Magnesium in PDB 7rdy: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class

All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class:
2.7.7.48; 3.6.4.12; 3.6.4.13;

The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Aluminium	(Al)	2 atoms
Zinc	(Zn)	8 atoms

The binding sites of Magnesium atom in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class (pdb code 7rdy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class, PDB code: 7rdy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:55.2 occ:1.00 O1B A:ADP1004 2.1 63.2 1.0 OD2 A:ASP218 2.1 53.3 1.0 OD1 A:ASN209 2.1 42.2 1.0 O2B A:ADP1004 2.3 63.2 1.0 PB A:ADP1004 2.6 63.2 1.0 O1A A:ADP1004 2.7 63.2 1.0 CG A:ASP218 2.8 53.3 1.0 CG A:ASN209 3.2 42.2 1.0 CB A:ASP218 3.3 53.3 1.0 O3A A:ADP1004 3.6 63.2 1.0 PA A:ADP1004 3.7 63.2 1.0 ND2 A:ASN209 3.7 42.2 1.0 OD1 A:ASP218 3.8 53.3 1.0 O3B A:ADP1004 3.8 63.2 1.0 OD2 A:ASP208 4.1 40.4 1.0 C5' A:ADP1004 4.2 63.2 1.0 O5' A:ADP1004 4.3 63.2 1.0 CB A:ASN209 4.4 42.2 1.0 C4' A:ADP1004 4.7 63.2 1.0 O A:ASP208 4.7 40.4 1.0 CA A:ASP218 4.7 53.3 1.0 CA A:ASN209 4.8 42.2 1.0

Magnesium binding site 2 out of 3 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1004 b:99.9 occ:1.00 OG E:SER289 2.0 94.9 1.0 O3B E:ADP1003 2.1 102.8 1.0 O2B E:ADP1003 2.1 102.8 1.0 F3 E:AF31005 2.1 102.9 1.0 PB E:ADP1003 2.5 102.8 1.0 CB E:SER289 3.0 94.9 1.0 O1A E:ADP1003 3.3 102.8 1.0 AL E:AF31005 3.4 102.9 1.0 O1B E:ADP1003 3.6 102.8 1.0 O3A E:ADP1003 3.6 102.8 1.0 N E:SER289 3.8 94.9 1.0 PA E:ADP1003 3.9 102.8 1.0 O E:GLY538 3.9 105.8 1.0 CA E:SER289 4.0 94.9 1.0 F1 E:AF31005 4.0 102.9 1.0 CA E:GLY538 4.0 105.8 1.0 OD2 E:ASP374 4.1 87.0 1.0 OE2 E:GLU375 4.1 90.0 1.0 O2A E:ADP1003 4.4 102.8 1.0 C E:GLY538 4.4 105.8 1.0 OD1 E:ASP374 4.7 87.0 1.0 NH2 E:ARG443 4.7 108.4 1.0 CB E:LYS288 4.8 95.0 1.0 CE E:LYS288 4.8 95.0 1.0 CG E:ASP374 4.8 87.0 1.0 C E:LYS288 4.9 95.0 1.0 F2 E:AF31005 5.0 102.9 1.0

Magnesium binding site 3 out of 3 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1004 b:208.9 occ:1.00 N F:SER289 1.9 206.1 1.0 OG F:SER289 2.0 206.1 1.0 CB F:SER289 2.2 206.1 1.0 CA F:SER289 2.4 206.1 1.0 O2B F:ADP1003 2.5 215.1 1.0 CG F:LYS288 2.9 208.3 1.0 C F:LYS288 3.0 208.3 1.0 O3B F:ADP1003 3.3 215.1 1.0 PB F:ADP1003 3.4 215.1 1.0 CA F:LYS288 3.6 208.3 1.0 CB F:LYS288 3.6 208.3 1.0 C F:SER289 3.7 206.1 1.0 N F:LYS288 3.8 208.3 1.0 O3A F:ADP1003 3.8 215.1 1.0 F3 F:AF31005 3.9 215.5 1.0 CD F:LYS288 4.0 208.3 1.0 O F:LYS288 4.0 208.3 1.0 N F:HIS290 4.0 206.7 1.0 NZ F:LYS320 4.2 205.9 1.0 AL F:AF31005 4.6 215.5 1.0 C F:GLY287 4.7 209.2 1.0 O F:SER289 4.8 206.1 1.0 O1B F:ADP1003 4.8 215.1 1.0

J.Chen, Q.Wang, B.Malone, E.Llewellyn, Y.Pechersky, K.Maruthi, E.T.Eng, J.K.Perry, E.A.Campbell, D.E.Shaw, S.A.Darst. Ensemble Cryo-Electron Microscopy Reveals Conformational States of the NSP13 Helicase in the Sars-Cov-2 Helicase Replication-Transcription Complex Biorxiv 2021.
DOI: 10.1101/2021.11.10.468168