Magnesium in PDB 6mc2: Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex

The structure of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex, PDB code: 6mc2 was solved by B.Chu, P.J.Paukstelis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.48 / 1.05
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	25.960, 46.960, 35.963, 90.00, 101.12, 90.00
R / Rfree (%)	10.7 / 13.7

The binding sites of Magnesium atom in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex (pdb code 6mc2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex, PDB code: 6mc2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:4.7 occ:1.00 OP2 A:DA5 2.0 5.7 1.0 O A:HOH238 2.1 5.1 1.0 O A:HOH246 2.1 6.2 1.0 O A:HOH242 2.1 5.4 1.0 O A:HOH262 2.1 5.4 1.0 O A:HOH249 2.1 4.8 1.0 P A:DA5 3.4 5.2 1.0 O5' A:DA5 3.9 8.1 1.0 O A:HOH247 3.9 7.2 1.0 O A:HOH224 4.1 9.9 1.0 O A:HOH213 4.1 6.3 0.5 OP1 A:DA5 4.2 7.9 1.0 O3' A:DA4 4.3 5.7 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:8.4 occ:0.40 O A:HOH260 1.9 22.4 1.0 O A:HOH253 1.9 20.1 0.7 OP1 A:DG7 1.9 10.3 0.5 O A:HOH234 2.0 7.7 0.7 O A:HOH225 2.1 14.3 1.0 O A:HOH206 2.1 3.4 0.3 OP1 A:DG7 2.2 7.9 0.5 O A:HOH253 2.2 10.0 0.3 O A:HOH241 2.3 20.1 1.0 OP2 A:DG7 3.2 8.1 0.5 P A:DG7 3.2 8.2 0.5 P A:DG7 3.3 8.5 0.5 O A:HOH234 3.3 9.7 0.3 O A:HOH222 3.8 23.7 1.0 OP2 A:DG7 3.9 13.3 0.5 O5' A:DG7 4.0 9.6 0.5 O A:HOH256 4.3 8.0 1.0 O5' A:DG7 4.3 7.9 0.5 O3' A:DG6 4.4 6.5 1.0 C5' A:DG7 4.4 9.7 0.5 C3' A:DG6 4.6 5.3 1.0 O A:HOH207 4.7 14.6 0.6 O A:HOH203 4.9 27.6 1.0 C5' A:DG7 4.9 7.9 0.5

Magnesium binding site 3 out of 5 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:9.5 occ:0.37 O A:HOH265 2.0 32.8 1.0 O A:HOH259 2.0 7.5 1.0 O A:HOH268 2.0 25.0 1.0 O A:HOH267 2.1 32.4 1.0 O A:HOH261 2.2 19.3 1.0 O A:HOH217 2.2 23.6 1.0 O A:HOH212 3.5 15.8 0.4 O A:HOH258 3.6 39.2 1.0 O A:HOH235 4.1 41.6 1.0 O A:HOH212 4.2 7.5 0.6 OP1 A:DA5 4.2 7.9 1.0 O A:HOH244 4.8 13.1 1.0 O A:HOH224 4.9 9.9 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:6.9 occ:1.00 OP2 B:DA4 2.0 7.8 1.0 O B:HOH216 2.1 12.4 1.0 O B:HOH233 2.1 10.3 1.0 O B:HOH227 2.1 19.8 1.0 O B:HOH251 2.1 12.5 1.0 P B:DA4 3.3 6.6 1.0 O3' B:DT3 4.0 7.0 1.0 OP1 B:DA4 4.0 7.0 1.0 O B:HOH239 4.1 28.4 1.0 N1 B:DA5 4.2 6.1 1.0 O B:HOH229 4.4 34.4 1.0 O5' B:DA4 4.5 6.9 0.7 O5' B:DA4 4.5 7.3 0.3 N6 B:DA5 4.8 7.0 1.0 C5' B:DA4 4.8 6.7 0.7 C5' B:DA4 4.8 7.2 0.3 C6 B:DA5 5.0 5.5 1.0 C2 B:DA5 5.0 6.5 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:4.8 occ:0.51 O B:HOH205 1.9 4.3 0.5 O A:HOH209 2.0 5.0 0.5 O B:HOH205 2.0 5.3 0.5 O A:HOH243 2.1 5.9 0.6 O A:HOH201 2.1 5.7 0.5 O A:HOH201 2.1 6.8 0.5 O A:HOH243 2.3 5.4 0.4 O A:HOH209 3.0 7.1 0.6 O6 A:DG7 3.6 5.9 0.5 N7 A:DG7 3.8 5.8 0.5 O6 B:DG7 3.9 11.6 1.0 N7 B:DG7 3.9 9.9 1.0 O A:HOH205 4.0 6.2 0.5 N7 A:DG7 4.3 6.5 0.5 C6 A:DG7 4.3 5.2 0.5 O6 A:DG7 4.3 5.4 0.5 C5 A:DG7 4.4 5.2 0.5 C6 B:DG7 4.6 9.1 1.0 C5 B:DG7 4.7 7.6 1.0 C2' B:DG6 4.7 8.8 1.0 N3 B:DG6 4.7 5.9 1.0 C1' B:DG6 4.8 6.3 1.0 C4 B:DG6 4.9 5.7 1.0 N9 B:DG6 4.9 6.1 1.0 N3 A:DG6 4.9 5.8 1.0 C8 A:DG7 5.0 5.2 0.5

B.Chu, D.Zhang, W.Hwang, P.J.Paukstelis. Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex. J. Am. Chem. Soc. V. 140 16291 2018.
ISSN: ESSN 1520-5126
PubMed: 30384604
DOI: 10.1021/JACS.8B10153