Zinc in PDB 8gwi: A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
Enzymatic activity of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
All present enzymatic activity of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors:
2.7.7.48;
Zinc Binding Sites:
The binding sites of Zinc atom in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
(pdb code 8gwi). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors, PDB code: 8gwi:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 8gwi
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Zinc Binding Sites List in 8gwi
Zinc binding site 1 out
of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1001
b:128.0
occ:1.00
|
ND1
|
A:HIS295
|
2.1
|
84.1
|
1.0
|
SG
|
A:CYS301
|
2.3
|
87.0
|
1.0
|
SG
|
A:CYS310
|
2.3
|
84.8
|
1.0
|
SG
|
A:CYS306
|
2.3
|
84.9
|
1.0
|
CE1
|
A:HIS295
|
2.9
|
71.8
|
1.0
|
CG
|
A:HIS295
|
3.2
|
70.8
|
1.0
|
O
|
A:CYS306
|
3.3
|
88.6
|
1.0
|
CB
|
A:CYS301
|
3.4
|
87.7
|
1.0
|
CB
|
A:CYS306
|
3.6
|
72.0
|
1.0
|
CB
|
A:HIS295
|
3.6
|
58.8
|
1.0
|
CB
|
A:CYS310
|
3.7
|
71.2
|
1.0
|
C
|
A:CYS306
|
3.8
|
74.6
|
1.0
|
CA
|
A:CYS301
|
3.8
|
81.2
|
1.0
|
NE2
|
A:HIS295
|
4.1
|
58.4
|
1.0
|
CA
|
A:CYS306
|
4.2
|
71.9
|
1.0
|
CD2
|
A:HIS295
|
4.3
|
66.6
|
1.0
|
N
|
A:HIS295
|
4.3
|
63.5
|
1.0
|
N
|
A:ILE307
|
4.6
|
70.0
|
1.0
|
N
|
A:CYS301
|
4.6
|
81.3
|
1.0
|
CA
|
A:HIS295
|
4.6
|
52.9
|
1.0
|
O
|
A:THR293
|
4.9
|
77.3
|
1.0
|
N
|
A:CYS310
|
4.9
|
69.1
|
1.0
|
CA
|
A:CYS310
|
4.9
|
55.8
|
1.0
|
N
|
A:LEU302
|
5.0
|
93.1
|
1.0
|
CA
|
A:ILE307
|
5.0
|
73.3
|
1.0
|
C
|
A:CYS301
|
5.0
|
88.8
|
1.0
|
|
Zinc binding site 2 out
of 8 in 8gwi
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Zinc Binding Sites List in 8gwi
Zinc binding site 2 out
of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1002
b:141.5
occ:1.00
|
ND1
|
A:HIS642
|
2.1
|
91.1
|
1.0
|
SG
|
A:CYS487
|
2.3
|
95.9
|
1.0
|
SG
|
A:CYS646
|
2.3
|
89.0
|
1.0
|
SG
|
A:CYS645
|
2.3
|
97.8
|
1.0
|
CE1
|
A:HIS642
|
3.0
|
87.8
|
1.0
|
CG
|
A:HIS642
|
3.1
|
77.6
|
1.0
|
CB
|
A:HIS642
|
3.4
|
76.6
|
1.0
|
CB
|
A:CYS645
|
3.5
|
92.4
|
1.0
|
CB
|
A:CYS487
|
3.7
|
94.1
|
1.0
|
CB
|
A:CYS646
|
3.7
|
84.0
|
1.0
|
C
|
A:CYS645
|
4.1
|
98.8
|
1.0
|
N
|
A:CYS487
|
4.1
|
88.2
|
1.0
|
NE2
|
A:HIS642
|
4.1
|
81.8
|
1.0
|
N
|
A:CYS646
|
4.1
|
93.5
|
1.0
|
CD2
|
A:HIS642
|
4.2
|
77.7
|
1.0
|
CE1
|
A:PHE571
|
4.2
|
71.7
|
1.0
|
CA
|
A:HIS642
|
4.3
|
74.9
|
1.0
|
O
|
A:CYS645
|
4.3
|
101.0
|
1.0
|
CA
|
A:CYS645
|
4.4
|
89.7
|
1.0
|
CA
|
A:CYS487
|
4.4
|
90.7
|
1.0
|
CA
|
A:CYS646
|
4.4
|
86.6
|
1.0
|
C
|
A:GLY486
|
4.7
|
84.6
|
1.0
|
CD1
|
A:PHE571
|
4.7
|
83.5
|
1.0
|
O
|
A:HIS642
|
4.8
|
97.3
|
1.0
|
CA
|
A:GLY486
|
4.9
|
82.0
|
1.0
|
NZ
|
A:LYS532
|
4.9
|
74.1
|
1.0
|
CZ
|
A:PHE571
|
4.9
|
68.8
|
1.0
|
N
|
A:CYS645
|
5.0
|
93.9
|
1.0
|
|
Zinc binding site 3 out
of 8 in 8gwi
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Zinc Binding Sites List in 8gwi
Zinc binding site 3 out
of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn701
b:254.8
occ:1.00
|
CE1
|
F:HIS33
|
2.1
|
185.9
|
1.0
|
ND1
|
F:HIS39
|
2.1
|
181.9
|
1.0
|
NE2
|
F:HIS33
|
2.1
|
188.1
|
1.0
|
SG
|
F:CYS19
|
2.3
|
198.1
|
1.0
|
SG
|
F:CYS16
|
2.3
|
183.4
|
1.0
|
CE1
|
F:HIS39
|
2.4
|
182.1
|
1.0
|
CB
|
F:CYS19
|
3.1
|
193.2
|
1.0
|
CG
|
F:HIS39
|
3.2
|
180.3
|
1.0
|
CB
|
F:CYS16
|
3.2
|
178.1
|
1.0
|
ND1
|
F:HIS33
|
3.4
|
183.8
|
1.0
|
CD2
|
F:HIS33
|
3.5
|
186.4
|
1.0
|
NE2
|
F:HIS39
|
3.5
|
182.8
|
1.0
|
O
|
F:ALA18
|
3.7
|
181.8
|
1.0
|
CD2
|
F:HIS39
|
3.9
|
182.4
|
1.0
|
CB
|
F:HIS39
|
4.0
|
180.1
|
1.0
|
CG
|
F:HIS33
|
4.0
|
186.3
|
1.0
|
CA
|
F:CYS19
|
4.1
|
193.4
|
1.0
|
C
|
F:ALA18
|
4.4
|
182.1
|
1.0
|
CG
|
F:PRO23
|
4.6
|
165.5
|
1.0
|
N
|
F:CYS19
|
4.6
|
193.9
|
1.0
|
CA
|
F:CYS16
|
4.7
|
175.7
|
1.0
|
|
Zinc binding site 4 out
of 8 in 8gwi
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Zinc Binding Sites List in 8gwi
Zinc binding site 4 out
of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn702
b:239.8
occ:1.00
|
CB
|
F:CYS29
|
2.2
|
167.7
|
1.0
|
SG
|
F:CYS8
|
2.3
|
185.1
|
1.0
|
SG
|
F:CYS26
|
2.3
|
172.3
|
1.0
|
SG
|
F:CYS5
|
2.3
|
183.0
|
1.0
|
SG
|
F:CYS29
|
2.3
|
175.2
|
1.0
|
CB
|
F:CYS8
|
3.3
|
187.9
|
1.0
|
N
|
F:CYS26
|
3.5
|
162.7
|
1.0
|
CB
|
F:CYS26
|
3.7
|
165.0
|
1.0
|
CA
|
F:CYS29
|
3.8
|
165.3
|
1.0
|
CB
|
F:CYS5
|
3.8
|
182.1
|
1.0
|
CA
|
F:CYS26
|
4.2
|
164.1
|
1.0
|
N
|
F:CYS8
|
4.3
|
188.2
|
1.0
|
CA
|
F:CYS8
|
4.4
|
188.8
|
1.0
|
N
|
F:CYS29
|
4.4
|
166.2
|
1.0
|
C
|
F:LEU25
|
4.5
|
157.2
|
1.0
|
CA
|
F:LEU25
|
4.5
|
158.7
|
1.0
|
CD1
|
F:LEU7
|
4.6
|
187.5
|
1.0
|
C
|
F:CYS29
|
4.7
|
165.1
|
1.0
|
CG
|
F:LEU7
|
4.7
|
188.1
|
1.0
|
C
|
F:CYS26
|
4.9
|
164.9
|
1.0
|
O
|
F:CYS26
|
4.9
|
166.6
|
1.0
|
|
Zinc binding site 5 out
of 8 in 8gwi
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Zinc Binding Sites List in 8gwi
Zinc binding site 5 out
of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_05.jpg) Mono view
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn703
b:243.0
occ:1.00
|
ND1
|
F:HIS75
|
2.1
|
179.1
|
1.0
|
SG
|
F:CYS72
|
2.3
|
168.2
|
1.0
|
SG
|
F:CYS55
|
2.3
|
165.0
|
1.0
|
SG
|
F:CYS50
|
2.3
|
158.7
|
1.0
|
CG
|
F:HIS75
|
2.7
|
177.0
|
1.0
|
CB
|
F:HIS75
|
2.8
|
177.8
|
1.0
|
O
|
F:HIS75
|
3.1
|
179.3
|
1.0
|
CB
|
F:CYS50
|
3.2
|
152.4
|
1.0
|
CE1
|
F:HIS75
|
3.2
|
177.2
|
1.0
|
CB
|
F:CYS55
|
3.5
|
160.6
|
1.0
|
CB
|
F:CYS72
|
3.6
|
164.6
|
1.0
|
CA
|
F:HIS75
|
3.7
|
179.3
|
1.0
|
C
|
F:HIS75
|
3.8
|
179.0
|
1.0
|
CD2
|
F:HIS75
|
3.9
|
174.9
|
1.0
|
N
|
F:HIS75
|
4.1
|
178.8
|
1.0
|
NE2
|
F:HIS75
|
4.1
|
175.3
|
1.0
|
N
|
F:CYS72
|
4.1
|
157.3
|
1.0
|
CA
|
F:CYS72
|
4.4
|
162.6
|
1.0
|
CA
|
F:CYS50
|
4.6
|
152.8
|
1.0
|
C
|
F:CYS72
|
4.8
|
161.5
|
1.0
|
CA
|
F:CYS55
|
4.9
|
159.5
|
1.0
|
|
Zinc binding site 6 out
of 8 in 8gwi
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Zinc Binding Sites List in 8gwi
Zinc binding site 6 out
of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_06.jpg) Mono view
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn701
b:211.9
occ:1.00
|
NE2
|
E:HIS33
|
2.0
|
180.6
|
1.0
|
ND1
|
E:HIS39
|
2.0
|
185.1
|
1.0
|
SG
|
E:CYS19
|
2.3
|
179.2
|
1.0
|
SG
|
E:CYS16
|
2.3
|
165.6
|
1.0
|
CE1
|
E:HIS33
|
2.9
|
179.2
|
1.0
|
CG
|
E:HIS39
|
3.0
|
185.0
|
1.0
|
CE1
|
E:HIS39
|
3.0
|
184.1
|
1.0
|
CD2
|
E:HIS33
|
3.1
|
180.7
|
1.0
|
CB
|
E:HIS39
|
3.3
|
184.3
|
1.0
|
N
|
E:CYS19
|
3.7
|
176.5
|
1.0
|
CB
|
E:CYS16
|
3.7
|
158.2
|
1.0
|
CB
|
E:CYS19
|
3.7
|
174.0
|
1.0
|
C
|
E:ALA18
|
4.0
|
165.3
|
1.0
|
ND1
|
E:HIS33
|
4.1
|
179.2
|
1.0
|
NE2
|
E:HIS39
|
4.1
|
183.1
|
1.0
|
CB
|
E:ALA18
|
4.1
|
163.2
|
1.0
|
CD2
|
E:HIS39
|
4.2
|
183.9
|
1.0
|
CA
|
E:CYS19
|
4.2
|
175.9
|
1.0
|
CG
|
E:HIS33
|
4.2
|
179.8
|
1.0
|
CA
|
E:ALA18
|
4.4
|
164.4
|
1.0
|
N
|
E:ALA18
|
4.4
|
163.0
|
1.0
|
O
|
E:ALA18
|
4.6
|
163.9
|
1.0
|
CA
|
E:HIS39
|
4.7
|
184.6
|
1.0
|
CA
|
E:CYS16
|
4.9
|
158.5
|
1.0
|
|
Zinc binding site 7 out
of 8 in 8gwi
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Zinc Binding Sites List in 8gwi
Zinc binding site 7 out
of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_07.jpg) Mono view
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn702
b:250.9
occ:1.00
|
CB
|
E:CYS26
|
1.8
|
186.5
|
1.0
|
SG
|
E:CYS8
|
2.3
|
197.1
|
1.0
|
SG
|
E:CYS29
|
2.3
|
167.6
|
1.0
|
SG
|
E:CYS5
|
2.3
|
188.7
|
1.0
|
SG
|
E:CYS26
|
2.3
|
186.4
|
1.0
|
CB
|
E:CYS8
|
3.2
|
192.3
|
1.0
|
CA
|
E:CYS26
|
3.3
|
184.4
|
1.0
|
CB
|
E:CYS5
|
3.7
|
185.1
|
1.0
|
N
|
E:CYS26
|
3.8
|
184.1
|
1.0
|
N
|
E:CYS8
|
3.8
|
192.5
|
1.0
|
CB
|
E:CYS29
|
3.9
|
167.8
|
1.0
|
CA
|
E:CYS8
|
4.1
|
192.2
|
1.0
|
C
|
E:CYS26
|
4.2
|
185.1
|
1.0
|
N
|
E:CYS29
|
4.7
|
168.8
|
1.0
|
O
|
E:CYS26
|
4.8
|
185.3
|
1.0
|
CB
|
E:LEU7
|
4.9
|
181.8
|
1.0
|
N
|
E:CYS27
|
4.9
|
178.2
|
1.0
|
C
|
E:LEU7
|
4.9
|
183.4
|
1.0
|
CA
|
E:GLY99
|
4.9
|
182.4
|
1.0
|
C
|
E:CYS8
|
5.0
|
192.2
|
1.0
|
N
|
E:GLY99
|
5.0
|
183.3
|
1.0
|
CA
|
E:CYS29
|
5.0
|
167.9
|
1.0
|
|
Zinc binding site 8 out
of 8 in 8gwi
Go back to
Zinc Binding Sites List in 8gwi
Zinc binding site 8 out
of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_08.jpg) Mono view
![](/pictures/ZN/pdb/gw/8gwi-ZN-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn703
b:238.1
occ:1.00
|
ND1
|
E:HIS75
|
2.1
|
182.7
|
1.0
|
CE1
|
E:HIS75
|
2.2
|
182.8
|
1.0
|
SG
|
E:CYS50
|
2.3
|
176.1
|
1.0
|
SG
|
E:CYS72
|
2.3
|
187.7
|
1.0
|
SG
|
E:CYS55
|
2.3
|
192.5
|
1.0
|
CB
|
E:CYS55
|
3.1
|
188.9
|
1.0
|
CG
|
E:HIS75
|
3.3
|
180.3
|
1.0
|
NE2
|
E:HIS75
|
3.4
|
180.7
|
1.0
|
CB
|
E:CYS72
|
3.4
|
183.8
|
1.0
|
CB
|
E:ALA52
|
3.6
|
187.3
|
1.0
|
CB
|
E:CYS50
|
3.7
|
172.6
|
1.0
|
CD2
|
E:HIS75
|
3.9
|
180.1
|
1.0
|
N
|
E:CYS72
|
4.1
|
183.4
|
1.0
|
OG
|
E:SER74
|
4.1
|
179.7
|
1.0
|
CB
|
E:HIS75
|
4.2
|
178.6
|
1.0
|
CA
|
E:CYS72
|
4.3
|
183.5
|
1.0
|
CG2
|
E:VAL57
|
4.5
|
174.6
|
1.0
|
CA
|
E:CYS55
|
4.6
|
189.3
|
1.0
|
CA
|
E:ALA52
|
4.8
|
189.4
|
1.0
|
N
|
E:HIS75
|
4.8
|
178.9
|
1.0
|
N
|
E:ALA52
|
4.8
|
188.7
|
1.0
|
|
Reference:
L.Yan,
Y.Huang,
J.Ge,
Z.Liu,
P.Lu,
B.Huang,
S.Gao,
J.Wang,
L.Tan,
S.Ye,
F.Yu,
W.Lan,
S.Xu,
F.Zhou,
L.Shi,
L.W.Guddat,
Y.Gao,
Z.Rao,
Z.Lou.
A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analog Inhibitors. Cell V. 185 4347 2022.
ISSN: ISSN 1097-4172
PubMed: 36335936
DOI: 10.1016/J.CELL.2022.09.037
Page generated: Sat Apr 8 09:08:21 2023
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