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

Enzymatic activity of 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;

Other elements in 7re1:

The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc (Composite) 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 (Composite) (pdb code 7re1). 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 (Composite), PDB code: 7re1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7re1

Go back to Fluorine Binding Sites List in 7re1
Fluorine binding site 1 out of 6 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 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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F706

b:86.8
occ:1.00
 F1 E:AF3706 0.0 86.8 1.0
AL E:AF3706 1.8 86.8 1.0
NH2 E:ARG567 2.4 88.5 1.0
O3B E:ADP704 2.5 84.8 1.0
NH1 E:ARG443 2.6 85.4 1.0
O1B E:ADP704 3.0 84.8 1.0
F3 E:AF3706 3.1 86.8 1.0
F2 E:AF3706 3.1 86.8 1.0
PB E:ADP704 3.2 84.8 1.0
CZ E:ARG443 3.5 85.4 1.0
CZ E:ARG567 3.5 88.5 1.0
NH2 E:ARG443 3.5 85.4 1.0
N E:GLY285 3.6 84.9 1.0
CB E:PRO284 3.9 85.1 1.0
NE E:ARG567 4.0 88.5 1.0
O3A E:ADP704 4.1 84.8 1.0
MG E:MG705 4.1 86.2 1.0
CA E:PRO284 4.2 85.1 1.0
C E:PRO284 4.2 85.1 1.0
CA E:GLY285 4.3 84.9 1.0
N E:GLY538 4.4 92.0 1.0
CA E:GLY538 4.4 92.0 1.0
NH1 E:ARG567 4.5 88.5 1.0
O2B E:ADP704 4.6 84.8 1.0
NE2 E:GLN404 4.7 88.5 1.0
NE E:ARG443 4.7 85.4 1.0
C E:GLY538 4.8 92.0 1.0

Fluorine binding site 2 out of 6 in 7re1

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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 (Composite)


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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F706

b:86.8
occ:1.00
 F2 E:AF3706 0.0 86.8 1.0
AL E:AF3706 1.8 86.8 1.0
NE2 E:GLN404 2.3 88.5 1.0
F3 E:AF3706 3.1 86.8 1.0
F1 E:AF3706 3.1 86.8 1.0
CD E:GLN404 3.4 88.5 1.0
OE2 E:GLU375 3.4 87.3 1.0
CB E:PRO284 3.7 85.1 1.0
OE1 E:GLU375 3.9 87.3 1.0
O1B E:ADP704 3.9 84.8 1.0
CA E:PRO284 4.0 85.1 1.0
CG E:GLN404 4.0 88.5 1.0
CD E:GLU375 4.0 87.3 1.0
NH2 E:ARG567 4.1 88.5 1.0
NZ E:LYS288 4.1 83.4 1.0
OE1 E:GLN404 4.2 88.5 1.0
O3B E:ADP704 4.3 84.8 1.0
CG E:GLN537 4.4 91.7 1.0
CE E:LYS288 4.4 83.4 1.0
PB E:ADP704 4.6 84.8 1.0
OE1 E:GLN537 4.6 91.7 1.0
MG E:MG705 4.6 86.2 1.0
CZ E:ARG567 4.8 88.5 1.0
N E:GLY538 4.8 92.0 1.0
N E:PRO284 4.9 85.1 1.0
N E:GLY285 4.9 84.9 1.0
CG E:PRO284 5.0 85.1 1.0
CD E:GLN537 5.0 91.7 1.0

Fluorine binding site 3 out of 6 in 7re1

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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 (Composite)


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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F706

b:86.8
occ:1.00
 F3 E:AF3706 0.0 86.8 1.0
AL E:AF3706 1.8 86.8 1.0
MG E:MG705 1.9 86.2 1.0
O3B E:ADP704 2.3 84.8 1.0
OE2 E:GLU375 2.5 87.3 1.0
F2 E:AF3706 3.1 86.8 1.0
F1 E:AF3706 3.1 86.8 1.0
PB E:ADP704 3.2 84.8 1.0
CA E:GLY538 3.4 92.0 1.0
O2B E:ADP704 3.5 84.8 1.0
CD E:GLU375 3.6 87.3 1.0
O1B E:ADP704 3.7 84.8 1.0
OG E:SER289 3.7 20.0 1.0
N E:GLY538 4.0 92.0 1.0
C E:GLY538 4.3 92.0 1.0
O E:GLY538 4.4 92.0 1.0
OE1 E:GLU375 4.4 87.3 1.0
CG E:GLU375 4.5 87.3 1.0
O3A E:ADP704 4.6 84.8 1.0
O1A E:ADP704 4.7 84.8 1.0
CB E:SER289 4.9 20.0 1.0
CE E:LYS288 4.9 83.4 1.0

Fluorine binding site 4 out of 6 in 7re1

Go back to Fluorine Binding Sites List in 7re1
Fluorine binding site 4 out of 6 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 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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1005

b:106.5
occ:1.00
 F1 F:AF31005 0.0 106.5 1.0
AL F:AF31005 1.8 106.5 1.0
O3B F:ADP1003 2.8 108.4 1.0
NH2 F:ARG567 2.9 114.5 1.0
F2 F:AF31005 3.1 106.5 1.0
N F:GLY285 3.1 107.9 1.0
F3 F:AF31005 3.1 106.5 1.0
NH1 F:ARG443 3.7 110.8 1.0
CA F:PRO284 3.7 107.6 1.0
CZ F:ARG567 3.7 114.5 1.0
PB F:ADP1003 3.8 108.4 1.0
C F:PRO284 3.9 107.6 1.0
CA F:GLY285 4.0 107.9 1.0
NE2 F:GLN404 4.2 105.0 1.0
NH2 F:ARG443 4.3 110.8 1.0
O2B F:ADP1003 4.3 108.4 1.0
O1B F:ADP1003 4.3 108.4 1.0
CB F:PRO284 4.3 107.6 1.0
NE F:ARG567 4.4 114.5 1.0
NH1 F:ARG567 4.4 114.5 1.0
CZ F:ARG443 4.4 110.8 1.0
N F:GLY538 4.7 115.9 1.0
MG F:MG1004 4.7 106.9 1.0
N F:PRO284 4.9 107.6 1.0
NZ F:LYS288 4.9 102.9 1.0
O F:PRO283 4.9 105.9 1.0

Fluorine binding site 5 out of 6 in 7re1

Go back to Fluorine Binding Sites List in 7re1
Fluorine binding site 5 out of 6 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 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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1005

b:106.5
occ:1.00
 F2 F:AF31005 0.0 106.5 1.0
AL F:AF31005 1.8 106.5 1.0
NZ F:LYS288 2.3 102.9 1.0
O F:GLY282 2.4 102.3 1.0
O F:PRO283 2.8 105.9 1.0
F1 F:AF31005 3.1 106.5 1.0
F3 F:AF31005 3.1 106.5 1.0
C F:PRO283 3.2 105.9 1.0
CA F:PRO284 3.3 107.6 1.0
C F:GLY282 3.4 102.3 1.0
N F:GLY285 3.5 107.9 1.0
N F:PRO284 3.6 107.6 1.0
CE F:LYS288 3.6 102.9 1.0
OG1 F:THR286 3.7 106.9 1.0
C F:PRO284 3.9 107.6 1.0
O2B F:ADP1003 4.0 108.4 1.0
N F:PRO283 4.2 105.9 1.0
CA F:PRO283 4.2 105.9 1.0
O1B F:ADP1003 4.3 108.4 1.0
PB F:ADP1003 4.3 108.4 1.0
CA F:GLY282 4.3 102.3 1.0
O3B F:ADP1003 4.3 108.4 1.0
N F:THR286 4.4 106.9 1.0
CA F:GLY285 4.6 107.9 1.0
CB F:PRO284 4.6 107.6 1.0
CB F:ASP401 4.7 101.4 1.0
CD F:PRO284 4.8 107.6 1.0
CD F:LYS288 4.8 102.9 1.0
NE2 F:GLN404 4.8 105.0 1.0
MG F:MG1004 4.9 106.9 1.0
C F:GLY285 4.9 107.9 1.0
N F:GLY282 4.9 102.3 1.0
CG F:PRO284 5.0 107.6 1.0

Fluorine binding site 6 out of 6 in 7re1

Go back to Fluorine Binding Sites List in 7re1
Fluorine binding site 6 out of 6 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 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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1005

b:106.5
occ:1.00
 F3 F:AF31005 0.0 106.5 1.0
AL F:AF31005 1.8 106.5 1.0
MG F:MG1004 2.0 106.9 1.0
O2B F:ADP1003 2.4 108.4 1.0
O3B F:ADP1003 3.0 108.4 1.0
F1 F:AF31005 3.1 106.5 1.0
F2 F:AF31005 3.1 106.5 1.0
PB F:ADP1003 3.2 108.4 1.0
NZ F:LYS288 3.2 102.9 1.0
CE F:LYS288 3.6 102.9 1.0
OG F:SER289 3.9 102.8 1.0
CB F:LYS288 4.1 102.9 1.0
O1B F:ADP1003 4.2 108.4 1.0
OE2 F:GLU375 4.3 94.4 1.0
O3A F:ADP1003 4.4 108.4 1.0
N F:SER289 4.4 102.8 1.0
N F:LYS288 4.7 102.9 1.0
CD F:LYS288 4.8 102.9 1.0
CG F:LYS288 4.8 102.9 1.0
CA F:LYS288 4.9 102.9 1.0
CA F:GLY538 5.0 115.9 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 12:02:07 2024

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