Fluorine in PDB 7rdy: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class

Enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class

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

Other elements in 7rdy:

The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Aluminium (Al) 2 atoms
Zinc (Zn) 8 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class (pdb code 7rdy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class, PDB code: 7rdy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7rdy

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Fluorine binding site 1 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1005

b:102.9
occ:1.00
 F1 E:AF31005 0.0 102.9 1.0
AL E:AF31005 1.8 102.9 1.0
NH1 E:ARG443 2.3 108.4 1.0
O3B E:ADP1003 2.3 102.8 1.0
NH2 E:ARG567 2.3 108.5 1.0
CZ E:ARG443 3.1 108.4 1.0
F2 E:AF31005 3.1 102.9 1.0
F3 E:AF31005 3.1 102.9 1.0
NH2 E:ARG443 3.1 108.4 1.0
PB E:ADP1003 3.3 102.8 1.0
O1B E:ADP1003 3.4 102.8 1.0
CZ E:ARG567 3.5 108.5 1.0
N E:GLY285 3.7 102.6 1.0
CA E:GLY538 3.9 105.8 1.0
NE E:ARG567 3.9 108.5 1.0
MG E:MG1004 4.0 99.9 1.0
O3A E:ADP1003 4.1 102.8 1.0
C E:GLY538 4.2 105.8 1.0
N E:GLY538 4.2 105.8 1.0
O E:GLY538 4.3 105.8 1.0
NE E:ARG443 4.3 108.4 1.0
CA E:GLY285 4.3 102.6 1.0
CB E:PRO284 4.3 101.4 1.0
CA E:PRO284 4.5 101.4 1.0
NH1 E:ARG567 4.6 108.5 1.0
C E:PRO284 4.6 101.4 1.0
O2B E:ADP1003 4.6 102.8 1.0
O1A E:ADP1003 4.7 102.8 1.0
N E:SER539 4.8 108.8 1.0
O E:THR566 4.9 109.1 1.0

Fluorine binding site 2 out of 6 in 7rdy

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Fluorine binding site 2 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1005

b:102.9
occ:1.00
 F2 E:AF31005 0.0 102.9 1.0
AL E:AF31005 1.8 102.9 1.0
OE1 E:GLN404 2.1 98.8 1.0
F1 E:AF31005 3.1 102.9 1.0
F3 E:AF31005 3.1 102.9 1.0
CD E:GLN404 3.2 98.8 1.0
CB E:PRO284 3.2 101.4 1.0
NH2 E:ARG567 3.3 108.5 1.0
CA E:PRO284 3.5 101.4 1.0
NE2 E:GLN404 3.8 98.8 1.0
O1B E:ADP1003 3.8 102.8 1.0
O3B E:ADP1003 4.2 102.8 1.0
NZ E:LYS288 4.3 95.0 1.0
CG E:GLN404 4.3 98.8 1.0
CZ E:ARG567 4.3 108.5 1.0
N E:GLY285 4.4 102.6 1.0
CE E:LYS288 4.4 95.0 1.0
N E:PRO284 4.5 101.4 1.0
C E:PRO284 4.5 101.4 1.0
PB E:ADP1003 4.5 102.8 1.0
CG E:PRO284 4.5 101.4 1.0
NH1 E:ARG567 4.7 108.5 1.0
OE2 E:GLU375 4.8 90.0 1.0
CG E:GLN537 4.9 103.9 1.0
NH1 E:ARG443 4.9 108.4 1.0
CD E:PRO284 4.9 101.4 1.0
MG E:MG1004 5.0 99.9 1.0

Fluorine binding site 3 out of 6 in 7rdy

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Fluorine binding site 3 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1005

b:102.9
occ:1.00
 F3 E:AF31005 0.0 102.9 1.0
AL E:AF31005 1.8 102.9 1.0
MG E:MG1004 2.1 99.9 1.0
O3B E:ADP1003 2.5 102.8 1.0
OE2 E:GLU375 3.0 90.0 1.0
F1 E:AF31005 3.1 102.9 1.0
F2 E:AF31005 3.1 102.9 1.0
PB E:ADP1003 3.2 102.8 1.0
CA E:GLY538 3.3 105.8 1.0
O2B E:ADP1003 3.4 102.8 1.0
O1B E:ADP1003 3.6 102.8 1.0
OG E:SER289 3.8 94.9 1.0
CD E:GLU375 4.0 90.0 1.0
N E:GLY538 4.0 105.8 1.0
C E:GLY538 4.3 105.8 1.0
O E:GLY538 4.4 105.8 1.0
CE E:LYS288 4.4 95.0 1.0
OE1 E:GLU375 4.6 90.0 1.0
O3A E:ADP1003 4.7 102.8 1.0
NZ E:LYS288 4.7 95.0 1.0
NH2 E:ARG567 4.8 108.5 1.0
C E:GLN537 4.8 103.9 1.0
CG E:GLU375 4.8 90.0 1.0
OE1 E:GLN404 4.8 98.8 1.0
O1A E:ADP1003 4.9 102.8 1.0

Fluorine binding site 4 out of 6 in 7rdy

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Fluorine binding site 4 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1005

b:215.5
occ:1.00
 F1 F:AF31005 0.0 215.5 1.0
AL F:AF31005 1.8 215.5 1.0
O3B F:ADP1003 2.2 215.1 1.0
NH2 F:ARG443 2.4 228.1 1.0
NH1 F:ARG443 2.9 228.1 1.0
CZ F:ARG443 3.0 228.1 1.0
O1A F:ADP1003 3.1 215.1 1.0
F3 F:AF31005 3.1 215.5 1.0
F2 F:AF31005 3.1 215.5 1.0
CA F:GLY285 3.3 216.2 1.0
PB F:ADP1003 3.6 215.1 1.0
N F:GLY285 3.7 216.2 1.0
O1B F:ADP1003 4.0 215.1 1.0
NH2 F:ARG567 4.2 233.5 1.0
O3A F:ADP1003 4.3 215.1 1.0
PA F:ADP1003 4.3 215.1 1.0
NE F:ARG443 4.3 228.1 1.0
OE1 F:GLU540 4.4 231.2 1.0
C F:GLY285 4.6 216.2 1.0
O2B F:ADP1003 4.7 215.1 1.0
CB F:GLU540 4.8 231.2 1.0
NZ F:LYS288 4.9 208.3 1.0
C F:PRO284 4.9 215.3 1.0

Fluorine binding site 5 out of 6 in 7rdy

Go back to Fluorine Binding Sites List in 7rdy
Fluorine binding site 5 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1005

b:215.5
occ:1.00
 F2 F:AF31005 0.0 215.5 1.0
AL F:AF31005 1.8 215.5 1.0
N F:GLY285 2.3 216.2 1.0
NZ F:LYS288 2.5 208.3 1.0
F1 F:AF31005 3.1 215.5 1.0
F3 F:AF31005 3.1 215.5 1.0
C F:PRO284 3.2 215.3 1.0
CA F:GLY285 3.2 216.2 1.0
CE F:LYS288 3.2 208.3 1.0
CA F:PRO284 3.3 215.3 1.0
CD F:LYS288 3.4 208.3 1.0
O F:PRO283 3.8 212.4 1.0
O3B F:ADP1003 4.0 215.1 1.0
CG F:LYS288 4.1 208.3 1.0
CB F:PRO284 4.3 215.3 1.0
N F:PRO284 4.3 215.3 1.0
O F:PRO284 4.4 215.3 1.0
C F:GLY285 4.4 216.2 1.0
C F:PRO283 4.4 212.4 1.0
N F:THR286 4.4 213.1 1.0
NH1 F:ARG443 4.5 228.1 1.0
OE1 F:GLN404 4.8 211.3 1.0
NH2 F:ARG443 5.0 228.1 1.0

Fluorine binding site 6 out of 6 in 7rdy

Go back to Fluorine Binding Sites List in 7rdy
Fluorine binding site 6 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1005

b:215.5
occ:1.00
 F3 F:AF31005 0.0 215.5 1.0
AL F:AF31005 1.8 215.5 1.0
F1 F:AF31005 3.1 215.5 1.0
F2 F:AF31005 3.1 215.5 1.0
O3B F:ADP1003 3.3 215.1 1.0
OE1 F:GLU375 3.3 196.8 1.0
CD F:LYS288 3.4 208.3 1.0
CG F:LYS288 3.8 208.3 1.0
MG F:MG1004 3.9 208.9 1.0
CA F:GLY538 4.2 225.2 1.0
N F:GLY538 4.4 225.2 1.0
CE F:LYS288 4.5 208.3 1.0
CD F:GLU375 4.5 196.8 1.0
NZ F:LYS288 4.6 208.3 1.0
PB F:ADP1003 4.6 215.1 1.0
OG F:SER289 4.8 206.1 1.0
O2B F:ADP1003 4.9 215.1 1.0

Reference:

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
Page generated: Fri Aug 2 12:01:50 2024

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