Magnesium in PDB 7k16: Tamana Bat Virus XRRNA1

The structure of Tamana Bat Virus XRRNA1, PDB code: 7k16 was solved by R.A.Jones, J.S.Kieft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.55 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	79.100, 79.100, 40.690, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 24.6

The structure of Tamana Bat Virus XRRNA1 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Tamana Bat Virus XRRNA1 (pdb code 7k16). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tamana Bat Virus XRRNA1, PDB code: 7k16:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tamana Bat Virus XRRNA1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tamana Bat Virus XRRNA1 within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:38.5 occ:1.00 O P:HOH221 1.9 50.4 1.0 O P:HOH220 2.0 36.7 1.0 OP1 P:A34 2.0 38.5 1.0 O P:HOH215 2.2 34.3 1.0 O P:HOH209 2.3 26.5 1.0 O P:HOH218 2.3 29.2 1.0 P P:A34 3.4 40.2 1.0 H5'' P:A34 3.7 46.1 1.0 O5' P:A34 4.0 39.4 1.0 OP2 P:A34 4.0 41.3 1.0 O P:HOH230 4.1 42.0 1.0 O P:HOH228 4.2 31.8 1.0 O6 P:G27 4.2 34.7 1.0 N7 P:G26 4.3 34.7 1.0 N7 P:G27 4.3 34.6 1.0 C5' P:A34 4.3 38.4 1.0 O P:HOH243 4.4 46.2 1.0 OP2 P:A35 4.4 39.6 1.0 O2' P:C3 4.4 36.5 1.0 O6 P:G26 4.5 34.9 1.0 H42 P:C28 4.5 39.2 1.0 O3' P:G33 4.5 42.8 1.0 H5' P:A34 4.7 46.1 1.0 C4 P:C3 4.9 32.6 1.0 N3 P:C3 4.9 32.6 1.0 HO2' P:C3 4.9 43.9 1.0 C5 P:G26 5.0 34.2 1.0 N4 P:C28 5.0 32.6 1.0 C2 P:C3 5.0 33.0 1.0 C5 P:C3 5.0 33.4 1.0 H41 P:C28 5.0 39.2 1.0

Magnesium binding site 2 out of 5 in the Tamana Bat Virus XRRNA1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tamana Bat Virus XRRNA1 within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg102 b:30.5 occ:1.00 OP2 P:A4 1.9 36.6 1.0 O P:HOH207 2.0 36.1 1.0 O P:HOH244 2.1 31.5 1.0 O P:HOH235 2.1 32.0 1.0 OP1 P:C3 2.1 31.8 1.0 O P:HOH217 2.2 30.8 1.0 P P:A4 3.2 37.7 1.0 H62 P:A5 3.4 57.4 1.0 P P:C3 3.5 32.2 1.0 H5'' P:C3 3.6 42.1 1.0 H8 P:A4 3.8 48.4 1.0 OP1 P:A4 3.8 39.0 1.0 H42 P:C46 3.8 43.2 1.0 H3' P:C3 3.8 42.9 1.0 O5' P:C3 3.9 34.0 1.0 O5' P:A4 4.0 38.0 1.0 O6 P:G6 4.0 42.2 1.0 N7 P:A4 4.2 40.6 1.0 N6 P:A5 4.2 47.8 1.0 N7 P:A5 4.2 47.5 1.0 O P:HOH237 4.2 29.6 1.0 C5' P:C3 4.2 35.1 1.0 O P:HOH227 4.2 28.4 1.0 C8 P:A4 4.3 40.4 1.0 H42 P:C45 4.3 41.4 1.0 O3' P:C3 4.4 35.5 1.0 OP2 P:C3 4.4 33.6 1.0 C3' P:C3 4.4 35.8 1.0 H41 P:C45 4.4 41.4 1.0 N3 P:C47 4.5 41.6 1.0 O3' P:G2 4.6 33.9 1.0 N3 P:C46 4.6 35.8 1.0 N4 P:C46 4.6 36.0 1.0 H61 P:A5 4.6 57.4 1.0 N4 P:C45 4.6 34.5 1.0 H41 P:C47 4.7 47.9 1.0 C4' P:C3 4.7 35.3 1.0 C6 P:G6 4.8 44.3 1.0 H4' P:C3 4.8 42.3 1.0 C5 P:A5 4.9 49.4 1.0 O2 P:C47 5.0 44.3 1.0 C6 P:A5 5.0 49.4 1.0

Magnesium binding site 3 out of 5 in the Tamana Bat Virus XRRNA1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tamana Bat Virus XRRNA1 within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg103 b:47.8 occ:1.00 O P:HOH241 1.9 52.8 1.0 OP2 P:C44 1.9 42.3 1.0 O P:HOH229 2.0 46.5 1.0 O P:HOH212 2.0 42.6 1.0 O P:HOH234 2.0 51.1 1.0 O P:HOH226 2.7 47.8 1.0 P P:C44 3.4 46.2 1.0 HO2' P:A23 3.5 48.0 1.0 H5'' P:C44 3.6 50.0 1.0 H3' P:U43 3.8 58.5 1.0 HO2' P:C42 4.0 50.9 1.0 H22 P:G2 4.0 36.1 1.0 HN22 P:5GP1 4.0 49.6 1.0 O5' P:C44 4.1 43.6 1.0 H1' P:G2 4.1 40.6 1.0 O2' P:A23 4.1 40.0 1.0 O P:HOH233 4.2 34.7 1.0 HN21 P:5GP1 4.2 49.6 1.0 C5' P:C44 4.3 41.6 1.0 OP1 P:C44 4.3 43.8 1.0 O3' P:A23 4.3 35.7 1.0 OP2 P:G24 4.3 35.7 1.0 O3' P:U43 4.4 48.1 1.0 O2 P:C42 4.4 36.6 1.0 H1' P:C42 4.5 49.2 1.0 H5' P:C44 4.5 50.0 1.0 N2 P:5GP1 4.5 41.4 1.0 C3' P:U43 4.5 48.7 1.0 N3 P:G2 4.5 32.0 1.0 O5' P:U43 4.6 50.1 1.0 H6 P:C44 4.7 41.6 1.0 H5'' P:U43 4.7 58.8 1.0 N2 P:G2 4.8 30.1 1.0 O3' P:C42 4.8 45.9 1.0 O2' P:G2 4.8 34.5 1.0 O2' P:C42 4.8 42.4 1.0 P P:G24 4.8 34.9 1.0 OP1 P:U43 4.9 48.2 1.0

Magnesium binding site 4 out of 5 in the Tamana Bat Virus XRRNA1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tamana Bat Virus XRRNA1 within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg104 b:48.3 occ:1.00 OP2 P:C47 1.9 51.1 1.0 O P:HOH231 2.1 40.9 1.0 O P:HOH208 2.1 48.3 1.0 O P:HOH245 2.2 45.6 1.0 O P:HOH250 2.3 47.5 1.0 P P:C47 3.4 51.1 1.0 H3' P:C46 3.5 56.6 1.0 H5 P:C47 3.9 52.2 1.0 O5' P:C46 4.1 50.0 1.0 O5' P:C47 4.2 52.0 1.0 O3' P:C46 4.2 48.9 1.0 OP1 P:C47 4.2 53.4 1.0 C3' P:C46 4.3 47.2 1.0 OP2 P:C46 4.3 49.3 1.0 H6 P:C47 4.4 54.2 1.0 P P:C46 4.6 51.1 1.0 C5 P:C47 4.7 43.5 1.0 OP1 P:C46 4.7 55.7 1.0 O P:HOH251 4.9 40.3 1.0 H5'' P:C46 4.9 58.9 1.0 C6 P:C47 5.0 45.1 1.0

Magnesium binding site 5 out of 5 in the Tamana Bat Virus XRRNA1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tamana Bat Virus XRRNA1 within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg105 b:60.3 occ:0.90 O P:HOH232 1.8 57.5 1.0 O P:HOH254 2.3 46.5 1.0 O P:HOH252 2.3 37.4 1.0 OP2 P:G18 3.2 34.4 1.0 H8 P:G18 3.9 41.4 1.0 N7 P:G18 4.4 33.9 1.0 OP1 P:A17 4.4 36.9 1.0 C8 P:G18 4.4 34.5 1.0 P P:G18 4.5 33.2 1.0 H5'' P:A17 4.6 42.0 1.0 O5' P:A17 4.6 35.5 1.0 OP2 P:A17 4.7 35.3 1.0 O P:HOH214 4.8 53.3 1.0 P P:A17 4.8 37.5 1.0 H3' P:A17 4.8 41.4 1.0 OP1 P:G18 5.0 37.0 1.0

R.A.Jones, A.L.Steckelberg, Q.Vicens, M.J.Szucs, B.M.Akiyama, J.S.Kieft. Different Tertiary Interactions Create the Same Important 3-D Features in A Distinct Flavivirus Xrrna. Rna 2020.
ISSN: ESSN 1469-9001
PubMed: 33004436
DOI: 10.1261/RNA.077065.120