Magnesium in PDB 3u0u: Crystal Structure of the DB1883-D(Cgcgaattcgcg)2 Complex at 1.24 A Resolution

The structure of Crystal Structure of the DB1883-D(Cgcgaattcgcg)2 Complex at 1.24 A Resolution, PDB code: 3u0u was solved by D.G.Wei, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.16 / 1.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	23.940, 39.690, 65.640, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.2

The binding sites of Magnesium atom in the Crystal Structure of the DB1883-D(Cgcgaattcgcg)2 Complex at 1.24 A Resolution (pdb code 3u0u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the DB1883-D(Cgcgaattcgcg)2 Complex at 1.24 A Resolution, PDB code: 3u0u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the DB1883-D(Cgcgaattcgcg)2 Complex at 1.24 A Resolution


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 the DB1883-D(Cgcgaattcgcg)2 Complex at 1.24 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg14 b:10.2 occ:1.00 O B:HOH2 2.0 11.1 1.0 O B:HOH5 2.0 11.7 1.0 O A:HOH32 2.1 10.0 1.0 O B:HOH34 2.1 11.2 1.0 O B:HOH35 2.1 11.3 1.0 O A:HOH18 2.1 11.5 1.0 O B:HOH26 4.1 13.3 1.0 O6 B:DG22 4.2 9.1 1.0 O A:HOH20 4.2 21.5 1.0 C5 A:DC1 4.3 11.4 1.0 O A:HOH50 4.3 18.0 1.0 O B:HOH3 4.3 12.5 1.0 N7 A:DG2 4.4 9.3 1.0 O6 A:DG2 4.5 9.4 1.0 C6 A:DC1 4.7 13.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the DB1883-D(Cgcgaattcgcg)2 Complex at 1.24 A Resolution


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 the DB1883-D(Cgcgaattcgcg)2 Complex at 1.24 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:38.6 occ:1.00 O B:HOH84 1.6 20.3 1.0 O B:HOH87 2.1 35.6 1.0 O B:HOH88 2.2 22.6 0.5 O B:HOH86 2.3 29.5 1.0 OP1 B:DC21 2.5 20.7 1.0 P B:DC21 3.8 18.0 1.0 O B:HOH88 3.9 23.6 0.5 O B:HOH6 3.9 17.4 1.0 C5' B:DC21 4.1 13.7 1.0 O5' B:DC21 4.2 14.5 1.0 O B:HOH89 4.5 42.7 1.0 O3' B:DT20 4.8 15.2 1.0 OP2 B:DC21 4.8 20.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the DB1883-D(Cgcgaattcgcg)2 Complex at 1.24 A Resolution


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 the DB1883-D(Cgcgaattcgcg)2 Complex at 1.24 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg25 b:32.0 occ:1.00 OP2 B:DG16 2.0 22.2 1.0 O B:HOH9 2.2 42.0 1.0 O B:HOH90 2.3 36.2 1.0 O B:HOH91 2.4 35.7 1.0 O B:HOH11 3.1 49.0 1.0 P B:DG16 3.5 19.3 1.0 O B:HOH38 3.8 26.6 1.0 C8 B:DG16 4.2 15.1 1.0 OP1 B:DG16 4.3 22.8 1.0 N7 B:DG16 4.3 15.1 1.0 O B:HOH58 4.3 33.0 1.0 C3' B:DC15 4.3 16.2 1.0 O5' B:DG16 4.3 20.5 1.0 O3' B:DC15 4.3 17.5 1.0 C2' B:DC15 4.8 18.3 1.0

D.Wei, W.D.Wilson, S.Neidle. Small-Molecule Binding to the Dna Minor Groove Is Mediated By A Conserved Water Cluster. J.Am.Chem.Soc. V. 135 1369 2013.
ISSN: ISSN 0002-7863
PubMed: 23276263
DOI: 10.1021/JA308952Y