Fluorine 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
Magnesium	(Mg)	2 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(1)-Rtc, PDB code: 7re2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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 E:F706 b:121.1 occ:1.00 F1 E:AF3706 0.0 121.1 1.0 AL E:AF3706 1.8 121.1 1.0 NH2 E:ARG443 2.2 126.7 1.0 O3B E:ADP704 2.8 120.7 1.0 NH2 E:ARG567 2.8 126.2 1.0 F3 E:AF3706 3.1 121.1 1.0 F2 E:AF3706 3.1 121.1 1.0 CZ E:ARG443 3.1 126.7 1.0 NH1 E:ARG443 3.4 126.7 1.0 CA E:GLY538 3.6 127.4 1.0 O1B E:ADP704 3.6 120.7 1.0 CZ E:ARG567 3.6 126.2 1.0 PB E:ADP704 3.7 120.7 1.0 N E:GLY538 3.8 127.4 1.0 NE E:ARG567 4.1 126.2 1.0 C E:GLY538 4.1 127.4 1.0 MG E:MG705 4.1 99.1 1.0 NE E:ARG443 4.3 126.7 1.0 O3A E:ADP704 4.3 120.7 1.0 O1A E:ADP704 4.3 120.7 1.0 O E:GLY538 4.4 127.4 1.0 N E:GLY285 4.4 118.9 1.0 NH1 E:ARG567 4.4 126.2 1.0 NE2 E:GLN537 4.4 123.7 1.0 CB E:PRO284 4.5 118.8 1.0 CA E:PRO284 4.6 118.8 1.0 OE2 E:GLU375 4.7 110.4 1.0 N E:SER539 4.8 127.9 1.0 NZ E:LYS288 5.0 111.8 1.0

Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F 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:F706 b:121.1 occ:1.00 F2 E:AF3706 0.0 121.1 1.0 AL E:AF3706 1.8 121.1 1.0 NE2 E:GLN404 2.5 114.8 1.0 NE2 E:GLN537 3.0 123.7 1.0 F1 E:AF3706 3.1 121.1 1.0 F3 E:AF3706 3.1 121.1 1.0 CD E:GLN404 3.3 114.8 1.0 CB E:PRO284 3.5 118.8 1.0 CA E:PRO284 3.6 118.8 1.0 CG E:GLN404 3.7 114.8 1.0 NZ E:LYS288 3.9 111.8 1.0 OE2 E:GLU375 4.0 110.4 1.0 NH2 E:ARG567 4.1 126.2 1.0 O1B E:ADP704 4.2 120.7 1.0 OE1 E:GLU375 4.2 110.4 1.0 CD E:GLN537 4.2 123.7 1.0 OE1 E:GLN404 4.2 114.8 1.0 N E:PRO284 4.3 118.8 1.0 CE E:LYS288 4.3 111.8 1.0 CG E:PRO284 4.5 118.8 1.0 CD E:GLU375 4.5 110.4 1.0 O3B E:ADP704 4.5 120.7 1.0 CD E:PRO284 4.5 118.8 1.0 NH1 E:ARG567 4.8 126.2 1.0 CZ E:ARG567 4.8 126.2 1.0 C E:PRO284 4.8 118.8 1.0 PB E:ADP704 4.9 120.7 1.0 NH2 E:ARG443 4.9 126.7 1.0 N E:GLY285 4.9 118.9 1.0 OE1 E:GLN537 4.9 123.7 1.0

Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F binding site number 3 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:F706 b:121.1 occ:1.00 F3 E:AF3706 0.0 121.1 1.0 AL E:AF3706 1.8 121.1 1.0 OE2 E:GLU375 2.2 110.4 1.0 O3B E:ADP704 2.3 120.7 1.0 F1 E:AF3706 3.1 121.1 1.0 F2 E:AF3706 3.1 121.1 1.0 PB E:ADP704 3.2 120.7 1.0 MG E:MG705 3.2 99.1 1.0 CE E:LYS288 3.2 111.8 1.0 NZ E:LYS288 3.3 111.8 1.0 CD E:GLU375 3.4 110.4 1.0 O1B E:ADP704 3.5 120.7 1.0 O2B E:ADP704 3.7 120.7 1.0 OE1 E:GLU375 4.0 110.4 1.0 OG E:SER289 4.0 111.7 1.0 NE2 E:GLN537 4.2 123.7 1.0 NH2 E:ARG443 4.5 126.7 1.0 CA E:GLY538 4.5 127.4 1.0 CG E:GLU375 4.5 110.4 1.0 O3A E:ADP704 4.6 120.7 1.0 CD E:LYS288 4.6 111.8 1.0 CB E:LYS288 4.8 111.8 1.0 OE1 E:GLN537 4.9 123.7 1.0 OD1 E:ASP374 4.9 103.4 1.0 CD E:GLN537 5.0 123.7 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