Magnesium in PDB 7re1: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc (Composite)

All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc (Composite):
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 (Composite) 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 (Composite) (pdb code 7re1). 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 (Composite), PDB code: 7re1:
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 (Composite)


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 (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:70.2 occ:1.00 O1A A:ADP1004 1.8 77.3 1.0 OD1 A:ASN209 2.0 62.8 1.0 O1B A:ADP1004 2.0 77.3 1.0 OD2 A:ASP218 2.4 70.9 1.0 CG A:ASN209 3.2 62.8 1.0 PA A:ADP1004 3.2 77.3 1.0 CG A:ASP218 3.3 70.9 1.0 PB A:ADP1004 3.4 77.3 1.0 CB A:ASP218 3.7 70.9 1.0 OD2 A:ASP208 3.7 62.6 1.0 O3A A:ADP1004 3.8 77.3 1.0 ND2 A:ASN209 3.9 62.8 1.0 O2B A:ADP1004 4.0 77.3 1.0 O A:ASP208 4.1 62.6 1.0 O2A A:ADP1004 4.1 77.3 1.0 C5' A:ADP1004 4.2 77.3 1.0 O5' A:ADP1004 4.2 77.3 1.0 CB A:ASN209 4.3 62.8 1.0 OD1 A:ASP218 4.4 70.9 1.0 O A:HOH1105 4.4 63.8 1.0 C A:ASP208 4.4 62.6 1.0 CA A:ASN209 4.4 62.8 1.0 N A:ASN209 4.5 62.8 1.0 CG A:ASP208 4.5 62.6 1.0 O3B A:ADP1004 4.6 77.3 1.0 CB A:ASP208 4.8 62.6 1.0 CE1 A:PHE35 4.8 63.9 1.0 CE1 A:TYR217 4.9 65.3 1.0

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


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 (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg705 b:86.2 occ:1.00 F3 E:AF3706 1.9 86.8 1.0 O2B E:ADP704 2.0 84.8 1.0 O3B E:ADP704 2.1 84.8 1.0 OG E:SER289 2.1 20.0 1.0 PB E:ADP704 2.4 84.8 1.0 CB E:SER289 3.2 20.0 1.0 AL E:AF3706 3.2 86.8 1.0 O1A E:ADP704 3.4 84.8 1.0 O1B E:ADP704 3.5 84.8 1.0 N E:SER289 3.6 83.2 1.0 O3A E:ADP704 3.6 84.8 1.0 OE2 E:GLU375 3.6 87.3 1.0 PA E:ADP704 3.9 84.8 1.0 CA E:SER289 4.0 83.2 1.0 F1 E:AF3706 4.1 86.8 1.0 O2A E:ADP704 4.3 84.8 1.0 CB E:LYS288 4.6 83.4 1.0 CA E:GLY538 4.6 92.0 1.0 OD2 E:ASP374 4.6 83.9 1.0 C E:LYS288 4.6 83.4 1.0 F2 E:AF3706 4.6 86.8 1.0 O E:GLY538 4.7 92.0 1.0 OD1 E:ASP374 4.7 83.9 1.0 CD E:GLU375 4.8 87.3 1.0 CE E:LYS288 4.9 83.4 1.0

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


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 (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1004 b:106.9 occ:1.00 O2B F:ADP1003 2.0 108.4 1.0 F3 F:AF31005 2.0 106.5 1.0 OG F:SER289 2.1 102.8 1.0 N F:SER289 2.6 102.8 1.0 PB F:ADP1003 3.0 108.4 1.0 CB F:SER289 3.1 102.8 1.0 O3B F:ADP1003 3.2 108.4 1.0 CA F:SER289 3.3 102.8 1.0 O3A F:ADP1003 3.4 108.4 1.0 C F:LYS288 3.5 102.9 1.0 CB F:LYS288 3.5 102.9 1.0 AL F:AF31005 3.7 106.5 1.0 CA F:LYS288 3.8 102.9 1.0 N F:LYS288 3.9 102.9 1.0 O1B F:ADP1003 4.3 108.4 1.0 NZ F:LYS288 4.4 102.9 1.0 O F:LYS288 4.4 102.9 1.0 CE F:LYS288 4.4 102.9 1.0 F1 F:AF31005 4.7 106.5 1.0 O2A F:ADP1003 4.7 108.4 1.0 C F:SER289 4.7 102.8 1.0 PA F:ADP1003 4.7 108.4 1.0 OE2 F:GLU375 4.8 94.4 1.0 CG F:LYS288 4.8 102.9 1.0 C F:GLY287 4.9 103.6 1.0 F2 F:AF31005 4.9 106.5 1.0 OD1 F:ASP374 4.9 89.6 1.0 OD2 F:ASP374 5.0 89.6 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