2.1 151.7 1.0 OP1 X:DG20 2.1 52.1 1.0 P X:DG20 3.5 58.2 1.0 N A:MET244 4.1 98.5 1.0 O3' X:DA19 4.2 52.3 1.0 OP2 X:DG20 4.3 60.1 1.0 OG1 A:THR245 4.3 62.8 1.0 O X:HOH206 4.3 76.6 1.0 O5' X:DG20 4.5 58.5 1.0 CB A:MET244 4.7 91.2 1.0 C5' X:DG20 4.8 62.5 1.0 N A:THR245 4.8 69.8 1.0 CA A:MET244 4.9 87.4 1.0 CG A:MET244 5.0 89.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 X:Mg102 b:88.8 occ:1.00 O X:HOH207 2.1 88.4 1.0 O X:HOH204 2.1 83.6 1.0 O X:HOH202 2.1 119.2 1.0 O X:HOH208 2.3 79.7 1.0 C2' X:DG18 3.4 65.5 1.0 OP2 X:DA19 3.4 81.4 1.0 N7 X:DA19 3.5 72.2 1.0 C8 X:DA19 3.9 64.7 1.0 C3' X:DG18 4.4 67.5 1.0 C8 X:DG18 4.5 64.4 1.0 P X:DA19 4.6 74.2 1.0 C1' X:DG18 4.7 64.5 1.0 O6 X:DG20 4.7 70.2 1.0 O5' X:DA19 4.7 72.1 1.0 N9 X:DG18 4.8 60.4 1.0 C5 X:DA19 4.8 69.3 1.0 O3' X:DG18 5.0 70.3 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 X:Mg103 b:97.2 occ:1.00 O X:HOH205 2.7 84.7 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.
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