Magnesium in PDB 7re2: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(1)-Rtc

All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(1)-Rtc:
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(1)-Rtc also contains other interesting chemical elements:

Zinc	(Zn)	5 atoms
Aluminium	(Al)	1 atom
Fluorine	(F)	3 atoms

The binding sites of Magnesium atom in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(1)-Rtc (pdb code 7re2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(1)-Rtc, PDB code: 7re2:
Jump to Magnesium binding site number: 1; 2;

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


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(1)-Rtc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:46.5 occ:1.00 O1A A:ADP1004 1.9 52.6 1.0 OD1 A:ASN209 2.0 35.6 1.0 OD2 A:ASP218 2.0 41.8 1.0 O1B A:ADP1004 2.2 52.6 1.0 O2B A:ADP1004 2.5 52.6 1.0 PB A:ADP1004 2.7 52.6 1.0 CG A:ASP218 2.7 41.8 1.0 CG A:ASN209 3.0 35.6 1.0 CB A:ASP218 3.0 41.8 1.0 PA A:ADP1004 3.2 52.6 1.0 O3A A:ADP1004 3.4 52.6 1.0 ND2 A:ASN209 3.6 35.6 1.0 OD1 A:ASP208 3.6 34.5 1.0 OD1 A:ASP218 3.8 41.8 1.0 CB A:ASN209 4.1 35.6 1.0 O3B A:ADP1004 4.1 52.6 1.0 O A:ASP208 4.2 34.5 1.0 O5' A:ADP1004 4.2 52.6 1.0 O2A A:ADP1004 4.2 52.6 1.0 C5' A:ADP1004 4.3 52.6 1.0 CE1 A:TYR217 4.4 38.0 1.0 CA A:ASP218 4.4 41.8 1.0 CA A:ASN209 4.5 35.6 1.0 CG A:ASP208 4.8 34.5 1.0 C A:ASP208 4.8 34.5 1.0 N A:ASN209 4.9 35.6 1.0 CD1 A:TYR217 5.0 38.0 1.0

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


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(1)-Rtc within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg705 b:99.1 occ:1.00 O3B E:ADP704 2.0 120.7 1.0 OG E:SER289 2.0 111.7 1.0 CB E:SER289 2.5 111.7 1.0 O1A E:ADP704 2.9 120.7 1.0 PB E:ADP704 3.1 120.7 1.0 O2A E:ADP704 3.2 120.7 1.0 F3 E:AF3706 3.2 121.1 1.0 PA E:ADP704 3.3 120.7 1.0 O2B E:ADP704 3.4 120.7 1.0 CA E:SER289 3.7 111.7 1.0 O3A E:ADP704 3.7 120.7 1.0 N E:SER289 3.7 111.7 1.0 O E:GLY538 3.9 127.4 1.0 F1 E:AF3706 4.1 121.1 1.0 AL E:AF3706 4.2 121.1 1.0 NH2 E:ARG443 4.3 126.7 1.0 OE2 E:GLU375 4.4 110.4 1.0 O1B E:ADP704 4.4 120.7 1.0 CA E:GLY538 4.5 127.4 1.0 NZ E:LYS320 4.6 117.1 1.0 C E:GLY538 4.6 127.4 1.0 C E:SER289 4.7 111.7 1.0 OD2 E:ASP374 4.8 103.4 1.0 O5' E:ADP704 4.9 120.7 1.0 C E:LYS288 4.9 111.8 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