Magnesium in PDB 7rdx: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class
Enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class
All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class:
2.7.7.48;
3.6.4.12;
3.6.4.13;
Other elements in 7rdx:
The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class
(pdb code 7rdx). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class, PDB code: 7rdx:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 7rdx
Go back to
Magnesium Binding Sites List in 7rdx
Magnesium binding site 1 out
of 3 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class
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 - Open Class within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1003
b:42.3
occ:1.00
|
OD1
|
A:ASN209
|
1.9
|
32.5
|
1.0
|
O1A
|
A:ADP1004
|
1.9
|
50.3
|
1.0
|
OD2
|
A:ASP218
|
2.4
|
40.1
|
1.0
|
O2B
|
A:ADP1004
|
2.5
|
50.3
|
1.0
|
O1B
|
A:ADP1004
|
2.8
|
50.3
|
1.0
|
CG
|
A:ASN209
|
2.9
|
32.5
|
1.0
|
H5'1
|
A:ADP1004
|
2.9
|
50.3
|
1.0
|
HD21
|
A:ASN209
|
3.1
|
32.5
|
1.0
|
CG
|
A:ASP218
|
3.1
|
40.1
|
1.0
|
PB
|
A:ADP1004
|
3.1
|
50.3
|
1.0
|
HB2
|
A:ASP218
|
3.2
|
40.1
|
1.0
|
PA
|
A:ADP1004
|
3.3
|
50.3
|
1.0
|
HB3
|
A:ASP218
|
3.3
|
40.1
|
1.0
|
ND2
|
A:ASN209
|
3.4
|
32.5
|
1.0
|
CB
|
A:ASP218
|
3.4
|
40.1
|
1.0
|
OD2
|
A:ASP208
|
3.5
|
29.3
|
1.0
|
O3A
|
A:ADP1004
|
3.7
|
50.3
|
1.0
|
C5'
|
A:ADP1004
|
3.9
|
50.3
|
1.0
|
O5'
|
A:ADP1004
|
4.0
|
50.3
|
1.0
|
OD1
|
A:ASP218
|
4.0
|
40.1
|
1.0
|
HA
|
A:ASN209
|
4.1
|
32.5
|
1.0
|
HD22
|
A:ASN209
|
4.2
|
32.5
|
1.0
|
CB
|
A:ASN209
|
4.3
|
32.5
|
1.0
|
H4'
|
A:ADP1004
|
4.3
|
50.3
|
1.0
|
HB3
|
A:ASN209
|
4.5
|
32.5
|
1.0
|
O3B
|
A:ADP1004
|
4.5
|
50.3
|
1.0
|
O2A
|
A:ADP1004
|
4.5
|
50.3
|
1.0
|
H5'2
|
A:ADP1004
|
4.6
|
50.3
|
1.0
|
CG
|
A:ASP208
|
4.6
|
29.3
|
1.0
|
CA
|
A:ASN209
|
4.6
|
32.5
|
1.0
|
HG1
|
A:THR206
|
4.7
|
29.7
|
1.0
|
C4'
|
A:ADP1004
|
4.7
|
50.3
|
1.0
|
O
|
A:ASP208
|
4.7
|
29.3
|
1.0
|
HE1
|
A:TYR217
|
4.7
|
37.3
|
1.0
|
HB2
|
A:ASN209
|
4.9
|
32.5
|
1.0
|
CA
|
A:ASP218
|
4.9
|
40.1
|
1.0
|
HZ3
|
A:LYS73
|
4.9
|
49.8
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 7rdx
Go back to
Magnesium Binding Sites List in 7rdx
Magnesium binding site 2 out
of 3 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class
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 - Open Class within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg705
b:108.5
occ:1.00
|
O3B
|
E:ADP704
|
1.9
|
115.4
|
1.0
|
AL
|
E:AF3706
|
2.0
|
115.0
|
1.0
|
F1
|
E:AF3706
|
2.0
|
115.0
|
1.0
|
F3
|
E:AF3706
|
2.0
|
115.0
|
1.0
|
O2B
|
E:ADP704
|
2.1
|
115.4
|
1.0
|
OG
|
E:SER289
|
2.2
|
104.9
|
1.0
|
PB
|
E:ADP704
|
2.3
|
115.4
|
1.0
|
O1A
|
E:ADP704
|
2.7
|
115.4
|
1.0
|
H
|
E:SER289
|
3.0
|
104.9
|
1.0
|
O3A
|
E:ADP704
|
3.0
|
115.4
|
1.0
|
PA
|
E:ADP704
|
3.2
|
115.4
|
1.0
|
CB
|
E:SER289
|
3.3
|
104.9
|
1.0
|
HB2
|
E:SER289
|
3.3
|
104.9
|
1.0
|
F2
|
E:AF3706
|
3.4
|
115.0
|
1.0
|
HE2
|
E:LYS288
|
3.5
|
103.1
|
1.0
|
O2A
|
E:ADP704
|
3.6
|
115.4
|
1.0
|
HB2
|
E:LYS288
|
3.7
|
103.1
|
1.0
|
N
|
E:SER289
|
3.7
|
104.9
|
1.0
|
HH22
|
E:ARG443
|
3.8
|
130.5
|
1.0
|
O1B
|
E:ADP704
|
3.8
|
115.4
|
1.0
|
HB3
|
E:SER289
|
4.0
|
104.9
|
1.0
|
OE2
|
E:GLU375
|
4.1
|
96.7
|
1.0
|
CA
|
E:SER289
|
4.1
|
104.9
|
1.0
|
H
|
E:GLY285
|
4.2
|
119.3
|
1.0
|
H
|
E:LYS288
|
4.2
|
103.1
|
1.0
|
HA2
|
E:GLY538
|
4.3
|
123.4
|
1.0
|
NH2
|
E:ARG443
|
4.3
|
130.5
|
1.0
|
HH12
|
E:ARG443
|
4.3
|
130.5
|
1.0
|
HZ1
|
E:LYS288
|
4.3
|
103.1
|
1.0
|
CE
|
E:LYS288
|
4.4
|
103.1
|
1.0
|
HA
|
E:SER289
|
4.6
|
104.9
|
1.0
|
HA2
|
E:GLY285
|
4.6
|
119.3
|
1.0
|
CB
|
E:LYS288
|
4.7
|
103.1
|
1.0
|
HE3
|
E:LYS288
|
4.7
|
103.1
|
1.0
|
N
|
E:LYS288
|
4.7
|
103.1
|
1.0
|
HH21
|
E:ARG443
|
4.7
|
130.5
|
1.0
|
O5'
|
E:ADP704
|
4.7
|
115.4
|
1.0
|
H
|
E:GLY287
|
4.8
|
107.7
|
1.0
|
NH1
|
E:ARG443
|
4.8
|
130.5
|
1.0
|
C
|
E:LYS288
|
4.8
|
103.1
|
1.0
|
NZ
|
E:LYS288
|
4.8
|
103.1
|
1.0
|
CZ
|
E:ARG443
|
4.9
|
130.5
|
1.0
|
O
|
E:GLY538
|
4.9
|
123.4
|
1.0
|
N
|
E:GLY285
|
4.9
|
119.3
|
1.0
|
CA
|
E:LYS288
|
5.0
|
103.1
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 7rdx
Go back to
Magnesium Binding Sites List in 7rdx
Magnesium binding site 3 out
of 3 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class
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 - Open Class within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg1004
b:134.2
occ:1.00
|
N
|
F:SER289
|
2.1
|
170.8
|
1.0
|
H
|
F:LYS288
|
2.6
|
173.3
|
1.0
|
HB2
|
F:LYS288
|
2.6
|
173.3
|
1.0
|
N
|
F:LYS288
|
2.8
|
173.3
|
1.0
|
HB2
|
F:SER289
|
2.8
|
170.8
|
1.0
|
O2B
|
F:ADP1003
|
2.8
|
177.4
|
1.0
|
OG
|
F:SER289
|
2.9
|
170.8
|
1.0
|
C
|
F:LYS288
|
3.0
|
173.3
|
1.0
|
CB
|
F:SER289
|
3.1
|
170.8
|
1.0
|
CA
|
F:SER289
|
3.1
|
170.8
|
1.0
|
CA
|
F:LYS288
|
3.1
|
173.3
|
1.0
|
CB
|
F:LYS288
|
3.3
|
173.3
|
1.0
|
C
|
F:GLY287
|
3.5
|
171.8
|
1.0
|
HA2
|
F:GLY287
|
3.5
|
171.8
|
1.0
|
HA
|
F:SER289
|
3.7
|
170.8
|
1.0
|
H
|
F:HIS290
|
3.7
|
174.0
|
1.0
|
HZ1
|
F:LYS320
|
3.8
|
173.5
|
1.0
|
HZ2
|
F:LYS320
|
3.9
|
173.5
|
1.0
|
HB3
|
F:LYS288
|
4.0
|
173.3
|
1.0
|
CA
|
F:GLY287
|
4.0
|
171.8
|
1.0
|
HB3
|
F:SER289
|
4.0
|
170.8
|
1.0
|
HA
|
F:LYS288
|
4.1
|
173.3
|
1.0
|
PB
|
F:ADP1003
|
4.1
|
177.4
|
1.0
|
HE2
|
F:LYS288
|
4.1
|
173.3
|
1.0
|
O3A
|
F:ADP1003
|
4.2
|
177.4
|
1.0
|
O
|
F:LYS288
|
4.2
|
173.3
|
1.0
|
HG3
|
F:LYS288
|
4.2
|
173.3
|
1.0
|
O
|
F:GLY287
|
4.2
|
171.8
|
1.0
|
C
|
F:SER289
|
4.2
|
170.8
|
1.0
|
NZ
|
F:LYS320
|
4.3
|
173.5
|
1.0
|
N
|
F:HIS290
|
4.3
|
174.0
|
1.0
|
CG
|
F:LYS288
|
4.3
|
173.3
|
1.0
|
H
|
F:GLY287
|
4.5
|
171.8
|
1.0
|
HD12
|
F:ILE399
|
4.5
|
173.9
|
1.0
|
N
|
F:GLY287
|
4.7
|
171.8
|
1.0
|
HZ3
|
F:LYS320
|
4.7
|
173.5
|
1.0
|
HD2
|
F:LYS288
|
4.7
|
173.3
|
1.0
|
HA3
|
F:GLY287
|
4.8
|
171.8
|
1.0
|
CD
|
F:LYS288
|
4.9
|
173.3
|
1.0
|
CE
|
F:LYS288
|
5.0
|
173.3
|
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 Oct 3 07:49:15 2024
|