Zinc 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:
Zinc Binding Sites:
The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the
Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Open Class, PDB code: 7rdx:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 7rdx
Go back to
Zinc Binding Sites List in 7rdx
Zinc binding site 1 out
of 8 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 Zinc with other atoms in the Zn 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:Zn1001
b:46.7
occ:1.00
|
HD1
|
A:HIS295
|
1.3
|
28.0
|
1.0
|
ND1
|
A:HIS295
|
2.1
|
28.0
|
1.0
|
SG
|
A:CYS310
|
2.3
|
25.5
|
1.0
|
SG
|
A:CYS301
|
2.3
|
30.3
|
1.0
|
SG
|
A:CYS306
|
2.3
|
29.3
|
1.0
|
HE1
|
A:HIS295
|
2.8
|
28.0
|
1.0
|
CE1
|
A:HIS295
|
2.8
|
28.0
|
1.0
|
O
|
A:CYS306
|
2.9
|
29.3
|
1.0
|
HA
|
A:CYS301
|
3.0
|
30.3
|
1.0
|
CG
|
A:HIS295
|
3.3
|
28.0
|
1.0
|
CB
|
A:CYS301
|
3.4
|
30.3
|
1.0
|
HB2
|
A:HIS295
|
3.4
|
28.0
|
1.0
|
HB2
|
A:CYS310
|
3.5
|
25.5
|
1.0
|
H
|
A:HIS295
|
3.5
|
28.0
|
1.0
|
HB3
|
A:CYS301
|
3.6
|
30.3
|
1.0
|
CB
|
A:CYS310
|
3.6
|
25.5
|
1.0
|
CA
|
A:CYS301
|
3.7
|
30.3
|
1.0
|
CB
|
A:CYS306
|
3.7
|
29.3
|
1.0
|
C
|
A:CYS306
|
3.7
|
29.3
|
1.0
|
HB3
|
A:CYS306
|
3.8
|
29.3
|
1.0
|
CB
|
A:HIS295
|
3.9
|
28.0
|
1.0
|
NE2
|
A:HIS295
|
4.0
|
28.0
|
1.0
|
HB3
|
A:CYS310
|
4.0
|
25.5
|
1.0
|
H
|
A:LEU302
|
4.1
|
31.6
|
1.0
|
H
|
A:CYS310
|
4.2
|
25.5
|
1.0
|
CA
|
A:CYS306
|
4.2
|
29.3
|
1.0
|
N
|
A:HIS295
|
4.2
|
28.0
|
1.0
|
HB2
|
A:CYS301
|
4.3
|
30.3
|
1.0
|
CD2
|
A:HIS295
|
4.3
|
28.0
|
1.0
|
HD1
|
A:HIS309
|
4.3
|
25.3
|
1.0
|
HA
|
A:CYS306
|
4.4
|
29.3
|
1.0
|
HA
|
A:ILE307
|
4.4
|
27.5
|
1.0
|
HB2
|
A:CYS306
|
4.5
|
29.3
|
1.0
|
N
|
A:CYS301
|
4.5
|
30.3
|
1.0
|
HA
|
A:CYS298
|
4.5
|
26.8
|
1.0
|
N
|
A:ILE307
|
4.6
|
27.5
|
1.0
|
CA
|
A:HIS295
|
4.7
|
28.0
|
1.0
|
HB3
|
A:HIS295
|
4.7
|
28.0
|
1.0
|
HA
|
A:TYR294
|
4.7
|
25.6
|
1.0
|
N
|
A:LEU302
|
4.7
|
31.6
|
1.0
|
HD13
|
A:LEU302
|
4.8
|
31.6
|
1.0
|
N
|
A:CYS310
|
4.8
|
25.5
|
1.0
|
C
|
A:CYS301
|
4.8
|
30.3
|
1.0
|
CA
|
A:CYS310
|
4.8
|
25.5
|
1.0
|
O
|
A:HIS295
|
4.8
|
28.0
|
1.0
|
H
|
A:CYS301
|
4.8
|
30.3
|
1.0
|
|
Zinc binding site 2 out
of 8 in 7rdx
Go back to
Zinc Binding Sites List in 7rdx
Zinc binding site 2 out
of 8 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 Zinc with other atoms in the Zn 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
|
A:Zn1002
b:52.4
occ:1.00
|
ND1
|
A:HIS642
|
2.1
|
33.3
|
1.0
|
SG
|
A:CYS646
|
2.3
|
36.1
|
1.0
|
SG
|
A:CYS487
|
2.3
|
34.5
|
1.0
|
SG
|
A:CYS645
|
2.3
|
38.6
|
1.0
|
HE1
|
A:PHE571
|
2.7
|
29.5
|
1.0
|
HB3
|
A:HIS642
|
2.9
|
33.3
|
1.0
|
CE1
|
A:HIS642
|
2.9
|
33.3
|
1.0
|
CG
|
A:HIS642
|
3.0
|
33.3
|
1.0
|
HE1
|
A:HIS642
|
3.1
|
33.3
|
1.0
|
HB2
|
A:CYS646
|
3.4
|
36.1
|
1.0
|
HB2
|
A:CYS487
|
3.4
|
34.5
|
1.0
|
CB
|
A:HIS642
|
3.5
|
33.3
|
1.0
|
CB
|
A:CYS646
|
3.5
|
36.1
|
1.0
|
CB
|
A:CYS487
|
3.5
|
34.5
|
1.0
|
CE1
|
A:PHE571
|
3.5
|
29.5
|
1.0
|
H
|
A:CYS487
|
3.6
|
34.5
|
1.0
|
HD1
|
A:PHE571
|
3.7
|
29.5
|
1.0
|
CB
|
A:CYS645
|
3.8
|
38.6
|
1.0
|
HB2
|
A:CYS645
|
3.8
|
38.6
|
1.0
|
N
|
A:CYS487
|
3.9
|
34.5
|
1.0
|
H
|
A:CYS646
|
3.9
|
36.1
|
1.0
|
N
|
A:CYS646
|
4.0
|
36.1
|
1.0
|
NE2
|
A:HIS642
|
4.0
|
33.3
|
1.0
|
CD1
|
A:PHE571
|
4.0
|
29.5
|
1.0
|
HE3
|
A:LYS532
|
4.1
|
30.0
|
1.0
|
HB2
|
A:HIS642
|
4.1
|
33.3
|
1.0
|
CD2
|
A:HIS642
|
4.1
|
33.3
|
1.0
|
CA
|
A:CYS487
|
4.2
|
34.5
|
1.0
|
CA
|
A:CYS646
|
4.2
|
36.1
|
1.0
|
HB3
|
A:CYS646
|
4.2
|
36.1
|
1.0
|
HB3
|
A:CYS487
|
4.3
|
34.5
|
1.0
|
C
|
A:CYS645
|
4.3
|
38.6
|
1.0
|
HA
|
A:CYS487
|
4.3
|
34.5
|
1.0
|
HA
|
A:HIS642
|
4.3
|
33.3
|
1.0
|
HA2
|
A:GLY486
|
4.3
|
32.4
|
1.0
|
HB3
|
A:CYS645
|
4.4
|
38.6
|
1.0
|
HA
|
A:CYS646
|
4.4
|
36.1
|
1.0
|
HZ
|
A:PHE528
|
4.5
|
31.6
|
1.0
|
CA
|
A:HIS642
|
4.6
|
33.3
|
1.0
|
C
|
A:GLY486
|
4.6
|
32.4
|
1.0
|
CZ
|
A:PHE571
|
4.6
|
29.5
|
1.0
|
HZ1
|
A:LYS532
|
4.6
|
30.0
|
1.0
|
CA
|
A:CYS645
|
4.6
|
38.6
|
1.0
|
HZ
|
A:PHE571
|
4.7
|
29.5
|
1.0
|
HZ2
|
A:LYS532
|
4.7
|
30.0
|
1.0
|
HE2
|
A:HIS642
|
4.7
|
33.3
|
1.0
|
O
|
A:CYS645
|
4.9
|
38.6
|
1.0
|
CE
|
A:LYS532
|
4.9
|
30.0
|
1.0
|
HD2
|
A:HIS642
|
4.9
|
33.3
|
1.0
|
NZ
|
A:LYS532
|
4.9
|
30.0
|
1.0
|
CA
|
A:GLY486
|
5.0
|
32.4
|
1.0
|
|
Zinc binding site 3 out
of 8 in 7rdx
Go back to
Zinc Binding Sites List in 7rdx
Zinc binding site 3 out
of 8 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 Zinc with other atoms in the Zn 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
|
E:Zn701
b:113.3
occ:1.00
|
HB3
|
E:CYS26
|
1.3
|
86.4
|
1.0
|
HB2
|
E:CYS26
|
1.6
|
86.4
|
1.0
|
CB
|
E:CYS26
|
1.7
|
86.4
|
1.0
|
SG
|
E:CYS8
|
2.3
|
86.1
|
1.0
|
SG
|
E:CYS29
|
2.3
|
90.1
|
1.0
|
SG
|
E:CYS5
|
2.4
|
81.4
|
1.0
|
SG
|
E:CYS26
|
2.4
|
86.4
|
1.0
|
HB2
|
E:CYS29
|
3.0
|
90.1
|
1.0
|
H
|
E:CYS26
|
3.1
|
86.4
|
1.0
|
CA
|
E:CYS26
|
3.1
|
86.4
|
1.0
|
HB2
|
E:CYS5
|
3.1
|
81.4
|
1.0
|
CB
|
E:CYS5
|
3.2
|
81.4
|
1.0
|
HB3
|
E:CYS5
|
3.3
|
81.4
|
1.0
|
CB
|
E:CYS29
|
3.3
|
90.1
|
1.0
|
N
|
E:CYS26
|
3.5
|
86.4
|
1.0
|
H
|
E:CYS29
|
3.5
|
90.1
|
1.0
|
HA
|
E:CYS26
|
3.6
|
86.4
|
1.0
|
HA2
|
E:GLY99
|
3.7
|
94.3
|
1.0
|
HB3
|
E:CYS8
|
3.7
|
86.1
|
1.0
|
CB
|
E:CYS8
|
3.7
|
86.1
|
1.0
|
HB3
|
E:CYS29
|
3.9
|
90.1
|
1.0
|
C
|
E:CYS26
|
4.0
|
86.4
|
1.0
|
HD12
|
E:LEU7
|
4.0
|
88.3
|
1.0
|
HB3
|
E:SER10
|
4.2
|
79.9
|
1.0
|
H
|
E:CYS27
|
4.2
|
87.9
|
1.0
|
H
|
E:CYS8
|
4.2
|
86.1
|
1.0
|
O
|
E:VAL98
|
4.2
|
90.4
|
1.0
|
N
|
E:CYS29
|
4.2
|
90.1
|
1.0
|
HB2
|
E:CYS8
|
4.4
|
86.1
|
1.0
|
N
|
E:CYS27
|
4.4
|
87.9
|
1.0
|
CA
|
E:CYS29
|
4.4
|
90.1
|
1.0
|
H
|
E:SER10
|
4.5
|
79.9
|
1.0
|
N
|
E:CYS8
|
4.6
|
86.1
|
1.0
|
HG
|
E:LEU7
|
4.6
|
88.3
|
1.0
|
HD11
|
E:LEU7
|
4.6
|
88.3
|
1.0
|
CA
|
E:GLY99
|
4.6
|
94.3
|
1.0
|
CA
|
E:CYS5
|
4.7
|
81.4
|
1.0
|
CA
|
E:CYS8
|
4.7
|
86.1
|
1.0
|
CD1
|
E:LEU7
|
4.7
|
88.3
|
1.0
|
HB3
|
E:CYS97
|
4.8
|
86.0
|
1.0
|
C
|
E:LEU25
|
4.8
|
84.2
|
1.0
|
HA
|
E:CYS5
|
4.9
|
81.4
|
1.0
|
O
|
E:CYS26
|
4.9
|
86.4
|
1.0
|
H
|
E:LYS28
|
4.9
|
89.1
|
1.0
|
C
|
E:VAL98
|
4.9
|
90.4
|
1.0
|
H
|
E:CYS30
|
5.0
|
89.1
|
1.0
|
|
Zinc binding site 4 out
of 8 in 7rdx
Go back to
Zinc Binding Sites List in 7rdx
Zinc binding site 4 out
of 8 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 Zinc with other atoms in the Zn binding
site number 4 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:Zn702
b:172.1
occ:1.00
|
HD1
|
E:HIS75
|
1.5
|
126.8
|
1.0
|
ND1
|
E:HIS75
|
2.1
|
126.8
|
1.0
|
SG
|
E:CYS72
|
2.3
|
122.3
|
1.0
|
SG
|
E:CYS55
|
2.3
|
128.2
|
1.0
|
SG
|
E:CYS50
|
2.3
|
117.1
|
1.0
|
HE1
|
E:HIS75
|
2.6
|
126.8
|
1.0
|
CE1
|
E:HIS75
|
2.6
|
126.8
|
1.0
|
HB3
|
E:CYS72
|
2.7
|
122.3
|
1.0
|
CB
|
E:CYS72
|
3.0
|
122.3
|
1.0
|
HB3
|
E:CYS55
|
3.1
|
128.2
|
1.0
|
HB2
|
E:ALA52
|
3.1
|
127.1
|
1.0
|
CB
|
E:CYS55
|
3.1
|
128.2
|
1.0
|
H
|
E:CYS72
|
3.1
|
122.3
|
1.0
|
HB2
|
E:CYS55
|
3.2
|
128.2
|
1.0
|
CG
|
E:HIS75
|
3.3
|
126.8
|
1.0
|
CB
|
E:CYS50
|
3.4
|
117.1
|
1.0
|
HB3
|
E:CYS50
|
3.4
|
117.1
|
1.0
|
HB3
|
E:ALA52
|
3.5
|
127.1
|
1.0
|
HB2
|
E:HIS75
|
3.5
|
126.8
|
1.0
|
HB2
|
E:CYS50
|
3.5
|
117.1
|
1.0
|
HB2
|
E:CYS72
|
3.7
|
122.3
|
1.0
|
CB
|
E:ALA52
|
3.7
|
127.1
|
1.0
|
HG
|
E:SER74
|
3.8
|
127.3
|
1.0
|
NE2
|
E:HIS75
|
3.8
|
126.8
|
1.0
|
N
|
E:CYS72
|
3.9
|
122.3
|
1.0
|
H
|
E:ALA52
|
3.9
|
127.1
|
1.0
|
H
|
E:HIS75
|
4.0
|
126.8
|
1.0
|
CB
|
E:HIS75
|
4.0
|
126.8
|
1.0
|
CA
|
E:CYS72
|
4.1
|
122.3
|
1.0
|
OG
|
E:SER74
|
4.1
|
127.3
|
1.0
|
CD2
|
E:HIS75
|
4.2
|
126.8
|
1.0
|
HB1
|
E:ALA52
|
4.3
|
127.1
|
1.0
|
HG23
|
E:VAL57
|
4.4
|
115.9
|
1.0
|
HB
|
E:VAL57
|
4.4
|
115.9
|
1.0
|
HG21
|
E:VAL57
|
4.5
|
115.9
|
1.0
|
CA
|
E:CYS55
|
4.6
|
128.2
|
1.0
|
HB3
|
E:HIS75
|
4.6
|
126.8
|
1.0
|
N
|
E:ALA52
|
4.6
|
127.1
|
1.0
|
N
|
E:HIS75
|
4.7
|
126.8
|
1.0
|
HA
|
E:CYS72
|
4.8
|
122.3
|
1.0
|
HA
|
E:TYR71
|
4.8
|
117.2
|
1.0
|
CA
|
E:CYS50
|
4.8
|
117.1
|
1.0
|
CG2
|
E:VAL57
|
4.8
|
115.9
|
1.0
|
H
|
E:ASN51
|
4.8
|
118.4
|
1.0
|
CA
|
E:ALA52
|
4.8
|
127.1
|
1.0
|
HA
|
E:CYS55
|
4.9
|
128.2
|
1.0
|
C
|
E:CYS72
|
4.9
|
122.3
|
1.0
|
CA
|
E:HIS75
|
5.0
|
126.8
|
1.0
|
|
Zinc binding site 5 out
of 8 in 7rdx
Go back to
Zinc Binding Sites List in 7rdx
Zinc binding site 5 out
of 8 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 Zinc with other atoms in the Zn binding
site number 5 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:Zn703
b:135.0
occ:1.00
|
ND1
|
E:HIS39
|
2.0
|
100.6
|
1.0
|
NE2
|
E:HIS33
|
2.0
|
91.3
|
1.0
|
SG
|
E:CYS19
|
2.3
|
96.5
|
1.0
|
SG
|
E:CYS16
|
2.3
|
90.5
|
1.0
|
HB3
|
E:HIS39
|
2.5
|
100.6
|
1.0
|
CG
|
E:HIS39
|
2.8
|
100.6
|
1.0
|
CE1
|
E:HIS33
|
2.8
|
91.3
|
1.0
|
HB2
|
E:HIS39
|
2.9
|
100.6
|
1.0
|
CB
|
E:HIS39
|
2.9
|
100.6
|
1.0
|
HE1
|
E:HIS33
|
2.9
|
91.3
|
1.0
|
H
|
E:CYS19
|
3.0
|
96.5
|
1.0
|
CE1
|
E:HIS39
|
3.2
|
100.6
|
1.0
|
CD2
|
E:HIS33
|
3.2
|
91.3
|
1.0
|
HB3
|
E:CYS16
|
3.3
|
90.5
|
1.0
|
N
|
E:CYS19
|
3.4
|
96.5
|
1.0
|
CB
|
E:CYS16
|
3.5
|
90.5
|
1.0
|
HD2
|
E:HIS33
|
3.5
|
91.3
|
1.0
|
HE1
|
E:HIS39
|
3.5
|
100.6
|
1.0
|
H
|
E:ALA18
|
3.6
|
99.0
|
1.0
|
CB
|
E:CYS19
|
3.6
|
96.5
|
1.0
|
HB2
|
E:CYS16
|
3.9
|
90.5
|
1.0
|
HB2
|
E:CYS19
|
3.9
|
96.5
|
1.0
|
HB3
|
E:ALA18
|
3.9
|
99.0
|
1.0
|
CA
|
E:CYS19
|
3.9
|
96.5
|
1.0
|
CD2
|
E:HIS39
|
4.0
|
100.6
|
1.0
|
ND1
|
E:HIS33
|
4.0
|
91.3
|
1.0
|
C
|
E:ALA18
|
4.1
|
99.0
|
1.0
|
HA
|
E:CYS19
|
4.1
|
96.5
|
1.0
|
NE2
|
E:HIS39
|
4.1
|
100.6
|
1.0
|
N
|
E:ALA18
|
4.2
|
99.0
|
1.0
|
H
|
E:GLY17
|
4.2
|
93.3
|
1.0
|
HB1
|
E:ALA110
|
4.2
|
94.4
|
1.0
|
CG
|
E:HIS33
|
4.2
|
91.3
|
1.0
|
CA
|
E:HIS39
|
4.4
|
100.6
|
1.0
|
HB3
|
E:CYS19
|
4.4
|
96.5
|
1.0
|
CA
|
E:ALA18
|
4.5
|
99.0
|
1.0
|
N
|
E:GLY17
|
4.6
|
93.3
|
1.0
|
CB
|
E:ALA18
|
4.6
|
99.0
|
1.0
|
HA
|
E:HIS39
|
4.7
|
100.6
|
1.0
|
CA
|
E:CYS16
|
4.7
|
90.5
|
1.0
|
HD1
|
E:HIS33
|
4.8
|
91.3
|
1.0
|
HD2
|
E:HIS39
|
4.8
|
100.6
|
1.0
|
HD11
|
E:LEU25
|
4.8
|
84.2
|
1.0
|
HZ
|
E:PHE106
|
4.8
|
91.2
|
1.0
|
O
|
E:ALA18
|
4.8
|
99.0
|
1.0
|
HB3
|
E:ALA110
|
4.9
|
94.4
|
1.0
|
HB1
|
E:ALA18
|
4.9
|
99.0
|
1.0
|
C
|
E:CYS16
|
4.9
|
90.5
|
1.0
|
CB
|
E:ALA110
|
4.9
|
94.4
|
1.0
|
HE2
|
E:HIS39
|
5.0
|
100.6
|
1.0
|
HG12
|
E:VAL34
|
5.0
|
95.0
|
1.0
|
H
|
E:HIS39
|
5.0
|
100.6
|
1.0
|
|
Zinc binding site 6 out
of 8 in 7rdx
Go back to
Zinc Binding Sites List in 7rdx
Zinc binding site 6 out
of 8 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 Zinc with other atoms in the Zn binding
site number 6 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:Zn1000
b:194.1
occ:1.00
|
SG
|
F:CYS26
|
2.3
|
125.2
|
1.0
|
SG
|
F:CYS8
|
2.3
|
128.6
|
1.0
|
SG
|
F:CYS29
|
2.3
|
130.3
|
1.0
|
SG
|
F:CYS5
|
2.3
|
124.1
|
1.0
|
HB2
|
F:CYS29
|
2.8
|
130.3
|
1.0
|
H
|
F:CYS26
|
2.9
|
125.2
|
1.0
|
HB3
|
F:CYS26
|
3.0
|
125.2
|
1.0
|
HD23
|
F:LEU7
|
3.1
|
130.8
|
1.0
|
CB
|
F:CYS29
|
3.1
|
130.3
|
1.0
|
CB
|
F:CYS26
|
3.2
|
125.2
|
1.0
|
HB3
|
F:CYS5
|
3.3
|
124.1
|
1.0
|
CB
|
F:CYS5
|
3.3
|
124.1
|
1.0
|
HG
|
F:SER10
|
3.4
|
124.7
|
1.0
|
H
|
F:CYS29
|
3.5
|
130.3
|
1.0
|
HB2
|
F:CYS5
|
3.5
|
124.1
|
1.0
|
N
|
F:CYS26
|
3.7
|
125.2
|
1.0
|
HB3
|
F:CYS29
|
3.8
|
130.3
|
1.0
|
OG
|
F:SER10
|
3.8
|
124.7
|
1.0
|
HD21
|
F:LEU7
|
3.8
|
130.8
|
1.0
|
CD2
|
F:LEU7
|
3.8
|
130.8
|
1.0
|
HG
|
F:LEU7
|
4.0
|
130.8
|
1.0
|
CA
|
F:CYS26
|
4.0
|
125.2
|
1.0
|
CB
|
F:CYS8
|
4.0
|
128.6
|
1.0
|
O
|
F:VAL98
|
4.0
|
127.6
|
1.0
|
HB2
|
F:CYS26
|
4.0
|
125.2
|
1.0
|
H
|
F:CYS8
|
4.1
|
128.6
|
1.0
|
N
|
F:CYS29
|
4.1
|
130.3
|
1.0
|
HB3
|
F:CYS8
|
4.2
|
128.6
|
1.0
|
CA
|
F:CYS29
|
4.3
|
130.3
|
1.0
|
CG
|
F:LEU7
|
4.5
|
130.8
|
1.0
|
N
|
F:CYS8
|
4.5
|
128.6
|
1.0
|
HA
|
F:LEU25
|
4.5
|
121.7
|
1.0
|
HB2
|
F:CYS8
|
4.6
|
128.6
|
1.0
|
HB2
|
F:LYS28
|
4.6
|
129.3
|
1.0
|
HD22
|
F:LEU7
|
4.6
|
130.8
|
1.0
|
H
|
F:LEU7
|
4.6
|
130.8
|
1.0
|
C
|
F:CYS26
|
4.7
|
125.2
|
1.0
|
HB3
|
F:SER100
|
4.7
|
132.4
|
1.0
|
HA
|
F:CYS29
|
4.7
|
130.3
|
1.0
|
H
|
F:SER10
|
4.8
|
124.7
|
1.0
|
CA
|
F:CYS5
|
4.8
|
124.1
|
1.0
|
HA
|
F:CYS26
|
4.8
|
125.2
|
1.0
|
CA
|
F:CYS8
|
4.8
|
128.6
|
1.0
|
O
|
F:CYS26
|
4.8
|
125.2
|
1.0
|
C
|
F:LEU25
|
4.8
|
121.7
|
1.0
|
HD11
|
F:LEU7
|
4.9
|
130.8
|
1.0
|
|
Zinc binding site 7 out
of 8 in 7rdx
Go back to
Zinc Binding Sites List in 7rdx
Zinc binding site 7 out
of 8 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 Zinc with other atoms in the Zn binding
site number 7 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:Zn1001
b:204.1
occ:1.00
|
HE1
|
F:HIS75
|
1.2
|
149.7
|
1.0
|
CE1
|
F:HIS75
|
1.7
|
149.7
|
1.0
|
HE2
|
F:HIS75
|
2.0
|
149.7
|
1.0
|
NE2
|
F:HIS75
|
2.1
|
149.7
|
1.0
|
SG
|
F:CYS50
|
2.3
|
138.9
|
1.0
|
SG
|
F:CYS55
|
2.3
|
147.3
|
1.0
|
SG
|
F:CYS72
|
2.3
|
144.3
|
1.0
|
ND1
|
F:HIS75
|
2.9
|
149.7
|
1.0
|
H
|
F:CYS72
|
3.1
|
144.3
|
1.0
|
CB
|
F:CYS55
|
3.2
|
147.3
|
1.0
|
HB3
|
F:CYS55
|
3.2
|
147.3
|
1.0
|
HB2
|
F:CYS55
|
3.3
|
147.3
|
1.0
|
CD2
|
F:HIS75
|
3.4
|
149.7
|
1.0
|
CB
|
F:CYS50
|
3.4
|
138.9
|
1.0
|
HB3
|
F:CYS50
|
3.4
|
138.9
|
1.0
|
HB2
|
F:CYS50
|
3.5
|
138.9
|
1.0
|
CB
|
F:CYS72
|
3.8
|
144.3
|
1.0
|
CG
|
F:HIS75
|
3.8
|
149.7
|
1.0
|
HB3
|
F:CYS72
|
3.8
|
144.3
|
1.0
|
HG23
|
F:VAL57
|
3.9
|
140.6
|
1.0
|
HB3
|
F:ALA52
|
3.9
|
144.3
|
1.0
|
N
|
F:CYS72
|
4.0
|
144.3
|
1.0
|
HB2
|
F:ALA52
|
4.0
|
144.3
|
1.0
|
HG21
|
F:VAL57
|
4.0
|
140.6
|
1.0
|
HD2
|
F:HIS75
|
4.1
|
149.7
|
1.0
|
HB
|
F:VAL57
|
4.2
|
140.6
|
1.0
|
HB3
|
F:SER74
|
4.3
|
150.5
|
1.0
|
CG2
|
F:VAL57
|
4.3
|
140.6
|
1.0
|
CB
|
F:ALA52
|
4.4
|
144.3
|
1.0
|
HA
|
F:TYR71
|
4.4
|
137.6
|
1.0
|
CA
|
F:CYS72
|
4.4
|
144.3
|
1.0
|
HB2
|
F:CYS72
|
4.5
|
144.3
|
1.0
|
CA
|
F:CYS55
|
4.7
|
147.3
|
1.0
|
H
|
F:HIS75
|
4.7
|
149.7
|
1.0
|
HB1
|
F:ALA52
|
4.8
|
144.3
|
1.0
|
CA
|
F:CYS50
|
4.8
|
138.9
|
1.0
|
CB
|
F:VAL57
|
4.8
|
140.6
|
1.0
|
HB3
|
F:TYR71
|
4.8
|
137.6
|
1.0
|
H
|
F:ASP56
|
4.9
|
143.4
|
1.0
|
HD1
|
F:TYR71
|
5.0
|
137.6
|
1.0
|
HA
|
F:CYS55
|
5.0
|
147.3
|
1.0
|
H
|
F:ALA52
|
5.0
|
144.3
|
1.0
|
|
Zinc binding site 8 out
of 8 in 7rdx
Go back to
Zinc Binding Sites List in 7rdx
Zinc binding site 8 out
of 8 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 Zinc with other atoms in the Zn binding
site number 8 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:Zn1002
b:151.9
occ:1.00
|
HD1
|
F:HIS39
|
1.4
|
135.5
|
1.0
|
NE2
|
F:HIS33
|
2.0
|
135.6
|
1.0
|
ND1
|
F:HIS39
|
2.0
|
135.5
|
1.0
|
SG
|
F:CYS19
|
2.3
|
129.6
|
1.0
|
SG
|
F:CYS16
|
2.3
|
121.1
|
1.0
|
HE1
|
F:HIS39
|
2.4
|
135.5
|
1.0
|
CE1
|
F:HIS39
|
2.5
|
135.5
|
1.0
|
CD2
|
F:HIS33
|
2.8
|
135.6
|
1.0
|
HD2
|
F:HIS33
|
2.9
|
135.6
|
1.0
|
CE1
|
F:HIS33
|
3.1
|
135.6
|
1.0
|
HB3
|
F:CYS16
|
3.3
|
121.1
|
1.0
|
CG
|
F:HIS39
|
3.3
|
135.5
|
1.0
|
CB
|
F:CYS16
|
3.4
|
121.1
|
1.0
|
HE1
|
F:HIS33
|
3.4
|
135.6
|
1.0
|
H
|
F:CYS19
|
3.4
|
129.6
|
1.0
|
CB
|
F:CYS19
|
3.5
|
129.6
|
1.0
|
HB2
|
F:CYS19
|
3.5
|
129.6
|
1.0
|
HB2
|
F:CYS16
|
3.7
|
121.1
|
1.0
|
N
|
F:CYS19
|
3.7
|
129.6
|
1.0
|
NE2
|
F:HIS39
|
3.8
|
135.5
|
1.0
|
HB3
|
F:ALA18
|
3.8
|
127.9
|
1.0
|
HB3
|
F:HIS39
|
3.9
|
135.5
|
1.0
|
HA
|
F:CYS19
|
3.9
|
129.6
|
1.0
|
CA
|
F:CYS19
|
4.0
|
129.6
|
1.0
|
CG
|
F:HIS33
|
4.0
|
135.6
|
1.0
|
HE1
|
F:PHE106
|
4.1
|
138.3
|
1.0
|
CB
|
F:HIS39
|
4.1
|
135.5
|
1.0
|
ND1
|
F:HIS33
|
4.1
|
135.6
|
1.0
|
HB1
|
F:ALA110
|
4.1
|
143.2
|
1.0
|
HB2
|
F:HIS39
|
4.2
|
135.5
|
1.0
|
CD2
|
F:HIS39
|
4.2
|
135.5
|
1.0
|
HB3
|
F:CYS19
|
4.3
|
129.6
|
1.0
|
HD11
|
F:LEU25
|
4.4
|
121.7
|
1.0
|
C
|
F:ALA18
|
4.5
|
127.9
|
1.0
|
HD2
|
F:PRO23
|
4.6
|
122.9
|
1.0
|
CB
|
F:ALA18
|
4.6
|
127.9
|
1.0
|
HB3
|
F:ALA110
|
4.7
|
143.2
|
1.0
|
O
|
F:CYS16
|
4.7
|
121.1
|
1.0
|
CA
|
F:CYS16
|
4.7
|
121.1
|
1.0
|
CB
|
F:ALA110
|
4.8
|
143.2
|
1.0
|
HB1
|
F:ALA18
|
4.8
|
127.9
|
1.0
|
H
|
F:ALA18
|
4.8
|
127.9
|
1.0
|
HD1
|
F:HIS33
|
4.9
|
135.6
|
1.0
|
HG2
|
F:PRO23
|
5.0
|
122.9
|
1.0
|
CE1
|
F:PHE106
|
5.0
|
138.3
|
1.0
|
HB2
|
F:ALA110
|
5.0
|
143.2
|
1.0
|
C
|
F:CYS16
|
5.0
|
121.1
|
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: Wed Oct 30 10:14:53 2024
|