Zinc 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:

Aluminium	(Al)	1 atom
Magnesium	(Mg)	2 atoms
Fluorine	(F)	3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(1)-Rtc, PDB code: 7re2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 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 Zinc with other atoms in the Zn 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:Zn1001 b:60.2 occ:1.00 ND1 A:HIS295 2.1 42.2 1.0 SG A:CYS310 2.3 36.7 1.0 SG A:CYS306 2.3 34.6 1.0 SG A:CYS301 2.3 38.6 1.0 CE1 A:HIS295 2.9 42.2 1.0 O A:CYS306 3.0 34.6 1.0 CG A:HIS295 3.2 42.2 1.0 CB A:CYS301 3.4 38.6 1.0 CB A:CYS310 3.5 36.7 1.0 CB A:CYS306 3.7 34.6 1.0 CB A:HIS295 3.7 42.2 1.0 CA A:CYS301 3.7 38.6 1.0 C A:CYS306 3.8 34.6 1.0 NE2 A:HIS295 4.1 42.2 1.0 N A:HIS295 4.2 42.2 1.0 CD2 A:HIS295 4.3 42.2 1.0 CA A:CYS306 4.3 34.6 1.0 CA A:HIS295 4.6 42.2 1.0 N A:CYS301 4.6 38.6 1.0 N A:ILE307 4.7 31.1 1.0 N A:LEU302 4.7 37.4 1.0 CA A:CYS310 4.8 36.7 1.0 O A:HIS295 4.8 42.2 1.0 C A:CYS301 4.8 38.6 1.0 N A:CYS310 4.8 36.7 1.0 O A:THR293 4.9 39.4 1.0

Zinc binding site 2 out of 5 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 Zinc with other atoms in the Zn 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 A:Zn1002 b:60.4 occ:1.00 ND1 A:HIS642 2.1 36.7 1.0 SG A:CYS487 2.3 37.4 1.0 SG A:CYS646 2.3 40.0 1.0 SG A:CYS645 2.3 43.0 1.0 CE1 A:HIS642 2.9 36.7 1.0 CG A:HIS642 3.2 36.7 1.0 CB A:CYS487 3.5 37.4 1.0 CB A:CYS646 3.5 40.0 1.0 CB A:HIS642 3.6 36.7 1.0 CB A:CYS645 3.7 43.0 1.0 CE1 A:PHE571 3.7 29.5 1.0 N A:CYS487 3.7 37.4 1.0 N A:CYS646 3.9 40.0 1.0 NE2 A:HIS642 4.1 36.7 1.0 CA A:CYS487 4.1 37.4 1.0 CD1 A:PHE571 4.1 29.5 1.0 CA A:CYS646 4.2 40.0 1.0 CD2 A:HIS642 4.2 36.7 1.0 C A:CYS645 4.2 43.0 1.0 NZ A:LYS532 4.3 27.3 1.0 CA A:CYS645 4.6 43.0 1.0 C A:GLY486 4.6 36.2 1.0 CZ A:PHE571 4.6 29.5 1.0 CE A:LYS532 4.6 27.3 1.0 CA A:HIS642 4.7 36.7 1.0 O A:CYS645 4.8 43.0 1.0 CA A:GLY486 4.9 36.2 1.0

Zinc binding site 3 out of 5 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 Zinc with other atoms in the Zn 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:Zn701 b:101.5 occ:1.00 SG E:CYS8 2.3 83.5 1.0 SG E:CYS26 2.3 82.7 1.0 SG E:CYS5 2.3 79.5 1.0 SG E:CYS29 2.3 87.3 1.0 CB E:CYS26 2.7 82.7 1.0 CB E:CYS29 2.9 87.3 1.0 CB E:CYS5 3.2 79.5 1.0 N E:CYS26 3.3 82.7 1.0 CA E:CYS26 3.5 82.7 1.0 CB E:CYS8 3.6 83.5 1.0 N E:CYS29 3.9 87.3 1.0 CA E:CYS29 4.0 87.3 1.0 C E:CYS26 4.2 82.7 1.0 O E:CYS26 4.5 82.7 1.0 C E:LEU25 4.5 79.7 1.0 CA E:CYS5 4.6 79.5 1.0 N E:CYS8 4.6 83.5 1.0 CA E:CYS8 4.7 83.5 1.0 O E:VAL98 4.9 96.8 1.0 CG E:LEU7 4.9 83.6 1.0 CA E:LEU25 5.0 79.7 1.0 CA E:GLY99 5.0 102.7 1.0 N E:CYS27 5.0 85.5 1.0

Zinc binding site 4 out of 5 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 Zinc with other atoms in the Zn binding site number 4 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:Zn702 b:156.9 occ:1.00 SG E:CYS55 2.3 120.0 1.0 SG E:CYS72 2.3 122.4 1.0 ND1 E:HIS75 2.3 122.1 1.0 SG E:CYS50 2.5 116.5 1.0 CB E:CYS72 3.0 122.4 1.0 CE1 E:HIS75 3.0 122.1 1.0 CG E:HIS75 3.0 122.1 1.0 CB E:CYS55 3.1 120.0 1.0 CB E:HIS75 3.5 122.1 1.0 CB E:CYS50 3.6 116.5 1.0 NE2 E:HIS75 3.9 122.1 1.0 N E:CYS72 3.9 122.4 1.0 CD2 E:HIS75 3.9 122.1 1.0 CB E:ALA52 4.0 116.6 1.0 CA E:CYS72 4.0 122.4 1.0 N E:HIS75 4.5 122.1 1.0 CA E:CYS55 4.6 120.0 1.0 CA E:HIS75 4.6 122.1 1.0 CG2 E:VAL57 4.8 118.1 1.0 C E:CYS72 4.8 122.4 1.0

Zinc binding site 5 out of 5 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 Zinc with other atoms in the Zn binding site number 5 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:Zn703 b:124.3 occ:1.00 NE2 E:HIS33 2.0 97.7 1.0 ND1 E:HIS39 2.0 104.5 1.0 SG E:CYS16 2.3 93.0 1.0 SG E:CYS19 2.3 100.2 1.0 CD2 E:HIS33 2.8 97.7 1.0 CE1 E:HIS39 2.9 104.5 1.0 CG E:HIS39 3.1 104.5 1.0 CE1 E:HIS33 3.1 97.7 1.0 CB E:CYS16 3.2 93.0 1.0 CB E:HIS39 3.5 104.5 1.0 CB E:CYS19 3.6 100.2 1.0 CG E:HIS33 4.0 97.7 1.0 NE2 E:HIS39 4.1 104.5 1.0 N E:CYS19 4.1 100.2 1.0 ND1 E:HIS33 4.1 97.7 1.0 CD2 E:HIS39 4.2 104.5 1.0 CA E:CYS19 4.2 100.2 1.0 CB E:ALA110 4.4 102.7 1.0 CA E:CYS16 4.6 93.0 1.0 CE2 E:PHE106 4.8 100.0 1.0 CZ E:PHE106 4.9 100.0 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