Magnesium in PDB 5w20: Crystal Structure of Inosine-Substituted Duplex Dna

The structure of Crystal Structure of Inosine-Substituted Duplex Dna, PDB code: 5w20 was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.73 / 1.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.190, 35.043, 41.336, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 18.1

The binding sites of Magnesium atom in the Crystal Structure of Inosine-Substituted Duplex Dna (pdb code 5w20). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Inosine-Substituted Duplex Dna, PDB code: 5w20:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Inosine-Substituted Duplex Dna


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 Inosine-Substituted Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:10.8 occ:1.00 O A:HOH224 2.0 9.9 1.0 O B:HOH211 2.1 9.7 1.0 O B:HOH270 2.1 11.1 1.0 O A:HOH250 2.1 11.4 1.0 O B:HOH217 4.1 15.0 0.5 O4' A:DC6 4.2 9.2 1.0 O4' B:DT8 4.2 9.5 1.0 O2 B:DC7 4.2 9.0 1.0 O B:HOH276 4.2 16.4 1.0 O4' A:DI5 4.3 8.0 1.0 O B:HOH236 4.3 16.2 1.0 C4' B:DT8 4.5 10.4 0.5 C2 A:DI4 4.5 7.4 1.0 C4' A:DC6 4.5 9.2 1.0 C4' A:DI5 4.5 9.2 1.0 O A:HOH272 4.5 28.2 1.0 N3 A:DI5 4.6 6.4 1.0 C4' B:DT8 4.6 9.2 0.6 N3 A:DI4 4.7 7.1 1.0 C5' B:DT8 4.8 10.5 0.5 C5' A:DC6 4.8 9.4 1.0 C1' A:DI5 4.9 8.1 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Inosine-Substituted Duplex Dna


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 Inosine-Substituted Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:9.8 occ:1.00 O A:HOH226 1.9 13.9 1.0 O A:HOH232 2.0 16.0 1.0 O A:HOH212 2.1 15.4 1.0 O A:HOH284 2.1 14.7 1.0 O A:HOH233 4.1 16.2 1.0 O A:HOH258 4.1 18.9 1.0 O B:HOH252 4.1 14.7 1.0 O6 A:DI5 4.2 7.6 1.0 O A:HOH216 4.3 14.3 1.0 O B:HOH291 4.3 26.5 1.0 O6 A:DI4 4.3 7.6 1.0 O A:HOH278 4.3 24.2 1.0 N7 A:DI4 4.4 7.3 1.0 N4 B:DC6 4.6 7.7 1.0 N7 A:DA3 4.9 6.8 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Inosine-Substituted Duplex Dna


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 Inosine-Substituted Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:20.3 occ:1.00 O A:HOH229 2.2 29.0 1.0 OP2 A:DA3 4.5 14.8 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Inosine-Substituted Duplex Dna


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 Inosine-Substituted Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:10.7 occ:1.00 O B:HOH257 2.1 12.1 1.0 O B:HOH226 2.1 11.3 1.0 O B:HOH237 2.2 11.2 1.0 O A:HOH268 3.9 16.6 0.5 O A:HOH269 4.0 24.8 1.0 N7 B:DI4 4.3 7.8 1.0 O B:HOH222 4.3 15.1 1.0 O B:HOH214 4.3 15.9 1.0 O B:HOH242 4.3 12.8 1.0 O6 B:DI4 4.3 7.9 1.0 O A:HOH248 4.4 22.4 1.0 N7 B:DA3 4.4 7.7 1.0 O B:HOH286 4.5 20.3 1.0 C8 B:DA3 4.6 8.5 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Inosine-Substituted Duplex Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Inosine-Substituted Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:9.1 occ:1.00 O B:HOH247 2.0 11.2 1.0 O B:HOH271 2.1 9.3 1.0 O A:HOH261 2.1 9.1 1.0 O B:HOH244 2.1 9.3 1.0 O A:HOH223 2.1 8.3 1.0 O A:HOH270 2.2 9.5 1.0 O4' A:DT8 4.2 7.0 1.0 O A:HOH225 4.2 14.3 1.0 O4' B:DI5 4.2 8.1 1.0 O B:HOH274 4.3 16.5 1.0 N3 B:DI5 4.3 7.5 1.0 O B:HOH266 4.3 24.7 1.0 O A:HOH210 4.4 8.4 1.0 O2 A:DC7 4.4 7.9 1.0 C4' A:DT8 4.4 6.7 1.0 O B:HOH275 4.5 17.4 1.0 O B:HOH272 4.5 24.2 1.0 C1' B:DI5 4.6 6.7 1.0 C5' A:DT8 4.8 6.8 1.0 O4' B:DC6 4.9 8.5 1.0 C2 B:DI5 4.9 7.2 1.0 C4 B:DI5 5.0 7.0 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Inosine-Substituted Duplex Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Inosine-Substituted Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:16.0 occ:0.70 O B:HOH246 2.0 19.6 1.0 O B:HOH262 2.3 29.6 1.0 OP1 B:DC2 4.3 16.9 1.0 OP2 B:DC2 4.7 15.5 1.0 P B:DC2 4.8 12.9 1.0 O3' B:DC1 4.9 13.2 1.0 C4' B:DC1 4.9 10.9 1.0 O B:HOH267 5.0 20.3 1.0

J.P.Peters, E.A.Kowal, P.S.Pallan, M.Egli, L.J.Maher 3Rd.. Comparative Analysis of Inosine-Substituted Duplex Dna By Circular Dichroism and X-Ray Crystallography. J. Biomol. Struct. Dyn. V. 36 2753 2018.
ISSN: ESSN 1538-0254
PubMed: 28818035
DOI: 10.1080/07391102.2017.1369164