Magnesium in PDB 7re3: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer

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

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

Other elements in 7re3:

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

Fluorine (F) 12 atoms
Zinc (Zn) 16 atoms
Aluminium (Al) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer (pdb code 7re3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer, PDB code: 7re3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7re3

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:53.9
occ:1.00
 O1A A:ADP2003 2.1 65.0 1.0
OD2 A:ASP218 2.2 55.6 1.0
OD1 A:ASN209 2.2 47.9 1.0
O2B A:ADP2003 2.4 65.0 1.0
O1B A:ADP2003 2.9 65.0 1.0
CG A:ASP218 3.0 55.6 1.0
PB A:ADP2003 3.1 65.0 1.0
CG A:ASN209 3.3 47.9 1.0
PA A:ADP2003 3.3 65.0 1.0
OD2 A:ASP208 3.3 47.3 1.0
CB A:ASP218 3.5 55.6 1.0
C5' A:ADP2003 3.5 65.0 1.0
O5' A:ADP2003 3.6 65.0 1.0
O3A A:ADP2003 3.6 65.0 1.0
ND2 A:ASN209 3.8 47.9 1.0
OD1 A:ASP218 4.0 55.6 1.0
CB A:ASN209 4.5 47.9 1.0
O3B A:ADP2003 4.5 65.0 1.0
C4' A:ADP2003 4.5 65.0 1.0
CG A:ASP208 4.5 47.3 1.0
O A:ASP208 4.6 47.3 1.0
O2A A:ADP2003 4.7 65.0 1.0
CA A:ASN209 4.8 47.9 1.0
CA A:ASP218 5.0 55.6 1.0
C A:ASP208 5.0 47.3 1.0

Magnesium binding site 2 out of 6 in 7re3

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg705

b:318.9
occ:1.00
 F1 E:AF3706 2.1 322.7 1.0
O1B E:ADP704 2.1 316.0 1.0
OG E:SER289 2.1 311.6 1.0
F3 E:AF3706 2.2 322.7 1.0
AL E:AF3706 2.3 322.7 1.0
O1A E:ADP704 2.3 316.0 1.0
O3B E:ADP704 2.8 316.0 1.0
PB E:ADP704 2.8 316.0 1.0
CB E:SER289 3.0 311.6 1.0
PA E:ADP704 3.1 316.0 1.0
O3A E:ADP704 3.4 316.0 1.0
O2A E:ADP704 3.6 316.0 1.0
N E:SER289 3.6 311.6 1.0
CA E:SER289 3.9 311.6 1.0
F2 E:AF3706 4.0 322.7 1.0
O2B E:ADP704 4.3 316.0 1.0
O5' E:ADP704 4.6 316.0 1.0
C E:LYS288 4.8 313.1 1.0
O E:GLY538 4.8 353.4 1.0
N E:LYS288 4.9 313.1 1.0
CB E:LYS288 5.0 313.1 1.0

Magnesium binding site 3 out of 6 in 7re3

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1004

b:188.2
occ:1.00
 N F:SER289 2.2 187.1 1.0
O2B F:ADP1003 2.3 194.2 1.0
OG F:SER289 2.8 187.1 1.0
N F:LYS288 3.0 189.9 1.0
CB F:SER289 3.0 187.1 1.0
C F:LYS288 3.1 189.9 1.0
CA F:SER289 3.1 187.1 1.0
CA F:LYS288 3.2 189.9 1.0
CB F:LYS288 3.3 189.9 1.0
PB F:ADP1003 3.6 194.2 1.0
O3A F:ADP1003 3.7 194.2 1.0
C F:GLY287 3.8 190.8 1.0
NZ F:LYS320 4.1 179.9 1.0
O F:LYS288 4.2 189.9 1.0
C F:SER289 4.2 187.1 1.0
CA F:GLY287 4.3 190.8 1.0
N F:HIS290 4.3 187.5 1.0
CG F:LYS288 4.4 189.9 1.0
O1B F:ADP1003 4.5 194.2 1.0
O F:GLY287 4.6 190.8 1.0
O3B F:ADP1003 4.7 194.2 1.0
N F:GLY287 4.9 190.8 1.0
CD F:LYS288 4.9 189.9 1.0

Magnesium binding site 4 out of 6 in 7re3

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg2002

b:62.0
occ:1.00
 O2A G:ADP2003 2.1 70.9 1.0
OD2 G:ASP218 2.2 59.4 1.0
OD1 G:ASN209 2.2 51.9 1.0
O1B G:ADP2003 2.4 70.9 1.0
O2B G:ADP2003 2.9 70.9 1.0
CG G:ASP218 3.0 59.4 1.0
PB G:ADP2003 3.1 70.9 1.0
CG G:ASN209 3.3 51.9 1.0
PA G:ADP2003 3.3 70.9 1.0
OD2 G:ASP208 3.3 52.6 1.0
CB G:ASP218 3.5 59.4 1.0
C5' G:ADP2003 3.5 70.9 1.0
O3A G:ADP2003 3.6 70.9 1.0
O5' G:ADP2003 3.6 70.9 1.0
ND2 G:ASN209 3.8 51.9 1.0
OD1 G:ASP218 4.0 59.4 1.0
CB G:ASN209 4.5 51.9 1.0
O3B G:ADP2003 4.5 70.9 1.0
CG G:ASP208 4.5 52.6 1.0
C4' G:ADP2003 4.5 70.9 1.0
O G:ASP208 4.6 52.6 1.0
O1A G:ADP2003 4.7 70.9 1.0
CA G:ASN209 4.8 51.9 1.0
CA G:ASP218 5.0 59.4 1.0

Magnesium binding site 5 out of 6 in 7re3

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Magnesium binding site 5 out of 6 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg705

b:418.4
occ:1.00
 F1 K:AF3706 2.1 422.9 1.0
O2B K:ADP704 2.1 417.9 1.0
OG K:SER289 2.1 412.2 1.0
F3 K:AF3706 2.2 422.9 1.0
AL K:AF3706 2.3 422.9 1.0
O2A K:ADP704 2.3 417.9 1.0
O3B K:ADP704 2.8 417.9 1.0
PB K:ADP704 2.8 417.9 1.0
CB K:SER289 3.0 412.2 1.0
PA K:ADP704 3.1 417.9 1.0
O3A K:ADP704 3.4 417.9 1.0
O1A K:ADP704 3.6 417.9 1.0
N K:SER289 3.6 412.2 1.0
CA K:SER289 3.9 412.2 1.0
F2 K:AF3706 4.0 422.9 1.0
O1B K:ADP704 4.3 417.9 1.0
O5' K:ADP704 4.6 417.9 1.0
C K:LYS288 4.8 413.4 1.0
O K:GLY538 4.8 451.8 1.0
N K:LYS288 4.9 413.4 1.0
CB K:LYS288 5.0 413.4 1.0

Magnesium binding site 6 out of 6 in 7re3

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1004

b:195.7
occ:1.00
 N L:SER289 2.2 192.7 1.0
O1B L:ADP1003 2.3 201.2 1.0
OG L:SER289 2.8 192.7 1.0
N L:LYS288 3.0 195.9 1.0
CB L:SER289 3.0 192.7 1.0
C L:LYS288 3.1 195.9 1.0
CA L:SER289 3.1 192.7 1.0
CA L:LYS288 3.2 195.9 1.0
CB L:LYS288 3.3 195.9 1.0
PB L:ADP1003 3.6 201.2 1.0
O3A L:ADP1003 3.7 201.2 1.0
C L:GLY287 3.8 197.0 1.0
NZ L:LYS320 4.1 185.9 1.0
O L:LYS288 4.2 195.9 1.0
C L:SER289 4.2 192.7 1.0
CA L:GLY287 4.3 197.0 1.0
N L:HIS290 4.3 192.5 1.0
CG L:LYS288 4.4 195.9 1.0
O2B L:ADP1003 4.5 201.2 1.0
O L:GLY287 4.6 197.0 1.0
O3B L:ADP1003 4.7 201.2 1.0
N L:GLY287 4.9 197.0 1.0
CD L:LYS288 4.9 195.9 1.0

Reference:

J.Chen, Q.Wang, B.Malone, E.C.Llewellyn, K.Maruthi, E.T.Eng, J.Perry, E.A.Campbell, D.E.Shaw, S.A.Darst. Ensemble Cryo-Electron Microscopy Reveals Conformational States of the Sars-Cov-2 Helicase Replication-Transcription Complex Biorxiv 2021.
DOI: 10.1101/2021.11.10.468168
Page generated: Thu Nov 25 10:09:30 2021

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