Magnesium in PDB 6d4l: Joint X-Ray/Neutron Structure of Dna Oligonucleotide D(Gtggccac)2 with 2'-SECH3 Modification on CYT5

The structure of Joint X-Ray/Neutron Structure of Dna Oligonucleotide D(Gtggccac)2 with 2'-SECH3 Modification on CYT5, PDB code: 6d4l was solved by A.Kovalevsky, Z.Huang, V.G.Vandavasi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.56
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.695, 42.695, 24.410, 90.00, 90.00, 90.00
R / Rfree (%)	25 / 31.2

The binding sites of Magnesium atom in the Joint X-Ray/Neutron Structure of Dna Oligonucleotide D(Gtggccac)2 with 2'-SECH3 Modification on CYT5 (pdb code 6d4l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Joint X-Ray/Neutron Structure of Dna Oligonucleotide D(Gtggccac)2 with 2'-SECH3 Modification on CYT5, PDB code: 6d4l:

Magnesium binding site 1 out of 1 in the Joint X-Ray/Neutron Structure of Dna Oligonucleotide D(Gtggccac)2 with 2'-SECH3 Modification on CYT5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Joint X-Ray/Neutron Structure of Dna Oligonucleotide D(Gtggccac)2 with 2'-SECH3 Modification on CYT5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:34.3 occ:0.50 O A:DOD209 1.9 41.5 1.0 O A:DOD213 2.2 53.0 1.0 O A:DOD223 2.2 47.2 0.5 O A:DOD228 2.3 21.6 0.5 O A:DOD229 2.4 90.1 1.0 O A:DOD203 2.4 69.1 1.0 D2 A:DOD209 2.4 42.1 1.0 D1 A:DOD209 2.4 42.9 1.0 D1 A:DOD223 2.5 47.3 0.5 D2 A:DOD213 2.6 53.4 1.0 D1 A:DOD228 2.7 19.8 0.5 D1 A:DOD213 2.7 52.9 1.0 D2 A:DOD228 2.8 19.5 0.5 D1 A:DOD229 2.8 90.1 1.0 D2 A:DOD203 3.0 68.8 1.0 D1 A:DOD203 3.0 69.5 1.0 D2 A:DOD220 3.1 25.2 0.5 D2 A:DOD223 3.1 47.4 0.5 D2 A:DOD229 3.2 90.3 1.0 D1 A:DOD220 3.6 26.1 0.5 O A:DOD220 3.6 25.6 0.5 N7 A:DG3 3.8 19.3 1.0 D2 A:DOD210 3.9 33.7 0.5 O A:DOD216 3.9 42.7 1.0 D1 A:DOD226 4.0 37.4 0.5 O6 A:DG4 4.2 16.1 1.0 D1 A:DOD216 4.3 43.8 1.0 H71 A:DT2 4.3 19.4 1.0 D2 A:DOD226 4.3 37.5 0.5 N7 A:DG4 4.4 20.7 1.0 O6 A:DG3 4.5 16.8 1.0 C8 A:DG3 4.6 20.8 1.0 C5 A:DG3 4.6 19.1 1.0 O A:DOD226 4.7 38.1 0.5 D8 A:DG3 4.7 21.1 0.3 H8 A:DG3 4.7 21.1 0.7 D2 A:DOD216 4.8 43.7 1.0 O A:DOD210 4.8 34.6 0.5 C6 A:DG3 4.9 16.3 1.0 DN41 A:CSL5 4.9 19.0 1.0 C6 A:DG4 5.0 15.8 1.0 D1 A:DOD210 5.0 34.2 0.5

V.G.Vandavasi, M.P.Blakeley, D.A.Keen, L.R.Hu, Z.Huang, A.Kovalevsky. Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-Dna. Structure V. 26 1645 2018.
ISSN: ISSN 1878-4186
PubMed: 30244969
DOI: 10.1016/J.STR.2018.08.001