Magnesium in PDB 6mc3: Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex

The structure of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex, PDB code: 6mc3 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)	28.42 / 1.57
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	34.135, 46.430, 71.894, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex (pdb code 6mc3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex, PDB code: 6mc3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 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:54.7 occ:1.00 OP1 A:DA5 2.1 36.7 0.5 OP1 A:DA5 2.2 40.4 0.5 OP1 A:DT3 2.3 45.2 1.0 O A:HOH204 2.5 52.1 1.0 C3' A:DG4 3.3 45.7 0.5 P A:DA5 3.4 41.2 0.5 C2' A:DG4 3.6 41.8 0.5 P A:DA5 3.6 36.6 0.5 P A:DT3 3.7 47.2 1.0 O5' A:DA5 3.8 43.1 0.5 O3' A:DG4 3.9 41.9 0.5 O5' A:DA5 4.2 34.2 0.5 O5' A:DT3 4.2 48.2 1.0 C5' A:DT3 4.2 43.9 1.0 OP2 A:DA5 4.3 26.3 0.5 C4' A:DG4 4.5 39.1 0.5 C5' A:DG4 4.5 40.8 0.5 O3' A:DG2 4.6 52.4 1.0 C3' A:DG2 4.6 38.6 1.0 OP2 A:DT3 4.6 53.7 1.0 O3' A:DG4 4.7 30.7 0.5 OP2 A:DA5 4.8 32.3 0.5 C2' A:DG4 4.8 31.7 0.5 O A:HOH216 4.8 53.2 1.0 C3' A:DG4 5.0 31.9 0.5 C5' A:DA5 5.0 44.0 0.5

Magnesium binding site 2 out of 6 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 C:Mg101 b:48.0 occ:1.00 O B:HOH126 2.0 54.8 1.0 O B:HOH121 2.0 48.8 1.0 O B:HOH118 2.0 42.7 1.0 O C:HOH214 2.1 43.6 1.0 O C:HOH225 2.1 49.4 1.0 O C:HOH202 2.3 46.8 1.0 O B:HOH104 3.4 48.4 1.0 N3 C:DG9 4.1 35.1 1.0 N1 B:DA5 4.4 38.1 1.0 O3' C:DG9 4.5 60.5 1.0 C1' C:DG9 4.5 43.5 1.0 N2 C:DG9 4.6 31.9 1.0 C2 C:DG9 4.8 34.3 1.0 N6 B:DA5 4.9 35.8 1.0 O4' C:DG9 5.0 43.0 1.0

Magnesium binding site 3 out of 6 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 D:Mg101 b:32.9 occ:1.00 O C:HOH203 1.9 31.3 1.0 O D:HOH212 2.0 29.2 1.0 O C:HOH212 2.0 38.8 1.0 O A:HOH209 2.0 33.7 1.0 O B:HOH119 2.2 35.2 1.0 O D:HOH209 2.2 31.1 1.0 O A:HOH206 3.7 32.9 1.0 O C:HOH210 3.7 38.5 1.0 O A:HOH213 3.8 43.0 1.0 O6 D:DG7 3.9 35.6 1.0 N7 D:DG7 4.0 27.7 1.0 O6 C:DG7 4.2 28.6 1.0 N7 C:DG7 4.2 28.4 1.0 O6 A:DG7 4.2 36.7 1.0 C2' D:DG6 4.5 22.9 1.0 O6 B:DG7 4.6 34.2 1.0 N7 B:DG7 4.6 31.4 1.0 C6 D:DG7 4.7 34.1 1.0 N3 D:DG6 4.7 24.7 1.0 C5 D:DG7 4.7 28.3 1.0 C1' D:DG6 4.7 28.3 1.0 N3 C:DG6 4.8 25.4 1.0 C4 D:DG6 4.8 24.4 1.0 N9 D:DG6 4.9 26.6 1.0 C6 C:DG7 4.9 32.3 1.0 C5 C:DG7 4.9 28.3 1.0

Magnesium binding site 4 out of 6 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 D:Mg102 b:29.4 occ:1.00 OP1 D:DA5 1.9 28.3 1.0 O D:HOH218 2.0 32.7 1.0 O D:HOH208 2.0 30.2 1.0 OP1 D:DT3 2.0 26.9 1.0 O D:HOH224 2.1 28.5 1.0 O D:HOH226 2.2 30.8 1.0 P D:DA5 3.4 33.3 1.0 P D:DT3 3.5 30.5 1.0 OP2 D:DA5 4.1 30.9 1.0 O5' D:DT3 4.2 26.7 1.0 O5' D:DA5 4.2 29.4 1.0 O D:HOH232 4.2 39.6 1.0 C5' D:DT3 4.3 28.2 1.0 OP2 D:DT3 4.4 40.0 1.0 O3' D:DG4 4.4 37.6 1.0 C2' D:DG4 4.4 33.6 1.0 O D:HOH202 4.4 52.8 1.0 C3' D:DG2 4.4 33.5 1.0 O D:HOH206 4.4 38.9 1.0 O3' D:DG2 4.5 30.3 1.0 O D:HOH237 4.6 54.6 1.0 C3' D:DG4 4.6 35.0 1.0 OP1 D:DG2 4.8 33.9 1.0 C5' D:DG2 5.0 28.9 1.0

Magnesium binding site 5 out of 6 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 D:Mg103 b:51.3 occ:1.00 O A:HOH214 2.0 42.9 1.0 O D:HOH231 2.0 48.9 1.0 O A:HOH205 2.2 45.8 1.0 O A:HOH218 2.2 51.1 1.0 OP2 D:DG6 3.5 28.1 1.0 O D:HOH236 4.4 57.0 1.0 O A:HOH201 4.7 39.1 1.0 O6 A:DG9 4.7 32.7 1.0 C3' D:DA5 4.7 31.3 1.0 N7 A:DG9 4.8 34.1 1.0 O D:HOH217 4.9 44.6 1.0 P D:DG6 4.9 30.1 1.0 C2' D:DA5 4.9 29.3 1.0

Magnesium binding site 6 out of 6 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 6 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg104 b:43.3 occ:1.00 O D:HOH230 2.0 39.1 1.0 O D:HOH203 2.0 53.4 1.0 O D:HOH240 2.2 41.0 1.0 O D:HOH239 2.2 55.2 1.0 O D:HOH201 2.3 47.5 1.0 O D:HOH236 3.3 57.0 1.0 OP1 D:DG2 4.0 33.9 1.0 OP2 D:DA5 4.3 30.9 1.0 OP1 D:DG6 4.4 31.3 1.0 O D:HOH206 4.5 38.9 1.0 O3' D:DA5 4.8 27.3 1.0 O3' D:DC1 4.9 34.9 1.0

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