Magnesium in PDB 1qp5: Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract

The structure of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract, PDB code: 1qp5 was solved by Y.Timsit, E.Vilbois, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.60
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	65.900, 65.900, 47.100, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract (pdb code 1qp5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract, PDB code: 1qp5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg68 b:19.0 occ:0.81 O A:HOH71 2.0 17.0 0.2 O A:HOH74 2.0 10.5 1.0 O B:HOH70 2.0 16.7 0.7 O A:HOH72 2.0 11.3 0.8 O B:HOH73 2.0 16.9 0.3 O B:HOH69 2.0 21.4 0.4 O6 A:DG7 3.3 54.7 1.0 O6 B:DG17 3.6 20.5 1.0 N7 B:DG16 4.2 2.6 1.0 O B:HOH60 4.2 69.6 0.7 O B:HOH47 4.3 2.0 1.0 C6 A:DG7 4.5 47.7 1.0 C6 B:DG17 4.8 21.0 1.0 C8 B:DG16 4.9 2.0 1.0 C5 B:DG16 5.0 2.0 1.0

Magnesium binding site 2 out of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg75 b:3.7 occ:0.35 O A:HOH77 2.0 2.0 0.3 O A:HOH76 2.0 2.5 0.5 OP1 A:DA12 4.4 15.0 1.0

Magnesium binding site 3 out of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg80 b:9.9 occ:0.69 O A:HOH82 2.0 8.8 0.3 O A:HOH81 2.0 5.9 0.5 O A:HOH85 2.0 8.6 0.0 O A:HOH83 2.0 10.5 0.7 O A:HOH84 2.0 8.7 0.0 O A:HOH86 2.0 6.6 0.7 O B:HOH43 4.2 30.3 1.0

Magnesium binding site 4 out of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg87 b:4.7 occ:0.59 O A:HOH92 2.0 2.0 0.5 O A:HOH93 2.0 4.2 0.5 O A:HOH88 2.0 2.9 0.1 O A:HOH91 2.0 2.9 0.0 O A:HOH89 2.0 2.0 0.6 O A:HOH90 2.0 3.9 0.8 O A:HOH51 3.4 14.4 0.8 O A:HOH138 3.8 2.0 0.7 O A:HOH126 3.8 3.0 0.7 O4' A:DG5 4.4 20.7 1.0 C5' A:DG5 4.5 32.6 1.0 C4' A:DG5 4.6 32.6 1.0 O4' A:DG4 4.7 34.7 1.0 O A:HOH95 4.7 2.0 0.8 O A:HOH97 5.0 22.0 0.5

Magnesium binding site 5 out of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg99 b:24.4 occ:0.67 O A:HOH103 2.0 10.8 0.5 O A:HOH102 2.0 17.4 0.1 O A:HOH100 2.0 14.9 0.4 O A:HOH105 2.0 17.5 0.0 O A:HOH101 2.0 16.5 0.3 O A:HOH104 2.0 18.3 0.8 C5 A:DC9 3.9 47.5 1.0 O A:HOH134 3.9 2.0 0.8 O A:HOH25 4.4 14.1 1.0 C6 A:DC9 4.5 42.6 1.0 OP2 A:DC9 4.7 28.1 1.0 O A:HOH79 4.7 21.0 1.0 N4 A:DC9 4.8 41.6 1.0 C4 A:DC9 4.9 48.5 1.0

Magnesium binding site 6 out of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg112 b:26.6 occ:0.64 O A:HOH117 2.0 24.6 0.4 O A:HOH116 2.0 28.4 0.3 O A:HOH118 2.0 27.5 0.0 O A:HOH114 2.0 28.5 0.2 O A:HOH115 2.0 27.4 0.0 O A:HOH113 2.0 30.6 0.6 O2 A:DC2 4.0 32.6 1.0 C5' A:DC3 4.0 39.1 1.0 O4' A:DC3 4.1 31.7 1.0 C4' A:DC3 4.2 32.2 1.0 C1' A:DC2 4.3 18.3 1.0 O B:HOH98 4.4 36.1 0.9 O B:HOH32 4.7 21.7 1.0 O4' A:DC2 4.9 20.8 1.0 C2' A:DC2 4.9 18.2 1.0 O3' A:DC2 5.0 32.4 1.0 C2 A:DC2 5.0 29.1 1.0

Magnesium binding site 7 out of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg61 b:27.5 occ:1.00 O B:HOH66 2.0 28.8 0.6 O B:HOH63 2.0 27.9 0.6 O B:HOH62 2.0 25.9 0.5 O B:HOH67 2.0 25.6 0.4 O A:HOH65 2.0 26.0 0.4 O A:HOH64 2.0 28.4 0.1 O6 B:DG19 3.1 34.4 1.0 O A:HOH132 4.2 7.8 1.0 C6 B:DG19 4.2 33.5 1.0 C5 B:DC18 4.3 18.3 1.0 O6 A:DG5 4.6 29.7 1.0 N7 B:DG19 4.6 38.9 1.0 C5 B:DG19 4.8 37.2 1.0 C4 B:DC18 4.8 28.3 1.0 C6 B:DC18 4.9 28.4 1.0 N7 A:DG4 4.9 16.3 1.0 N4 B:DC18 4.9 26.0 1.0

Magnesium binding site 8 out of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg119 b:41.6 occ:0.55 O B:HOH121 2.0 37.6 0.4 O A:HOH123 2.0 38.0 0.5 O B:HOH124 2.0 40.8 0.8 O B:HOH125 2.0 39.0 0.0 O B:HOH120 2.0 33.4 0.9 O B:HOH122 2.0 43.2 1.0 O B:HOH44 4.0 2.0 1.0 O4' B:DG17 4.4 14.0 1.0 O3' B:DG17 4.9 18.2 1.0

Y.Timsit, E.Vilbois, D.Moras. Base-Pairing Shift in the Major Groove of (Ca)N Tracts By B-Dna Crystal Structures. Nature V. 354 167 1991.
ISSN: ISSN 0028-0836
PubMed: 1944598
DOI: 10.1038/354167A0