Magnesium in PDB 455d: A6/A18 Inter-Strand Dithiobis(Propane)-Crosslinked Dodecamer (Cgcgaattcgcg)2

The structure of A6/A18 Inter-Strand Dithiobis(Propane)-Crosslinked Dodecamer (Cgcgaattcgcg)2, PDB code: 455d was solved by T.K.Chiu, M.Kaczor-Grzeskowiak, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.544, 39.303, 66.964, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 27.6

The binding sites of Magnesium atom in the A6/A18 Inter-Strand Dithiobis(Propane)-Crosslinked Dodecamer (Cgcgaattcgcg)2 (pdb code 455d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the A6/A18 Inter-Strand Dithiobis(Propane)-Crosslinked Dodecamer (Cgcgaattcgcg)2, PDB code: 455d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the A6/A18 Inter-Strand Dithiobis(Propane)-Crosslinked Dodecamer (Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A6/A18 Inter-Strand Dithiobis(Propane)-Crosslinked Dodecamer (Cgcgaattcgcg)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg25 b:9.7 occ:1.00 O A:HOH171 2.0 9.0 1.0 O B:HOH172 2.0 10.0 1.0 O A:HOH168 2.1 8.8 1.0 O B:HOH170 2.1 9.6 1.0 O A:HOH169 2.1 7.7 1.0 O A:HOH167 2.1 8.6 1.0 O B:HOH77 4.1 8.9 1.0 O6 B:DG22 4.2 8.2 1.0 O A:HOH81 4.2 16.9 1.0 O A:HOH41 4.2 12.8 1.0 C5 A:DC1 4.3 10.2 1.0 O A:HOH74 4.3 11.9 1.0 O B:HOH47 4.3 10.4 1.0 O6 A:DG2 4.4 7.8 1.0 N7 A:DG2 4.4 8.0 1.0 C6 A:DC1 4.6 11.7 1.0

Magnesium binding site 2 out of 3 in the A6/A18 Inter-Strand Dithiobis(Propane)-Crosslinked Dodecamer (Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A6/A18 Inter-Strand Dithiobis(Propane)-Crosslinked Dodecamer (Cgcgaattcgcg)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg26 b:16.4 occ:1.00 O A:HOH178 2.0 17.0 1.0 O A:HOH175 2.0 15.9 1.0 O A:HOH174 2.0 15.6 1.0 O A:HOH177 2.0 16.6 1.0 O A:HOH176 2.1 14.5 1.0 O A:HOH173 2.1 15.1 1.0 OP1 A:DG12 3.8 14.1 1.0 O A:HOH123 3.9 31.7 1.0 O A:HOH156 3.9 25.9 1.0 O A:HOH69 4.1 17.3 1.0 O A:HOH94 4.2 15.9 1.0 OP2 A:DG12 4.4 13.6 1.0 P A:DG12 4.5 13.3 1.0 O5' A:DG12 5.0 11.5 1.0

Magnesium binding site 3 out of 3 in the A6/A18 Inter-Strand Dithiobis(Propane)-Crosslinked Dodecamer (Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A6/A18 Inter-Strand Dithiobis(Propane)-Crosslinked Dodecamer (Cgcgaattcgcg)2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg27 b:27.1 occ:1.00 O B:HOH183 2.0 26.9 1.0 O B:HOH179 2.0 26.1 1.0 O B:HOH184 2.1 26.5 1.0 O B:HOH180 2.1 26.2 1.0 O B:HOH182 2.1 25.9 1.0 OP1 B:DA17 2.2 13.7 1.0 P B:DA17 3.6 13.1 1.0 O B:HOH165 4.1 40.0 1.0 OP2 B:DA17 4.2 13.7 1.0 O5' B:DA17 4.2 11.9 1.0 O B:HOH141 4.4 25.9 1.0 C5' B:DA17 4.6 11.3 1.0 O3' B:DG16 4.6 12.4 1.0 O B:HOH157 4.6 31.0 1.0

T.K.Chiu, M.Kaczor-Grzeskowiak, R.E.Dickerson. Absence of Minor Groove Monovalent Cations in the Crosslinked Dodecamer C-G-C-G-A-A-T-T-C-G-C-G. J.Mol.Biol. V. 292 589 1999.
ISSN: ISSN 0022-2836
PubMed: 10497024
DOI: 10.1006/JMBI.1999.3075