Magnesium in PDB 6d54: Low Temperature Joint X-Ray/Neutron Structure of Dna Oligonucleotide D(Gtggccac)2 with 2'-SECH3 Modification on CYT5

The structure of Low Temperature Joint X-Ray/Neutron Structure of Dna Oligonucleotide D(Gtggccac)2 with 2'-SECH3 Modification on CYT5, PDB code: 6d54 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 / 1.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	41.884, 41.884, 24.307, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 26

The binding sites of Magnesium atom in the Low Temperature Joint X-Ray/Neutron Structure of Dna Oligonucleotide D(Gtggccac)2 with 2'-SECH3 Modification on CYT5 (pdb code 6d54). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Low Temperature Joint X-Ray/Neutron Structure of Dna Oligonucleotide D(Gtggccac)2 with 2'-SECH3 Modification on CYT5, PDB code: 6d54:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Low Temperature 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 Low Temperature 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:34.7 occ:1.00 O A:DOD210 1.9 28.2 1.0 O A:DOD237 2.0 47.2 1.0 O A:DOD208 2.1 25.8 1.0 O A:DOD238 2.1 41.2 1.0 O A:DOD209 2.2 54.3 1.0 O A:DOD235 2.2 60.8 1.0 D1 A:DOD237 2.5 48.1 1.0 D2 A:DOD210 2.5 30.0 1.0 D1 A:DOD210 2.5 29.7 1.0 D1 A:DOD238 2.6 43.0 1.0 D1 A:DOD208 2.7 27.4 1.0 D2 A:DOD237 2.7 47.5 1.0 D1 A:DOD209 2.8 54.0 1.0 D2 A:DOD208 2.8 26.9 1.0 D2 A:DOD209 2.8 54.8 1.0 D2 A:DOD238 2.8 40.0 1.0 D1 A:DOD235 2.9 61.2 1.0 D2 A:DOD235 2.9 61.5 1.0 D1 A:DOD221 3.2 43.4 1.0 D1 A:DOD232 3.7 37.0 1.0 N7 A:DG3 3.9 19.3 1.0 O A:DOD216 3.9 23.9 1.0 D2 A:DOD207 3.9 46.2 1.0 O A:DOD221 3.9 42.6 1.0 O6 A:DG4 4.1 17.2 1.0 D2 A:DOD232 4.1 36.7 1.0 H73 A:DT2 4.1 18.2 1.0 O A:DOD232 4.3 36.6 1.0 O6 A:DG3 4.3 18.1 1.0 N7 A:DG4 4.4 17.0 1.0 D2 A:DOD216 4.5 24.3 1.0 D2 A:DOD221 4.5 42.2 1.0 D1 A:DOD216 4.5 23.2 1.0 C5 A:DG3 4.6 18.1 1.0 C8 A:DG3 4.7 17.9 1.0 O A:DOD207 4.8 46.4 1.0 C6 A:DG3 4.8 19.1 1.0 H8 A:DG3 4.8 18.8 0.7 D8 A:DG3 4.8 18.8 0.3 D1 A:DOD207 4.9 45.6 1.0 C6 A:DG4 4.9 14.1 1.0 DN41 A:CSL5 4.9 18.8 1.0

Magnesium binding site 2 out of 2 in the Low Temperature 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 2 of Low Temperature 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:Mg102 b:27.1 occ:1.00 OP2 A:DA7 2.0 19.9 1.0 O A:DOD218 2.1 26.5 1.0 O A:DOD224 2.1 30.3 1.0 O A:DOD226 2.2 34.3 1.0 O A:DOD229 2.3 33.2 1.0 D2 A:DOD218 2.6 25.8 1.0 D2 A:DOD224 2.6 31.8 1.0 D1 A:DOD224 2.6 30.5 1.0 D1 A:DOD226 2.6 37.4 1.0 D2 A:DOD226 2.7 35.7 1.0 D1 A:DOD218 2.8 27.3 1.0 D2 A:DOD229 2.8 33.6 1.0 D1 A:DOD229 2.8 32.5 1.0 P A:DA7 3.4 19.9 1.0 H3' A:DC6 3.7 17.5 1.0 O A:DOD220 3.9 20.4 1.0 D1 A:DOD220 4.0 24.2 1.0 O5' A:DA7 4.1 18.6 1.0 O A:DOD217 4.1 29.8 1.0 H8 A:DA7 4.2 14.5 1.0 OP1 A:DA7 4.2 21.8 1.0 D1 A:DOD214 4.2 30.0 1.0 D2 A:DOD220 4.3 23.1 1.0 O A:DOD214 4.3 26.8 1.0 O3' A:DC6 4.4 18.9 1.0 D1 A:DOD217 4.4 30.8 1.0 O A:DOD206 4.5 33.2 1.0 C3' A:DC6 4.5 16.4 1.0 D1 A:DOD206 4.6 34.4 1.0 OP2 A:DC6 4.6 18.9 1.0 O5' A:DC6 4.7 17.8 1.0 D2 A:DOD214 5.0 28.6 1.0 D2 A:DOD217 5.0 30.7 1.0

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