Magnesium in PDB 8axf: Crystal Structure of Fmv N Bound to 42-Mer Ssrna

The structure of Crystal Structure of Fmv N Bound to 42-Mer Ssrna, PDB code: 8axf was solved by L.Izhaki-Tavor, I.Yechezkel, M.Dessau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.49 / 2.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.17, 151.82, 169.57, 90, 90, 90
R / Rfree (%)	22.2 / 24.2

The binding sites of Magnesium atom in the Crystal Structure of Fmv N Bound to 42-Mer Ssrna (pdb code 8axf). 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 Fmv N Bound to 42-Mer Ssrna, PDB code: 8axf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Fmv N Bound to 42-Mer Ssrna


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 Fmv N Bound to 42-Mer Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg101 b:89.7 occ:1.00 OP1 Q:U30 2.4 92.4 1.0 OE1 D:GLN182 2.6 77.4 1.0 OP2 Q:U31 2.8 74.6 1.0 OP1 Q:U29 3.2 85.6 1.0 P Q:U31 3.5 85.4 1.0 C5' Q:U30 3.6 60.5 1.0 OP1 Q:U31 3.7 81.5 1.0 P Q:U30 3.7 79.3 1.0 CD D:GLN182 3.7 73.8 1.0 C5' Q:U29 3.8 75.1 1.0 O3' Q:U30 3.9 97.0 1.0 ND2 D:ASN225 4.0 84.1 1.0 O5' Q:U30 4.1 66.8 1.0 O4 Q:U32 4.1 89.1 1.0 C3' Q:U29 4.2 72.3 1.0 C4' Q:U29 4.3 78.9 1.0 NE2 D:GLN182 4.4 80.3 1.0 C4' Q:U30 4.4 74.6 1.0 C3' Q:U30 4.4 84.3 1.0 O5' Q:U29 4.4 81.0 1.0 P Q:U29 4.4 75.2 1.0 O3' Q:U29 4.4 82.8 1.0 CG D:GLN182 4.9 78.8 1.0 OP2 Q:U30 4.9 78.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Fmv N Bound to 42-Mer Ssrna


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 Fmv N Bound to 42-Mer Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg102 b:88.7 occ:1.00 OP1 Q:U19 2.0 77.6 1.0 O Q:HOH204 3.2 81.6 1.0 P Q:U19 3.2 92.1 1.0 OP2 Q:U19 3.5 85.0 1.0 C5 Q:U21 4.1 84.4 1.0 O5' Q:U19 4.2 92.7 1.0 C6 Q:U21 4.3 84.6 1.0 O3' Q:U18 4.3 92.0 1.0 C3' Q:U18 4.4 88.3 1.0 C5' Q:U21 4.7 86.7 1.0 O4 Q:U22 4.7 73.5 1.0 OP1 Q:U20 4.9 80.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Fmv N Bound to 42-Mer Ssrna


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 Fmv N Bound to 42-Mer Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg103 b:72.8 occ:1.00 OP1 Q:U9 2.3 73.7 1.0 OE1 A:GLN182 2.7 60.6 1.0 OP2 Q:U10 2.9 68.4 1.0 P Q:U10 3.6 69.3 1.0 P Q:U9 3.7 55.3 1.0 CD A:GLN182 3.8 66.6 1.0 O3' Q:U9 3.8 78.1 1.0 OP1 Q:U10 3.8 73.4 1.0 O5' Q:U8 3.8 70.7 1.0 C5' Q:U9 3.8 61.0 1.0 ND2 A:ASN225 3.9 69.6 1.0 NE2 A:GLN182 4.2 61.2 1.0 O5' Q:U9 4.2 58.6 1.0 C5' Q:U8 4.3 54.0 1.0 C3' Q:U8 4.4 60.9 1.0 C3' Q:U9 4.5 68.5 1.0 C4' Q:U9 4.5 56.1 1.0 C4' Q:U8 4.6 66.5 1.0 O3' Q:U8 4.6 64.5 1.0 OP1 Q:U8 4.6 78.5 1.0 OP2 Q:U9 4.8 67.2 1.0 P Q:U8 4.9 62.4 1.0

L.Izhaki-Tavor, I.Yechezkel, J.Alter, A.Patel, M.Dessau. Rna Encapsulation Mode and Evolutionary Insights From the Crystal Structure of Emaravirus Nucleoprotein To Be Published 2023.
DOI: 10.1128/SPECTRUM.05018-22