Magnesium in PDB 5v0h: Rna Duplex with 2-Meimpg Analogue Bound-One Binding Site

The structure of Rna Duplex with 2-Meimpg Analogue Bound-One Binding Site, PDB code: 5v0h was solved by W.Zhang, C.P.Tam, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.11 / 1.90
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	42.852, 42.852, 83.841, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 27.2

The binding sites of Magnesium atom in the Rna Duplex with 2-Meimpg Analogue Bound-One Binding Site (pdb code 5v0h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rna Duplex with 2-Meimpg Analogue Bound-One Binding Site, PDB code: 5v0h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rna Duplex with 2-Meimpg Analogue Bound-One Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna Duplex with 2-Meimpg Analogue Bound-One Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:52.5 occ:0.33 O2' A:G15 2.3 48.7 1.0 O3' A:G15 2.4 49.9 1.0 C3' A:G15 3.2 47.8 1.0 C2' A:G15 3.3 51.2 1.0 C4' A:G15 3.7 53.6 1.0 C1' A:G15 4.4 47.4 1.0 O4' A:G15 4.5 52.2 1.0 C5' A:G15 4.9 50.8 1.0

Magnesium binding site 2 out of 2 in the Rna Duplex with 2-Meimpg Analogue Bound-One Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna Duplex with 2-Meimpg Analogue Bound-One Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:38.5 occ:0.33 O3' B:G15 2.3 44.2 1.0 O2' B:G15 2.4 39.9 1.0 C3' B:G15 3.2 44.2 1.0 C2' B:G15 3.3 41.1 1.0 C4' B:G15 3.7 44.4 1.0 C1' B:G15 4.5 41.3 1.0 O4' B:G15 4.6 41.0 1.0 C5' B:G15 4.9 45.2 1.0

W.Zhang, C.P.Tam, L.Zhou, S.S.Oh, J.Wang, J.W.Szostak. Structural Rationale For the Enhanced Catalysis of Nonenzymatic Rna Primer Extension By A Downstream Oligonucleotide. J. Am. Chem. Soc. V. 140 2829 2018.
ISSN: ESSN 1520-5126
PubMed: 29411978
DOI: 10.1021/JACS.7B11750