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

All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open 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 - Open 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 - Open Class (pdb code 7rdx). 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 - Open Class, PDB code: 7rdx:
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 - Open 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 - Open Class within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:42.3 occ:1.00 OD1 A:ASN209 1.9 32.5 1.0 O1A A:ADP1004 1.9 50.3 1.0 OD2 A:ASP218 2.4 40.1 1.0 O2B A:ADP1004 2.5 50.3 1.0 O1B A:ADP1004 2.8 50.3 1.0 CG A:ASN209 2.9 32.5 1.0 H5'1 A:ADP1004 2.9 50.3 1.0 HD21 A:ASN209 3.1 32.5 1.0 CG A:ASP218 3.1 40.1 1.0 PB A:ADP1004 3.1 50.3 1.0 HB2 A:ASP218 3.2 40.1 1.0 PA A:ADP1004 3.3 50.3 1.0 HB3 A:ASP218 3.3 40.1 1.0 ND2 A:ASN209 3.4 32.5 1.0 CB A:ASP218 3.4 40.1 1.0 OD2 A:ASP208 3.5 29.3 1.0 O3A A:ADP1004 3.7 50.3 1.0 C5' A:ADP1004 3.9 50.3 1.0 O5' A:ADP1004 4.0 50.3 1.0 OD1 A:ASP218 4.0 40.1 1.0 HA A:ASN209 4.1 32.5 1.0 HD22 A:ASN209 4.2 32.5 1.0 CB A:ASN209 4.3 32.5 1.0 H4' A:ADP1004 4.3 50.3 1.0 HB3 A:ASN209 4.5 32.5 1.0 O3B A:ADP1004 4.5 50.3 1.0 O2A A:ADP1004 4.5 50.3 1.0 H5'2 A:ADP1004 4.6 50.3 1.0 CG A:ASP208 4.6 29.3 1.0 CA A:ASN209 4.6 32.5 1.0 HG1 A:THR206 4.7 29.7 1.0 C4' A:ADP1004 4.7 50.3 1.0 O A:ASP208 4.7 29.3 1.0 HE1 A:TYR217 4.7 37.3 1.0 HB2 A:ASN209 4.9 32.5 1.0 CA A:ASP218 4.9 40.1 1.0 HZ3 A:LYS73 4.9 49.8 1.0

Magnesium binding site 2 out of 3 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open 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 - Open Class within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg705 b:108.5 occ:1.00 O3B E:ADP704 1.9 115.4 1.0 AL E:AF3706 2.0 115.0 1.0 F1 E:AF3706 2.0 115.0 1.0 F3 E:AF3706 2.0 115.0 1.0 O2B E:ADP704 2.1 115.4 1.0 OG E:SER289 2.2 104.9 1.0 PB E:ADP704 2.3 115.4 1.0 O1A E:ADP704 2.7 115.4 1.0 H E:SER289 3.0 104.9 1.0 O3A E:ADP704 3.0 115.4 1.0 PA E:ADP704 3.2 115.4 1.0 CB E:SER289 3.3 104.9 1.0 HB2 E:SER289 3.3 104.9 1.0 F2 E:AF3706 3.4 115.0 1.0 HE2 E:LYS288 3.5 103.1 1.0 O2A E:ADP704 3.6 115.4 1.0 HB2 E:LYS288 3.7 103.1 1.0 N E:SER289 3.7 104.9 1.0 HH22 E:ARG443 3.8 130.5 1.0 O1B E:ADP704 3.8 115.4 1.0 HB3 E:SER289 4.0 104.9 1.0 OE2 E:GLU375 4.1 96.7 1.0 CA E:SER289 4.1 104.9 1.0 H E:GLY285 4.2 119.3 1.0 H E:LYS288 4.2 103.1 1.0 HA2 E:GLY538 4.3 123.4 1.0 NH2 E:ARG443 4.3 130.5 1.0 HH12 E:ARG443 4.3 130.5 1.0 HZ1 E:LYS288 4.3 103.1 1.0 CE E:LYS288 4.4 103.1 1.0 HA E:SER289 4.6 104.9 1.0 HA2 E:GLY285 4.6 119.3 1.0 CB E:LYS288 4.7 103.1 1.0 HE3 E:LYS288 4.7 103.1 1.0 N E:LYS288 4.7 103.1 1.0 HH21 E:ARG443 4.7 130.5 1.0 O5' E:ADP704 4.7 115.4 1.0 H E:GLY287 4.8 107.7 1.0 NH1 E:ARG443 4.8 130.5 1.0 C E:LYS288 4.8 103.1 1.0 NZ E:LYS288 4.8 103.1 1.0 CZ E:ARG443 4.9 130.5 1.0 O E:GLY538 4.9 123.4 1.0 N E:GLY285 4.9 119.3 1.0 CA E:LYS288 5.0 103.1 1.0

Magnesium binding site 3 out of 3 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open 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 - Open Class within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1004 b:134.2 occ:1.00 N F:SER289 2.1 170.8 1.0 H F:LYS288 2.6 173.3 1.0 HB2 F:LYS288 2.6 173.3 1.0 N F:LYS288 2.8 173.3 1.0 HB2 F:SER289 2.8 170.8 1.0 O2B F:ADP1003 2.8 177.4 1.0 OG F:SER289 2.9 170.8 1.0 C F:LYS288 3.0 173.3 1.0 CB F:SER289 3.1 170.8 1.0 CA F:SER289 3.1 170.8 1.0 CA F:LYS288 3.1 173.3 1.0 CB F:LYS288 3.3 173.3 1.0 C F:GLY287 3.5 171.8 1.0 HA2 F:GLY287 3.5 171.8 1.0 HA F:SER289 3.7 170.8 1.0 H F:HIS290 3.7 174.0 1.0 HZ1 F:LYS320 3.8 173.5 1.0 HZ2 F:LYS320 3.9 173.5 1.0 HB3 F:LYS288 4.0 173.3 1.0 CA F:GLY287 4.0 171.8 1.0 HB3 F:SER289 4.0 170.8 1.0 HA F:LYS288 4.1 173.3 1.0 PB F:ADP1003 4.1 177.4 1.0 HE2 F:LYS288 4.1 173.3 1.0 O3A F:ADP1003 4.2 177.4 1.0 O F:LYS288 4.2 173.3 1.0 HG3 F:LYS288 4.2 173.3 1.0 O F:GLY287 4.2 171.8 1.0 C F:SER289 4.2 170.8 1.0 NZ F:LYS320 4.3 173.5 1.0 N F:HIS290 4.3 174.0 1.0 CG F:LYS288 4.3 173.3 1.0 H F:GLY287 4.5 171.8 1.0 HD12 F:ILE399 4.5 173.9 1.0 N F:GLY287 4.7 171.8 1.0 HZ3 F:LYS320 4.7 173.5 1.0 HD2 F:LYS288 4.7 173.3 1.0 HA3 F:GLY287 4.8 171.8 1.0 CD F:LYS288 4.9 173.3 1.0 CE F:LYS288 5.0 173.3 1.0

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