Magnesium in PDB 5w1z: Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)

The structure of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4), PDB code: 5w1z 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)	32.24 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	24.884, 32.798, 34.034, 90.25, 107.32, 111.04
R / Rfree (%)	20.7 / 23.4

The structure of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) also contains other interesting chemical elements:

Bromine	(Br)	4 atoms
Sodium	(Na)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) (pdb code 5w1z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4), PDB code: 5w1z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


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 Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:27.9 occ:0.70 O A:HOH203 1.9 16.2 0.5 O A:HOH233 2.0 31.6 1.0 O A:HOH231 2.2 11.0 0.3 O2 A:DC1 4.1 20.4 1.0 C5' A:DC2 4.3 23.5 1.0 O4' A:DC2 4.4 20.0 1.0 C4' A:DC2 4.5 23.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


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 Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:23.0 occ:1.00 O C:HOH223 1.9 24.4 1.0 O D:HOH213 2.2 21.9 1.0 O C:HOH224 2.2 27.5 1.0 O D:HOH233 2.2 24.4 1.0 O C:HOH209 2.3 23.5 1.0 O4' D:DA13 4.1 25.2 1.0 O D:HOH211 4.1 27.0 1.0 O D:HOH212 4.3 16.5 0.5 N3 C:DI10 4.3 19.1 1.0 O2 D:DC12 4.3 19.0 1.0 C4' D:DA13 4.6 27.1 1.0 O4' C:DI10 4.6 20.7 1.0 O3' C:DI10 4.7 24.3 1.0 C1' C:DI10 4.8 20.2 1.0 C4' C:DI10 4.9 22.4 1.0 C2 C:DI10 4.9 20.1 1.0 O4' D:DC12 5.0 24.1 0.5

Magnesium binding site 3 out of 3 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


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 Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:33.7 occ:1.00 O D:HOH228 2.1 33.8 1.0 O D:HOH212 4.2 16.5 0.5 OP1 D:DC12 4.3 28.6 0.5 OP1 D:DC12 4.5 29.5 0.5 C5' D:DC12 4.5 26.7 0.5 O3' D:DC11 4.6 29.2 1.0 C5' D:DC12 4.8 27.0 0.5

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