Magnesium in PDB 1qc1: Crystal Structure of the Self-Fitted B-Dna Decamer D(Ccgccggcgg)

The structure of Crystal Structure of the Self-Fitted B-Dna Decamer D(Ccgccggcgg), PDB code: 1qc1 was solved by Y.Timsit, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 2.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	53.700, 53.700, 45.000, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Crystal Structure of the Self-Fitted B-Dna Decamer D(Ccgccggcgg) (pdb code 1qc1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Self-Fitted B-Dna Decamer D(Ccgccggcgg), PDB code: 1qc1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Self-Fitted B-Dna Decamer D(Ccgccggcgg)


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 Self-Fitted B-Dna Decamer D(Ccgccggcgg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:5.5 occ:0.81 O A:HOH128 2.0 7.8 0.2 O A:HOH126 2.0 12.5 0.5 O A:HOH127 2.0 7.8 0.4 O A:HOH129 2.0 6.5 0.1 O A:HOH130 2.0 12.8 1.0 O A:HOH139 3.8 31.7 0.8 C5' A:DC8 4.1 26.2 1.0 O A:HOH140 4.3 29.7 0.7 C4' A:DC8 4.6 30.2 1.0 OP1 A:DC8 4.6 16.6 1.0 OP1 A:DG9 4.7 16.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Self-Fitted B-Dna Decamer D(Ccgccggcgg)


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 Self-Fitted B-Dna Decamer D(Ccgccggcgg) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:20.7 occ:0.60 O A:HOH117 2.0 21.7 0.2 O A:HOH116 2.0 21.6 0.9 O B:HOH120 2.0 24.2 0.8 O B:HOH119 2.0 22.8 0.1 O A:HOH118 2.0 22.7 0.0 O B:HOH121 2.0 25.6 0.9 O4' B:DG17 3.9 2.5 1.0 C4' B:DG17 4.2 13.1 1.0 N2 B:DG16 4.7 8.2 1.0 O4' A:DG7 4.8 26.5 1.0 C4' A:DG7 4.9 19.3 1.0 C1' B:DG17 4.9 5.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Self-Fitted B-Dna Decamer D(Ccgccggcgg)


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 Self-Fitted B-Dna Decamer D(Ccgccggcgg) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:19.0 occ:0.95 O B:HOH141 2.0 20.8 0.2 O B:HOH139 2.0 21.2 0.1 O B:HOH142 2.0 21.4 0.1 O B:HOH140 2.0 21.5 0.0 O B:HOH143 2.0 21.7 0.1 O B:HOH109 3.8 52.9 1.0 O B:HOH122 4.0 27.4 1.0 C4' B:DC15 4.4 28.5 1.0 C5' B:DC15 4.6 32.6 1.0 O B:HOH115 4.7 33.3 0.8 O3' B:DC15 4.8 30.9 1.0 OP1 B:DG16 4.9 27.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Self-Fitted B-Dna Decamer D(Ccgccggcgg)


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 the Self-Fitted B-Dna Decamer D(Ccgccggcgg) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:15.2 occ:1.00 O B:HOH144 2.0 20.5 0.4 O B:HOH145 2.0 21.9 0.2 O B:HOH148 2.0 27.6 0.5 O A:HOH143 2.0 22.7 0.1 O A:HOH138 3.6 28.3 0.8 N7 B:DG17 3.8 17.9 1.0 C8 B:DG16 4.0 4.8 1.0 C2' B:DG16 4.1 9.8 1.0 N7 B:DG16 4.5 4.0 1.0 N9 B:DG16 4.5 2.0 1.0 O6 A:DG3 4.6 2.0 1.0 O6 B:DG17 4.7 18.3 1.0 C8 B:DG17 4.7 6.0 1.0 C5 B:DG17 4.8 13.7 1.0 C1' B:DG16 4.9 2.0 1.0

Y.Timsit, D.Moras. Dna Self-Fitting: the Double Helix Directs the Geometry of Its Supramolecular Assembly Embo J. V. 13 2737 1994.
ISSN: ISSN 0261-4189
PubMed: 8026458