Magnesium in PDB 6xez: Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc

All present enzymatic activity of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

The structure of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc 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 Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc (pdb code 6xez). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc, PDB code: 6xez:
Jump to Magnesium binding site number: 1; 2; 3;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:90.2 occ:1.00 O1B A:ADP1004 2.3 94.0 1.0 OD2 A:ASP218 2.3 79.9 1.0 O1A A:ADP1004 2.3 94.0 1.0 OD1 A:ASN209 2.4 69.9 1.0 O2B A:ADP1004 2.5 94.0 1.0 PB A:ADP1004 2.9 94.0 1.0 CG A:ASN209 3.2 69.9 1.0 CG A:ASP218 3.3 79.9 1.0 ND2 A:ASN209 3.5 69.9 1.0 PA A:ADP1004 3.6 94.0 1.0 O3A A:ADP1004 3.7 94.0 1.0 OD1 A:ASP208 3.8 68.0 1.0 C5' A:ADP1004 3.9 94.0 1.0 CB A:ASP218 4.0 79.9 1.0 O5' A:ADP1004 4.1 94.0 1.0 O3B A:ADP1004 4.2 94.0 1.0 OD1 A:ASP218 4.2 79.9 1.0 O A:ASP208 4.4 68.0 1.0 CB A:ASN209 4.5 69.9 1.0 O2A A:ADP1004 4.9 94.0 1.0 C4' A:ADP1004 4.9 94.0 1.0 CG A:ASP208 5.0 68.0 1.0 CA A:ASN209 5.0 69.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg706 b:0.9 occ:1.00 F2 E:AF3705 2.9 1.0 1.0 CB E:SER289 3.3 0.6 1.0 OG E:SER289 3.3 0.6 1.0 O E:LYS288 3.8 0.6 1.0 O3B E:ADP704 3.8 0.1 1.0 C E:LYS288 3.8 0.6 1.0 OD1 E:ASP374 3.9 0.2 1.0 CB E:LYS288 4.0 0.6 1.0 N E:SER289 4.0 0.6 1.0 CD1 E:LEU317 4.2 0.3 1.0 CD2 E:LEU317 4.2 0.3 1.0 CA E:SER289 4.2 0.6 1.0 AL E:AF3705 4.3 1.0 1.0 CA E:LYS288 4.6 0.6 1.0 CG E:LEU317 4.6 0.3 1.0 F1 E:AF3705 4.7 1.0 1.0 CG E:ASP374 4.8 0.2 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1005 b:0.0 occ:1.00 CB F:LYS288 2.8 0.3 1.0 F2 F:AF31004 2.9 0.4 1.0 C F:LYS288 2.9 0.3 1.0 N F:SER289 3.0 0.4 1.0 CB F:SER289 3.3 0.4 1.0 O F:LYS288 3.3 0.3 1.0 OD2 F:ASP374 3.4 0.3 1.0 CA F:LYS288 3.5 0.3 1.0 CA F:SER289 3.6 0.4 1.0 O3B F:ADP1003 3.8 0.5 1.0 CG F:ASP374 4.3 0.3 1.0 AL F:AF31004 4.3 0.4 1.0 N F:LYS288 4.6 0.3 1.0 F1 F:AF31004 4.7 0.4 1.0 OG F:SER289 4.7 0.4 1.0 OD1 F:ASP374 4.9 0.3 1.0 NZ F:LYS320 5.0 0.5 1.0

J.Chen, B.Malone, E.Llewellyn, M.Grasso, P.M.M.Shelton, P.D.B.Olinares, K.Maruthi, E.T.Eng, H.Vatandaslar, B.T.Chait, T.M.Kapoor, S.A.Darst, E.A.Campbell. Structural Basis For Helicase-Polymerase Coupling in the Sars-Cov-2 Replication-Transcription Complex. Cell V. 182 1560 2020.
ISSN: ISSN 1097-4172
PubMed: 32783916
DOI: 10.1016/J.CELL.2020.07.033