Zinc in PDB 7rdz: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo Class
Enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo Class
All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo Class:
2.7.7.48;
3.6.4.12;
3.6.4.13;
Other elements in 7rdz:
The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo 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 - Apo Class
(pdb code 7rdz). 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 - Apo Class, PDB code: 7rdz:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 7rdz
Go back to
Zinc Binding Sites List in 7rdz
Zinc binding site 1 out
of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo 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 - Apo Class within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2000
b:119.2
occ:1.00
|
ND1
|
A:HIS295
|
2.1
|
92.2
|
1.0
|
|
SG
|
A:CYS310
|
2.3
|
90.4
|
1.0
|
|
SG
|
A:CYS306
|
2.3
|
93.7
|
1.0
|
|
SG
|
A:CYS301
|
2.3
|
96.2
|
1.0
|
|
HA
|
A:CYS301
|
2.9
|
96.2
|
1.0
|
|
CE1
|
A:HIS295
|
2.9
|
92.2
|
1.0
|
|
HB2
|
A:HIS295
|
3.0
|
92.2
|
1.0
|
|
HE1
|
A:HIS295
|
3.1
|
92.2
|
1.0
|
|
CG
|
A:HIS295
|
3.2
|
92.2
|
1.0
|
|
HB2
|
A:CYS310
|
3.4
|
90.4
|
1.0
|
|
O
|
A:CYS306
|
3.4
|
93.7
|
1.0
|
|
CB
|
A:CYS301
|
3.4
|
96.2
|
1.0
|
|
CB
|
A:CYS310
|
3.5
|
90.4
|
1.0
|
|
HB3
|
A:CYS301
|
3.6
|
96.2
|
1.0
|
|
CA
|
A:CYS301
|
3.6
|
96.2
|
1.0
|
|
CB
|
A:HIS295
|
3.6
|
92.2
|
1.0
|
|
H
|
A:HIS295
|
3.7
|
92.2
|
1.0
|
|
CB
|
A:CYS306
|
3.7
|
93.7
|
1.0
|
|
HB3
|
A:CYS306
|
3.7
|
93.7
|
1.0
|
|
C
|
A:CYS306
|
3.9
|
93.7
|
1.0
|
|
HB3
|
A:CYS310
|
4.0
|
90.4
|
1.0
|
|
NE2
|
A:HIS295
|
4.1
|
92.2
|
1.0
|
|
H
|
A:LEU302
|
4.2
|
93.6
|
1.0
|
|
H
|
A:CYS310
|
4.2
|
90.4
|
1.0
|
|
HA
|
A:CYS298
|
4.2
|
93.3
|
1.0
|
|
HB2
|
A:CYS301
|
4.2
|
96.2
|
1.0
|
|
CD2
|
A:HIS295
|
4.2
|
92.2
|
1.0
|
|
HD1
|
A:HIS309
|
4.3
|
87.4
|
1.0
|
|
HB3
|
A:HIS295
|
4.3
|
92.2
|
1.0
|
|
N
|
A:HIS295
|
4.3
|
92.2
|
1.0
|
|
HA
|
A:ILE307
|
4.3
|
92.7
|
1.0
|
|
CA
|
A:CYS306
|
4.3
|
93.7
|
1.0
|
|
N
|
A:CYS301
|
4.4
|
96.2
|
1.0
|
|
HB2
|
A:CYS306
|
4.4
|
93.7
|
1.0
|
|
HA
|
A:CYS306
|
4.5
|
93.7
|
1.0
|
|
CA
|
A:HIS295
|
4.6
|
92.2
|
1.0
|
|
N
|
A:ILE307
|
4.6
|
92.7
|
1.0
|
|
H
|
A:CYS301
|
4.6
|
96.2
|
1.0
|
|
CA
|
A:CYS310
|
4.7
|
90.4
|
1.0
|
|
N
|
A:LEU302
|
4.8
|
93.6
|
1.0
|
|
C
|
A:CYS301
|
4.8
|
96.2
|
1.0
|
|
N
|
A:CYS310
|
4.8
|
90.4
|
1.0
|
|
HD23
|
A:LEU302
|
4.8
|
93.6
|
1.0
|
|
O
|
A:HIS295
|
4.8
|
92.2
|
1.0
|
|
HE2
|
A:HIS295
|
4.9
|
92.2
|
1.0
|
|
HA
|
A:TYR294
|
4.9
|
90.9
|
1.0
|
|
CA
|
A:ILE307
|
5.0
|
92.7
|
1.0
|
|
Zinc binding site 2 out
of 8 in 7rdz
Go back to
Zinc Binding Sites List in 7rdz
Zinc binding site 2 out
of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo 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 - Apo Class within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2001
b:121.0
occ:1.00
|
ND1
|
A:HIS642
|
2.1
|
102.3
|
1.0
|
|
SG
|
A:CYS487
|
2.3
|
105.2
|
1.0
|
|
SG
|
A:CYS646
|
2.3
|
108.3
|
1.0
|
|
SG
|
A:CYS645
|
2.3
|
108.6
|
1.0
|
|
HE1
|
A:PHE571
|
2.6
|
101.8
|
1.0
|
|
CE1
|
A:HIS642
|
2.8
|
102.3
|
1.0
|
|
HE1
|
A:HIS642
|
3.0
|
102.3
|
1.0
|
|
HB3
|
A:HIS642
|
3.1
|
102.3
|
1.0
|
|
CG
|
A:HIS642
|
3.1
|
102.3
|
1.0
|
|
H
|
A:CYS487
|
3.2
|
105.2
|
1.0
|
|
HB2
|
A:CYS646
|
3.4
|
108.3
|
1.0
|
|
HZ1
|
A:LYS532
|
3.4
|
103.1
|
1.0
|
|
CE1
|
A:PHE571
|
3.5
|
101.8
|
1.0
|
|
HB2
|
A:CYS487
|
3.5
|
105.2
|
1.0
|
|
CB
|
A:CYS646
|
3.5
|
108.3
|
1.0
|
|
CB
|
A:CYS487
|
3.5
|
105.2
|
1.0
|
|
HB2
|
A:CYS645
|
3.6
|
108.6
|
1.0
|
|
CB
|
A:HIS642
|
3.6
|
102.3
|
1.0
|
|
HD1
|
A:PHE571
|
3.6
|
101.8
|
1.0
|
|
CB
|
A:CYS645
|
3.6
|
108.6
|
1.0
|
|
N
|
A:CYS487
|
3.8
|
105.2
|
1.0
|
|
HE2
|
A:LYS532
|
3.9
|
103.1
|
1.0
|
|
NE2
|
A:HIS642
|
3.9
|
102.3
|
1.0
|
|
CD1
|
A:PHE571
|
3.9
|
101.8
|
1.0
|
|
C
|
A:CYS645
|
4.0
|
108.6
|
1.0
|
|
HZ3
|
A:LYS532
|
4.0
|
103.1
|
1.0
|
|
CD2
|
A:HIS642
|
4.0
|
102.3
|
1.0
|
|
NZ
|
A:LYS532
|
4.0
|
103.1
|
1.0
|
|
O
|
A:CYS645
|
4.1
|
108.6
|
1.0
|
|
N
|
A:CYS646
|
4.1
|
108.3
|
1.0
|
|
HB2
|
A:HIS642
|
4.1
|
102.3
|
1.0
|
|
CA
|
A:CYS487
|
4.2
|
105.2
|
1.0
|
|
HB3
|
A:CYS646
|
4.2
|
108.3
|
1.0
|
|
HB3
|
A:CYS487
|
4.3
|
105.2
|
1.0
|
|
CA
|
A:CYS646
|
4.3
|
108.3
|
1.0
|
|
HB3
|
A:CYS645
|
4.3
|
108.6
|
1.0
|
|
HA
|
A:CYS487
|
4.4
|
105.2
|
1.0
|
|
HA2
|
A:GLY486
|
4.4
|
104.1
|
1.0
|
|
H
|
A:CYS646
|
4.4
|
108.3
|
1.0
|
|
CA
|
A:CYS645
|
4.4
|
108.6
|
1.0
|
|
CE
|
A:LYS532
|
4.5
|
103.1
|
1.0
|
|
HZ
|
A:PHE528
|
4.5
|
104.8
|
1.0
|
|
CZ
|
A:PHE571
|
4.5
|
101.8
|
1.0
|
|
HA
|
A:HIS642
|
4.6
|
102.3
|
1.0
|
|
HA
|
A:CYS646
|
4.6
|
108.3
|
1.0
|
|
HE2
|
A:HIS642
|
4.6
|
102.3
|
1.0
|
|
HZ
|
A:PHE571
|
4.7
|
101.8
|
1.0
|
|
CA
|
A:HIS642
|
4.7
|
102.3
|
1.0
|
|
C
|
A:GLY486
|
4.8
|
104.1
|
1.0
|
|
HZ2
|
A:LYS532
|
4.8
|
103.1
|
1.0
|
|
HE3
|
A:LYS532
|
4.8
|
103.1
|
1.0
|
|
HD2
|
A:HIS642
|
4.9
|
102.3
|
1.0
|
|
H
|
A:CYS645
|
4.9
|
108.6
|
1.0
|
|
Zinc binding site 3 out
of 8 in 7rdz
Go back to
Zinc Binding Sites List in 7rdz
Zinc binding site 3 out
of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo 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 - Apo Class within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn1000
b:200.7
occ:1.00
|
SG
|
E:CYS29
|
2.3
|
172.8
|
1.0
|
|
SG
|
E:CYS5
|
2.3
|
167.8
|
1.0
|
|
SG
|
E:CYS26
|
2.3
|
169.7
|
1.0
|
|
SG
|
E:CYS8
|
2.3
|
166.9
|
1.0
|
|
HB2
|
E:CYS29
|
2.4
|
172.8
|
1.0
|
|
HB3
|
E:CYS26
|
2.8
|
169.7
|
1.0
|
|
CB
|
E:CYS29
|
2.9
|
172.8
|
1.0
|
|
H
|
E:CYS26
|
3.0
|
169.7
|
1.0
|
|
HB3
|
E:CYS5
|
3.0
|
167.8
|
1.0
|
|
CB
|
E:CYS26
|
3.1
|
169.7
|
1.0
|
|
CB
|
E:CYS5
|
3.2
|
167.8
|
1.0
|
|
HB2
|
E:CYS5
|
3.3
|
167.8
|
1.0
|
|
H
|
E:CYS29
|
3.4
|
172.8
|
1.0
|
|
HB3
|
E:CYS29
|
3.4
|
172.8
|
1.0
|
|
HB3
|
E:CYS8
|
3.4
|
166.9
|
1.0
|
|
CB
|
E:CYS8
|
3.6
|
166.9
|
1.0
|
|
N
|
E:CYS26
|
3.7
|
169.7
|
1.0
|
|
HB2
|
E:CYS26
|
3.9
|
169.7
|
1.0
|
|
H
|
E:CYS8
|
3.9
|
166.9
|
1.0
|
|
HD12
|
E:LEU7
|
4.0
|
172.2
|
1.0
|
|
CA
|
E:CYS26
|
4.0
|
169.7
|
1.0
|
|
HG
|
E:LEU7
|
4.0
|
172.2
|
1.0
|
|
O
|
E:VAL98
|
4.0
|
166.3
|
1.0
|
|
N
|
E:CYS29
|
4.0
|
172.8
|
1.0
|
|
CA
|
E:CYS29
|
4.1
|
172.8
|
1.0
|
|
HB2
|
E:CYS8
|
4.2
|
166.9
|
1.0
|
|
HB3
|
E:SER10
|
4.3
|
163.3
|
1.0
|
|
N
|
E:CYS8
|
4.3
|
166.9
|
1.0
|
|
HA3
|
E:GLY99
|
4.4
|
166.4
|
1.0
|
|
HD12
|
E:LEU25
|
4.5
|
170.5
|
1.0
|
|
CA
|
E:CYS8
|
4.5
|
166.9
|
1.0
|
|
HA2
|
E:GLY99
|
4.5
|
166.4
|
1.0
|
|
HA
|
E:CYS29
|
4.6
|
172.8
|
1.0
|
|
H
|
E:SER10
|
4.6
|
163.3
|
1.0
|
|
CA
|
E:CYS5
|
4.6
|
167.8
|
1.0
|
|
CD1
|
E:LEU7
|
4.6
|
172.2
|
1.0
|
|
HD11
|
E:LEU7
|
4.6
|
172.2
|
1.0
|
|
C
|
E:CYS26
|
4.6
|
169.7
|
1.0
|
|
HA
|
E:LEU25
|
4.7
|
170.5
|
1.0
|
|
CG
|
E:LEU7
|
4.8
|
172.2
|
1.0
|
|
H
|
E:LEU7
|
4.8
|
172.2
|
1.0
|
|
HD13
|
E:LEU25
|
4.8
|
170.5
|
1.0
|
|
HA
|
E:CYS26
|
4.8
|
169.7
|
1.0
|
|
C
|
E:VAL98
|
4.8
|
166.3
|
1.0
|
|
O
|
E:CYS26
|
4.8
|
169.7
|
1.0
|
|
H
|
E:VAL98
|
4.8
|
166.3
|
1.0
|
|
HB2
|
E:CYS97
|
4.8
|
169.7
|
1.0
|
|
HB2
|
E:LYS28
|
4.9
|
169.7
|
1.0
|
|
CA
|
E:GLY99
|
4.9
|
166.4
|
1.0
|
|
C
|
E:LEU25
|
4.9
|
170.5
|
1.0
|
|
H
|
E:ASN9
|
4.9
|
166.2
|
1.0
|
|
HA
|
E:CYS5
|
5.0
|
167.8
|
1.0
|
|
Zinc binding site 4 out
of 8 in 7rdz
Go back to
Zinc Binding Sites List in 7rdz
Zinc binding site 4 out
of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo 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 - Apo Class within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn1001
b:208.0
occ:1.00
|
ND1
|
E:HIS75
|
2.1
|
178.9
|
1.0
|
|
SG
|
E:CYS55
|
2.3
|
176.9
|
1.0
|
|
SG
|
E:CYS72
|
2.3
|
178.8
|
1.0
|
|
SG
|
E:CYS50
|
2.3
|
176.6
|
1.0
|
|
CG
|
E:HIS75
|
2.5
|
178.9
|
1.0
|
|
CE1
|
E:HIS75
|
2.5
|
178.9
|
1.0
|
|
HB3
|
E:CYS72
|
2.6
|
178.8
|
1.0
|
|
HB3
|
E:CYS55
|
2.8
|
176.9
|
1.0
|
|
HB2
|
E:ALA52
|
2.9
|
179.6
|
1.0
|
|
HB2
|
E:HIS75
|
2.9
|
178.9
|
1.0
|
|
CB
|
E:CYS55
|
2.9
|
176.9
|
1.0
|
|
HE1
|
E:HIS75
|
3.0
|
178.9
|
1.0
|
|
HB2
|
E:CYS55
|
3.0
|
176.9
|
1.0
|
|
CB
|
E:CYS72
|
3.0
|
178.8
|
1.0
|
|
H
|
E:CYS72
|
3.1
|
178.8
|
1.0
|
|
NE2
|
E:HIS75
|
3.1
|
178.9
|
1.0
|
|
CD2
|
E:HIS75
|
3.1
|
178.9
|
1.0
|
|
CB
|
E:HIS75
|
3.2
|
178.9
|
1.0
|
|
HB3
|
E:CYS50
|
3.5
|
176.6
|
1.0
|
|
CB
|
E:CYS50
|
3.5
|
176.6
|
1.0
|
|
CB
|
E:ALA52
|
3.7
|
179.6
|
1.0
|
|
HB3
|
E:HIS75
|
3.7
|
178.9
|
1.0
|
|
HB2
|
E:CYS72
|
3.7
|
178.8
|
1.0
|
|
HE2
|
E:HIS75
|
3.8
|
178.9
|
1.0
|
|
N
|
E:CYS72
|
3.8
|
178.8
|
1.0
|
|
HB3
|
E:ALA52
|
3.8
|
179.6
|
1.0
|
|
HB2
|
E:CYS50
|
3.8
|
176.6
|
1.0
|
|
HD2
|
E:HIS75
|
3.8
|
178.9
|
1.0
|
|
HB1
|
E:ALA52
|
3.9
|
179.6
|
1.0
|
|
CA
|
E:CYS72
|
4.0
|
178.8
|
1.0
|
|
HG21
|
E:VAL57
|
4.1
|
175.6
|
1.0
|
|
HG23
|
E:VAL57
|
4.3
|
175.6
|
1.0
|
|
H
|
E:ALA52
|
4.4
|
179.6
|
1.0
|
|
CA
|
E:CYS55
|
4.4
|
176.9
|
1.0
|
|
H
|
E:HIS75
|
4.4
|
178.9
|
1.0
|
|
CA
|
E:HIS75
|
4.5
|
178.9
|
1.0
|
|
HB
|
E:VAL57
|
4.6
|
175.6
|
1.0
|
|
N
|
E:HIS75
|
4.6
|
178.9
|
1.0
|
|
CG2
|
E:VAL57
|
4.6
|
175.6
|
1.0
|
|
HA
|
E:CYS72
|
4.7
|
178.8
|
1.0
|
|
HA
|
E:TYR71
|
4.7
|
174.2
|
1.0
|
|
HA
|
E:CYS55
|
4.8
|
176.9
|
1.0
|
|
C
|
E:CYS72
|
4.8
|
178.8
|
1.0
|
|
HB3
|
E:TYR71
|
4.9
|
174.2
|
1.0
|
|
CA
|
E:CYS50
|
4.9
|
176.6
|
1.0
|
|
CA
|
E:ALA52
|
4.9
|
179.6
|
1.0
|
|
H
|
E:SER74
|
5.0
|
174.4
|
1.0
|
|
N
|
E:ALA52
|
5.0
|
179.6
|
1.0
|
|
C
|
E:TYR71
|
5.0
|
174.2
|
1.0
|
|
C
|
E:CYS55
|
5.0
|
176.9
|
1.0
|
|
O
|
E:CYS50
|
5.0
|
176.6
|
1.0
|
|
Zinc binding site 5 out
of 8 in 7rdz
Go back to
Zinc Binding Sites List in 7rdz
Zinc binding site 5 out
of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo 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 - Apo Class within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn1002
b:193.1
occ:1.00
|
NE2
|
E:HIS33
|
2.0
|
170.0
|
1.0
|
|
ND1
|
E:HIS39
|
2.0
|
168.2
|
1.0
|
|
SG
|
E:CYS19
|
2.3
|
176.8
|
1.0
|
|
SG
|
E:CYS16
|
2.3
|
177.7
|
1.0
|
|
CE1
|
E:HIS39
|
2.8
|
168.2
|
1.0
|
|
HB3
|
E:CYS16
|
2.8
|
177.7
|
1.0
|
|
HE1
|
E:HIS39
|
2.8
|
168.2
|
1.0
|
|
CE1
|
E:HIS33
|
2.8
|
170.0
|
1.0
|
|
CD2
|
E:HIS33
|
2.8
|
170.0
|
1.0
|
|
CB
|
E:CYS16
|
3.0
|
177.7
|
1.0
|
|
HE1
|
E:HIS33
|
3.1
|
170.0
|
1.0
|
|
HD2
|
E:HIS33
|
3.1
|
170.0
|
1.0
|
|
HB2
|
E:CYS16
|
3.1
|
177.7
|
1.0
|
|
CG
|
E:HIS39
|
3.2
|
168.2
|
1.0
|
|
H
|
E:CYS19
|
3.4
|
176.8
|
1.0
|
|
HB3
|
E:HIS39
|
3.4
|
168.2
|
1.0
|
|
CB
|
E:CYS19
|
3.5
|
176.8
|
1.0
|
|
HB2
|
E:CYS19
|
3.5
|
176.8
|
1.0
|
|
CB
|
E:HIS39
|
3.7
|
168.2
|
1.0
|
|
ND1
|
E:HIS33
|
3.8
|
170.0
|
1.0
|
|
N
|
E:CYS19
|
3.8
|
176.8
|
1.0
|
|
CG
|
E:HIS33
|
3.8
|
170.0
|
1.0
|
|
HB2
|
E:HIS39
|
3.8
|
168.2
|
1.0
|
|
NE2
|
E:HIS39
|
4.0
|
168.2
|
1.0
|
|
CA
|
E:CYS19
|
4.0
|
176.8
|
1.0
|
|
HA
|
E:CYS19
|
4.0
|
176.8
|
1.0
|
|
HB1
|
E:ALA110
|
4.1
|
180.5
|
1.0
|
|
HB3
|
E:ALA18
|
4.1
|
171.6
|
1.0
|
|
HZ
|
E:PHE106
|
4.1
|
177.2
|
1.0
|
|
HE2
|
E:PHE106
|
4.2
|
177.2
|
1.0
|
|
CD2
|
E:HIS39
|
4.2
|
168.2
|
1.0
|
|
HB3
|
E:CYS19
|
4.3
|
176.8
|
1.0
|
|
CA
|
E:CYS16
|
4.4
|
177.7
|
1.0
|
|
HD1
|
E:HIS33
|
4.5
|
170.0
|
1.0
|
|
HB2
|
E:ALA110
|
4.5
|
180.5
|
1.0
|
|
C
|
E:ALA18
|
4.7
|
171.6
|
1.0
|
|
HE2
|
E:HIS39
|
4.7
|
168.2
|
1.0
|
|
CB
|
E:ALA110
|
4.7
|
180.5
|
1.0
|
|
CZ
|
E:PHE106
|
4.7
|
177.2
|
1.0
|
|
CE2
|
E:PHE106
|
4.8
|
177.2
|
1.0
|
|
HA
|
E:CYS16
|
4.8
|
177.7
|
1.0
|
|
HD2
|
E:PRO23
|
4.8
|
174.4
|
1.0
|
|
O
|
E:CYS16
|
4.8
|
177.7
|
1.0
|
|
C
|
E:CYS16
|
4.9
|
177.7
|
1.0
|
|
CB
|
E:ALA18
|
4.9
|
171.6
|
1.0
|
|
Zinc binding site 6 out
of 8 in 7rdz
Go back to
Zinc Binding Sites List in 7rdz
Zinc binding site 6 out
of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo 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 - Apo Class within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn1000
b:208.5
occ:1.00
|
SG
|
F:CYS26
|
2.3
|
174.1
|
1.0
|
|
SG
|
F:CYS5
|
2.3
|
174.6
|
1.0
|
|
SG
|
F:CYS29
|
2.3
|
176.4
|
1.0
|
|
SG
|
F:CYS8
|
2.3
|
176.0
|
1.0
|
|
HB2
|
F:CYS29
|
2.5
|
176.4
|
1.0
|
|
HB3
|
F:CYS26
|
2.9
|
174.1
|
1.0
|
|
CB
|
F:CYS29
|
2.9
|
176.4
|
1.0
|
|
H
|
F:CYS26
|
3.0
|
174.1
|
1.0
|
|
HB3
|
F:CYS5
|
3.1
|
174.6
|
1.0
|
|
HB3
|
F:CYS8
|
3.1
|
176.0
|
1.0
|
|
CB
|
F:CYS26
|
3.2
|
174.1
|
1.0
|
|
CB
|
F:CYS5
|
3.2
|
174.6
|
1.0
|
|
CB
|
F:CYS8
|
3.3
|
176.0
|
1.0
|
|
HB2
|
F:CYS5
|
3.3
|
174.6
|
1.0
|
|
HD23
|
F:LEU7
|
3.3
|
179.3
|
1.0
|
|
O
|
F:VAL98
|
3.4
|
173.9
|
1.0
|
|
HB3
|
F:CYS29
|
3.5
|
176.4
|
1.0
|
|
H
|
F:CYS29
|
3.5
|
176.4
|
1.0
|
|
HG
|
F:SER10
|
3.7
|
171.7
|
1.0
|
|
N
|
F:CYS26
|
3.8
|
174.1
|
1.0
|
|
H
|
F:CYS8
|
3.8
|
176.0
|
1.0
|
|
OG
|
F:SER10
|
3.8
|
171.7
|
1.0
|
|
HB2
|
F:CYS26
|
3.9
|
174.1
|
1.0
|
|
HG
|
F:LEU7
|
4.0
|
179.3
|
1.0
|
|
CA
|
F:CYS26
|
4.0
|
174.1
|
1.0
|
|
HB2
|
F:CYS8
|
4.1
|
176.0
|
1.0
|
|
N
|
F:CYS8
|
4.1
|
176.0
|
1.0
|
|
CA
|
F:CYS29
|
4.1
|
176.4
|
1.0
|
|
HA2
|
F:GLY99
|
4.1
|
176.2
|
1.0
|
|
N
|
F:CYS29
|
4.1
|
176.4
|
1.0
|
|
CD2
|
F:LEU7
|
4.2
|
179.3
|
1.0
|
|
CA
|
F:CYS8
|
4.3
|
176.0
|
1.0
|
|
HD21
|
F:LEU7
|
4.4
|
179.3
|
1.0
|
|
H
|
F:SER10
|
4.4
|
171.7
|
1.0
|
|
C
|
F:VAL98
|
4.6
|
173.9
|
1.0
|
|
HA
|
F:CYS29
|
4.6
|
176.4
|
1.0
|
|
CA
|
F:CYS5
|
4.6
|
174.6
|
1.0
|
|
CG
|
F:LEU7
|
4.6
|
179.3
|
1.0
|
|
H
|
F:LEU7
|
4.7
|
179.3
|
1.0
|
|
HA
|
F:LEU25
|
4.7
|
175.2
|
1.0
|
|
C
|
F:CYS26
|
4.7
|
174.1
|
1.0
|
|
HA
|
F:CYS26
|
4.8
|
174.1
|
1.0
|
|
C
|
F:LEU7
|
4.9
|
179.3
|
1.0
|
|
C
|
F:CYS8
|
4.9
|
176.0
|
1.0
|
|
O
|
F:CYS26
|
4.9
|
174.1
|
1.0
|
|
H
|
F:ASN9
|
4.9
|
171.0
|
1.0
|
|
HD22
|
F:LEU7
|
4.9
|
179.3
|
1.0
|
|
HA
|
F:CYS5
|
4.9
|
174.6
|
1.0
|
|
HB3
|
F:SER10
|
4.9
|
171.7
|
1.0
|
|
HB2
|
F:LYS28
|
4.9
|
173.2
|
1.0
|
|
C
|
F:LEU25
|
5.0
|
175.2
|
1.0
|
|
CB
|
F:SER10
|
5.0
|
171.7
|
1.0
|
|
Zinc binding site 7 out
of 8 in 7rdz
Go back to
Zinc Binding Sites List in 7rdz
Zinc binding site 7 out
of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo 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 - Apo Class within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn1001
b:211.7
occ:1.00
|
HD1
|
F:HIS75
|
1.7
|
183.5
|
1.0
|
|
ND1
|
F:HIS75
|
2.1
|
183.5
|
1.0
|
|
SG
|
F:CYS50
|
2.3
|
181.4
|
1.0
|
|
SG
|
F:CYS55
|
2.3
|
185.0
|
1.0
|
|
SG
|
F:CYS72
|
2.3
|
180.9
|
1.0
|
|
CE1
|
F:HIS75
|
2.7
|
183.5
|
1.0
|
|
HE1
|
F:HIS75
|
2.9
|
183.5
|
1.0
|
|
HB3
|
F:CYS55
|
2.9
|
185.0
|
1.0
|
|
CG
|
F:HIS75
|
3.0
|
183.5
|
1.0
|
|
CB
|
F:CYS55
|
3.0
|
185.0
|
1.0
|
|
HB2
|
F:HIS75
|
3.1
|
183.5
|
1.0
|
|
HB2
|
F:CYS55
|
3.1
|
185.0
|
1.0
|
|
H
|
F:CYS72
|
3.1
|
180.9
|
1.0
|
|
HB2
|
F:ALA52
|
3.5
|
183.3
|
1.0
|
|
CB
|
F:HIS75
|
3.6
|
183.5
|
1.0
|
|
CB
|
F:CYS50
|
3.6
|
181.4
|
1.0
|
|
HB3
|
F:CYS72
|
3.6
|
180.9
|
1.0
|
|
HG23
|
F:VAL57
|
3.6
|
178.5
|
1.0
|
|
CB
|
F:CYS72
|
3.6
|
180.9
|
1.0
|
|
HB3
|
F:ALA52
|
3.7
|
183.3
|
1.0
|
|
NE2
|
F:HIS75
|
3.7
|
183.5
|
1.0
|
|
HB3
|
F:CYS50
|
3.7
|
181.4
|
1.0
|
|
HB2
|
F:CYS50
|
3.7
|
181.4
|
1.0
|
|
CD2
|
F:HIS75
|
3.9
|
183.5
|
1.0
|
|
N
|
F:CYS72
|
3.9
|
180.9
|
1.0
|
|
CB
|
F:ALA52
|
4.0
|
183.3
|
1.0
|
|
HB3
|
F:HIS75
|
4.2
|
183.5
|
1.0
|
|
HG21
|
F:VAL57
|
4.2
|
178.5
|
1.0
|
|
H
|
F:HIS75
|
4.3
|
183.5
|
1.0
|
|
HB3
|
F:SER74
|
4.4
|
181.9
|
1.0
|
|
CG2
|
F:VAL57
|
4.4
|
178.5
|
1.0
|
|
HB2
|
F:CYS72
|
4.4
|
180.9
|
1.0
|
|
CA
|
F:CYS72
|
4.4
|
180.9
|
1.0
|
|
HB3
|
F:TYR71
|
4.4
|
180.4
|
1.0
|
|
HB1
|
F:ALA52
|
4.4
|
183.3
|
1.0
|
|
CA
|
F:CYS55
|
4.5
|
185.0
|
1.0
|
|
N
|
F:HIS75
|
4.5
|
183.5
|
1.0
|
|
HA
|
F:TYR71
|
4.6
|
180.4
|
1.0
|
|
HD2
|
F:HIS75
|
4.7
|
183.5
|
1.0
|
|
CA
|
F:HIS75
|
4.7
|
183.5
|
1.0
|
|
H
|
F:ALA52
|
4.8
|
183.3
|
1.0
|
|
HA
|
F:CYS55
|
4.8
|
185.0
|
1.0
|
|
HB
|
F:VAL57
|
4.8
|
178.5
|
1.0
|
|
H
|
F:SER74
|
4.8
|
181.9
|
1.0
|
|
HD2
|
F:TYR71
|
4.9
|
180.4
|
1.0
|
|
CA
|
F:CYS50
|
5.0
|
181.4
|
1.0
|
|
H
|
F:ASP56
|
5.0
|
181.6
|
1.0
|
|
Zinc binding site 8 out
of 8 in 7rdz
Go back to
Zinc Binding Sites List in 7rdz
Zinc binding site 8 out
of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Apo 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 - Apo Class within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn1002
b:186.4
occ:1.00
|
NE2
|
F:HIS33
|
2.0
|
177.4
|
1.0
|
|
ND1
|
F:HIS39
|
2.0
|
176.2
|
1.0
|
|
SG
|
F:CYS19
|
2.3
|
178.3
|
1.0
|
|
SG
|
F:CYS16
|
2.3
|
177.1
|
1.0
|
|
CE1
|
F:HIS33
|
2.8
|
177.4
|
1.0
|
|
CE1
|
F:HIS39
|
2.8
|
176.2
|
1.0
|
|
HE1
|
F:HIS39
|
2.9
|
176.2
|
1.0
|
|
HE1
|
F:HIS33
|
2.9
|
177.4
|
1.0
|
|
CD2
|
F:HIS33
|
3.1
|
177.4
|
1.0
|
|
CG
|
F:HIS39
|
3.1
|
176.2
|
1.0
|
|
HB3
|
F:CYS16
|
3.2
|
177.1
|
1.0
|
|
HD2
|
F:HIS33
|
3.3
|
177.4
|
1.0
|
|
CB
|
F:CYS16
|
3.4
|
177.1
|
1.0
|
|
H
|
F:CYS19
|
3.4
|
178.3
|
1.0
|
|
HB2
|
F:HIS39
|
3.5
|
176.2
|
1.0
|
|
HB3
|
F:HIS39
|
3.5
|
176.2
|
1.0
|
|
CB
|
F:CYS19
|
3.6
|
178.3
|
1.0
|
|
CB
|
F:HIS39
|
3.6
|
176.2
|
1.0
|
|
HB2
|
F:CYS16
|
3.6
|
177.1
|
1.0
|
|
HB2
|
F:CYS19
|
3.7
|
178.3
|
1.0
|
|
N
|
F:CYS19
|
3.8
|
178.3
|
1.0
|
|
HB3
|
F:ALA18
|
3.9
|
176.0
|
1.0
|
|
ND1
|
F:HIS33
|
3.9
|
177.4
|
1.0
|
|
HG1
|
F:THR37
|
4.0
|
177.3
|
1.0
|
|
NE2
|
F:HIS39
|
4.0
|
176.2
|
1.0
|
|
HB1
|
F:ALA110
|
4.1
|
183.7
|
1.0
|
|
CG
|
F:HIS33
|
4.1
|
177.4
|
1.0
|
|
CA
|
F:CYS19
|
4.1
|
178.3
|
1.0
|
|
HA
|
F:CYS19
|
4.1
|
178.3
|
1.0
|
|
HE2
|
F:PHE106
|
4.2
|
181.0
|
1.0
|
|
CD2
|
F:HIS39
|
4.2
|
176.2
|
1.0
|
|
HB3
|
F:CYS19
|
4.4
|
178.3
|
1.0
|
|
HB3
|
F:ALA110
|
4.6
|
183.7
|
1.0
|
|
HD1
|
F:HIS33
|
4.7
|
177.4
|
1.0
|
|
CB
|
F:ALA110
|
4.7
|
183.7
|
1.0
|
|
CA
|
F:CYS16
|
4.7
|
177.1
|
1.0
|
|
HD11
|
F:LEU25
|
4.7
|
175.2
|
1.0
|
|
C
|
F:ALA18
|
4.7
|
176.0
|
1.0
|
|
CB
|
F:ALA18
|
4.7
|
176.0
|
1.0
|
|
HB2
|
F:ALA110
|
4.7
|
183.7
|
1.0
|
|
HE2
|
F:HIS39
|
4.8
|
176.2
|
1.0
|
|
OG1
|
F:THR37
|
4.8
|
177.3
|
1.0
|
|
HZ
|
F:PHE106
|
4.8
|
181.0
|
1.0
|
|
O
|
F:CYS16
|
4.8
|
177.1
|
1.0
|
|
HB1
|
F:ALA18
|
4.9
|
176.0
|
1.0
|
|
CE2
|
F:PHE106
|
4.9
|
181.0
|
1.0
|
|
H
|
F:ALA18
|
5.0
|
176.0
|
1.0
|
|
HA
|
F:CYS16
|
5.0
|
177.1
|
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 10:15:05 2024
|
