Magnesium in PDB 9e9q: Sars-Cov-2 SL5 Crystal Structure Native

The structure of Sars-Cov-2 SL5 Crystal Structure Native, PDB code: 9e9q was solved by C.P.Jones, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.36 / 3.33
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.717, 96.717, 114.823, 90, 90, 120
R / Rfree (%)	15.8 / 20.4

The binding sites of Magnesium atom in the Sars-Cov-2 SL5 Crystal Structure Native (pdb code 9e9q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Sars-Cov-2 SL5 Crystal Structure Native, PDB code: 9e9q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Sars-Cov-2 SL5 Crystal Structure Native


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sars-Cov-2 SL5 Crystal Structure Native within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:254.2 occ:1.00 O A:HOH303 2.2 192.4 1.0 O A:HOH314 2.2 181.8 1.0 O A:HOH318 2.2 213.7 1.0 O A:HOH329 2.2 231.9 1.0 O A:HOH308 2.2 211.8 1.0 O A:HOH320 2.2 211.4 1.0 N7 A:G84 3.7 165.5 1.0 C5 A:G84 4.4 160.0 1.0 C8 A:G84 4.4 159.2 1.0 O6 A:G84 4.5 202.4 1.0 OP1 A:A86 4.6 157.8 1.0 OP2 A:A86 4.6 163.8 1.0 C6 A:G84 4.7 182.9 1.0 OP1 A:G80 4.9 170.3 1.0

Magnesium binding site 2 out of 5 in the Sars-Cov-2 SL5 Crystal Structure Native


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sars-Cov-2 SL5 Crystal Structure Native within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:253.6 occ:1.00 O A:HOH301 2.2 217.1 1.0 O A:HOH323 2.2 197.9 1.0 O A:HOH307 2.2 209.9 1.0 O A:HOH326 2.2 195.4 1.0 O A:HOH330 2.2 210.2 1.0 O A:HOH324 2.2 189.5 1.0 OP2 A:G78 4.3 173.8 1.0 OP1 A:C53 4.6 170.5 1.0 OP2 A:C53 4.9 170.7 1.0

Magnesium binding site 3 out of 5 in the Sars-Cov-2 SL5 Crystal Structure Native


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sars-Cov-2 SL5 Crystal Structure Native within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:250.7 occ:1.00 O A:HOH304 2.2 220.7 1.0 O A:HOH309 2.2 184.8 1.0 O A:HOH322 2.2 238.2 1.0 O A:HOH321 2.2 188.0 1.0 O A:HOH313 2.2 200.0 1.0 O A:HOH315 2.2 202.9 1.0 OP2 A:C46 3.6 166.3 1.0 N7 A:G47 4.1 193.3 1.0 O6 A:G47 4.4 191.8 1.0 P A:C46 4.4 165.4 1.0 OP2 A:G47 4.6 164.2 1.0 OP1 A:C46 4.6 167.5 1.0 O5' A:C46 4.7 163.7 1.0 C5 A:G47 4.9 166.7 1.0

Magnesium binding site 4 out of 5 in the Sars-Cov-2 SL5 Crystal Structure Native


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sars-Cov-2 SL5 Crystal Structure Native within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:236.9 occ:1.00 O A:HOH319 2.2 223.3 1.0 O A:HOH311 2.2 197.7 1.0 O2 A:C50 2.6 212.1 1.0 C2 A:C50 3.8 207.1 1.0 O4 A:U52 4.3 187.2 1.0 N3 A:C50 4.5 205.9 1.0 N1 A:C50 4.8 191.7 1.0 C1' A:C50 4.8 199.2 1.0 O2' A:C50 5.0 197.3 1.0

Magnesium binding site 5 out of 5 in the Sars-Cov-2 SL5 Crystal Structure Native


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Sars-Cov-2 SL5 Crystal Structure Native within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:249.6 occ:1.00 O A:HOH312 2.2 186.1 1.0 O A:HOH327 2.2 222.3 1.0 O A:HOH305 2.2 192.7 1.0 O A:HOH328 2.2 224.7 1.0 O A:HOH310 2.2 191.2 1.0 O A:HOH316 2.2 196.3 1.0 N7 A:G18 3.8 186.7 1.0 O6 A:G18 4.3 176.7 1.0 C5 A:G18 4.5 164.0 1.0 N7 A:G19 4.6 168.2 1.0 C8 A:G18 4.6 158.6 1.0 OP2 A:A17 4.6 181.5 1.0 C6 A:G18 4.7 160.5 1.0 O6 A:G19 4.9 156.7 1.0

C.P.Jones, A.R.Ferre-D'amare. Crystallographic and Cryoem Analyses Reveal Sars-Cov-2 SL5 Is A Mobile T-Shaped Four-Way Junction with Deep Pockets. Rna V. 31 949 2025.
ISSN: ESSN 1469-9001
PubMed: 40527531
DOI: 10.1261/RNA.080413.125