Zinc in PDB 6rwn: Sivrcm Intasome in Complex with Dolutegravir
Other elements in 6rwn:
The structure of Sivrcm Intasome in Complex with Dolutegravir also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Sivrcm Intasome in Complex with Dolutegravir
(pdb code 6rwn). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Sivrcm Intasome in Complex with Dolutegravir, PDB code: 6rwn:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 6rwn
Go back to
Zinc Binding Sites List in 6rwn
Zinc binding site 1 out
of 8 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:43.0
occ:1.00
|
NE2
|
A:HIS12
|
2.0
|
7.8
|
1.0
|
ND1
|
A:HIS16
|
2.2
|
7.3
|
1.0
|
SG
|
A:CYS40
|
2.4
|
9.4
|
1.0
|
SG
|
A:CYS43
|
2.4
|
10.1
|
1.0
|
CE1
|
A:HIS16
|
2.8
|
7.3
|
1.0
|
CE1
|
A:HIS12
|
2.9
|
7.8
|
1.0
|
CD2
|
A:HIS12
|
3.1
|
7.8
|
1.0
|
CB
|
A:CYS40
|
3.2
|
9.4
|
1.0
|
CG
|
A:HIS16
|
3.5
|
7.3
|
1.0
|
CB
|
A:CYS43
|
3.8
|
10.1
|
1.0
|
ND1
|
A:HIS12
|
4.0
|
7.8
|
1.0
|
NE2
|
A:HIS16
|
4.0
|
7.3
|
1.0
|
CG
|
A:HIS12
|
4.1
|
7.8
|
1.0
|
CB
|
A:HIS16
|
4.1
|
7.3
|
1.0
|
N
|
A:CYS43
|
4.2
|
10.1
|
1.0
|
CD2
|
A:HIS16
|
4.4
|
7.3
|
1.0
|
CA
|
A:HIS16
|
4.4
|
7.3
|
1.0
|
CA
|
A:CYS43
|
4.6
|
10.1
|
1.0
|
CA
|
A:CYS40
|
4.7
|
9.4
|
1.0
|
O
|
A:HIS12
|
4.7
|
7.8
|
1.0
|
CB
|
A:LYS42
|
4.9
|
8.5
|
1.0
|
C
|
A:LYS42
|
5.0
|
8.5
|
1.0
|
|
Zinc binding site 2 out
of 8 in 6rwn
Go back to
Zinc Binding Sites List in 6rwn
Zinc binding site 2 out
of 8 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn500
b:45.4
occ:1.00
|
ND1
|
E:HIS16
|
2.2
|
22.9
|
1.0
|
NE2
|
E:HIS12
|
2.2
|
22.1
|
1.0
|
SG
|
E:CYS43
|
2.4
|
33.3
|
1.0
|
SG
|
E:CYS40
|
2.4
|
26.9
|
1.0
|
CE1
|
E:HIS16
|
2.9
|
22.9
|
1.0
|
CD2
|
E:HIS12
|
3.0
|
22.1
|
1.0
|
CE1
|
E:HIS12
|
3.1
|
22.1
|
1.0
|
CB
|
E:CYS40
|
3.3
|
26.9
|
1.0
|
CG
|
E:HIS16
|
3.3
|
22.9
|
1.0
|
CB
|
E:CYS43
|
3.5
|
33.3
|
1.0
|
CB
|
E:HIS16
|
3.8
|
22.9
|
1.0
|
CG
|
E:HIS12
|
4.1
|
22.1
|
1.0
|
ND1
|
E:HIS12
|
4.1
|
22.1
|
1.0
|
NE2
|
E:HIS16
|
4.1
|
22.9
|
1.0
|
CA
|
E:HIS16
|
4.3
|
22.9
|
1.0
|
CD2
|
E:HIS16
|
4.3
|
22.9
|
1.0
|
N
|
E:CYS43
|
4.3
|
33.3
|
1.0
|
O
|
E:HIS12
|
4.3
|
22.1
|
1.0
|
CA
|
E:CYS43
|
4.5
|
33.3
|
1.0
|
CA
|
E:CYS40
|
4.7
|
26.9
|
1.0
|
|
Zinc binding site 3 out
of 8 in 6rwn
Go back to
Zinc Binding Sites List in 6rwn
Zinc binding site 3 out
of 8 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Zn500
b:63.8
occ:1.00
|
NE2
|
K:HIS12
|
2.2
|
36.3
|
1.0
|
ND1
|
K:HIS16
|
2.2
|
29.9
|
1.0
|
SG
|
K:CYS40
|
2.4
|
46.0
|
1.0
|
SG
|
K:CYS43
|
2.4
|
40.4
|
1.0
|
CE1
|
K:HIS16
|
2.8
|
29.9
|
1.0
|
CE1
|
K:HIS12
|
2.9
|
36.3
|
1.0
|
CB
|
K:CYS40
|
3.0
|
46.0
|
1.0
|
CD2
|
K:HIS12
|
3.1
|
36.3
|
1.0
|
CG
|
K:HIS16
|
3.4
|
29.9
|
1.0
|
CB
|
K:CYS43
|
3.8
|
40.4
|
1.0
|
ND1
|
K:HIS12
|
4.0
|
36.3
|
1.0
|
CB
|
K:HIS16
|
4.0
|
29.9
|
1.0
|
NE2
|
K:HIS16
|
4.0
|
29.9
|
1.0
|
CG
|
K:HIS12
|
4.1
|
36.3
|
1.0
|
CD2
|
K:HIS16
|
4.3
|
29.9
|
1.0
|
N
|
K:CYS43
|
4.4
|
40.4
|
1.0
|
CA
|
K:HIS16
|
4.4
|
29.9
|
1.0
|
O
|
K:HIS12
|
4.5
|
36.3
|
1.0
|
CA
|
K:CYS40
|
4.5
|
46.0
|
1.0
|
CB
|
K:LYS42
|
4.7
|
36.7
|
1.0
|
CA
|
K:CYS43
|
4.7
|
40.4
|
1.0
|
C
|
K:LYS42
|
4.8
|
36.7
|
1.0
|
C
|
K:CYS40
|
5.0
|
46.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 6rwn
Go back to
Zinc Binding Sites List in 6rwn
Zinc binding site 4 out
of 8 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn500
b:55.1
occ:1.00
|
NE2
|
J:HIS12
|
2.2
|
25.1
|
1.0
|
ND1
|
J:HIS16
|
2.2
|
25.8
|
1.0
|
SG
|
J:CYS43
|
2.4
|
40.8
|
1.0
|
SG
|
J:CYS40
|
2.4
|
35.3
|
1.0
|
CE1
|
J:HIS16
|
2.9
|
25.8
|
1.0
|
CE1
|
J:HIS12
|
3.0
|
25.1
|
1.0
|
CB
|
J:CYS40
|
3.0
|
35.3
|
1.0
|
CD2
|
J:HIS12
|
3.2
|
25.1
|
1.0
|
CG
|
J:HIS16
|
3.4
|
25.8
|
1.0
|
CB
|
J:CYS43
|
3.7
|
40.8
|
1.0
|
CB
|
J:HIS16
|
4.0
|
25.8
|
1.0
|
NE2
|
J:HIS16
|
4.1
|
25.8
|
1.0
|
ND1
|
J:HIS12
|
4.1
|
25.1
|
1.0
|
CG
|
J:HIS12
|
4.2
|
25.1
|
1.0
|
N
|
J:CYS43
|
4.4
|
40.8
|
1.0
|
CD2
|
J:HIS16
|
4.4
|
25.8
|
1.0
|
CA
|
J:HIS16
|
4.4
|
25.8
|
1.0
|
CA
|
J:CYS40
|
4.5
|
35.3
|
1.0
|
CA
|
J:CYS43
|
4.6
|
40.8
|
1.0
|
O
|
J:HIS12
|
4.8
|
25.1
|
1.0
|
C
|
J:LYS42
|
4.8
|
37.7
|
1.0
|
|
Zinc binding site 5 out
of 8 in 6rwn
Go back to
Zinc Binding Sites List in 6rwn
Zinc binding site 5 out
of 8 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn301
b:44.4
occ:1.00
|
NE2
|
I:HIS12
|
2.0
|
8.0
|
1.0
|
ND1
|
I:HIS16
|
2.2
|
7.3
|
1.0
|
SG
|
I:CYS40
|
2.4
|
9.2
|
1.0
|
SG
|
I:CYS43
|
2.4
|
10.8
|
1.0
|
CE1
|
I:HIS16
|
2.8
|
7.3
|
1.0
|
CE1
|
I:HIS12
|
2.9
|
8.0
|
1.0
|
CD2
|
I:HIS12
|
3.1
|
8.0
|
1.0
|
CB
|
I:CYS40
|
3.2
|
9.2
|
1.0
|
CG
|
I:HIS16
|
3.5
|
7.3
|
1.0
|
CB
|
I:CYS43
|
3.9
|
10.8
|
1.0
|
ND1
|
I:HIS12
|
4.0
|
8.0
|
1.0
|
NE2
|
I:HIS16
|
4.0
|
7.3
|
1.0
|
CG
|
I:HIS12
|
4.1
|
8.0
|
1.0
|
CB
|
I:HIS16
|
4.1
|
7.3
|
1.0
|
N
|
I:CYS43
|
4.2
|
10.8
|
1.0
|
CD2
|
I:HIS16
|
4.4
|
7.3
|
1.0
|
CA
|
I:HIS16
|
4.4
|
7.3
|
1.0
|
CA
|
I:CYS43
|
4.6
|
10.8
|
1.0
|
CA
|
I:CYS40
|
4.7
|
9.2
|
1.0
|
O
|
I:HIS12
|
4.7
|
8.0
|
1.0
|
CB
|
I:LYS42
|
4.9
|
8.6
|
1.0
|
C
|
I:LYS42
|
5.0
|
8.6
|
1.0
|
|
Zinc binding site 6 out
of 8 in 6rwn
Go back to
Zinc Binding Sites List in 6rwn
Zinc binding site 6 out
of 8 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Zn500
b:46.9
occ:1.00
|
ND1
|
M:HIS16
|
2.2
|
22.8
|
1.0
|
NE2
|
M:HIS12
|
2.2
|
22.2
|
1.0
|
SG
|
M:CYS43
|
2.4
|
33.7
|
1.0
|
SG
|
M:CYS40
|
2.4
|
27.1
|
1.0
|
CE1
|
M:HIS16
|
2.9
|
22.8
|
1.0
|
CD2
|
M:HIS12
|
3.0
|
22.2
|
1.0
|
CE1
|
M:HIS12
|
3.1
|
22.2
|
1.0
|
CB
|
M:CYS40
|
3.3
|
27.1
|
1.0
|
CG
|
M:HIS16
|
3.3
|
22.8
|
1.0
|
CB
|
M:CYS43
|
3.5
|
33.7
|
1.0
|
CB
|
M:HIS16
|
3.8
|
22.8
|
1.0
|
CG
|
M:HIS12
|
4.1
|
22.2
|
1.0
|
ND1
|
M:HIS12
|
4.1
|
22.2
|
1.0
|
NE2
|
M:HIS16
|
4.1
|
22.8
|
1.0
|
CA
|
M:HIS16
|
4.3
|
22.8
|
1.0
|
CD2
|
M:HIS16
|
4.3
|
22.8
|
1.0
|
N
|
M:CYS43
|
4.3
|
33.7
|
1.0
|
O
|
M:HIS12
|
4.3
|
22.2
|
1.0
|
CA
|
M:CYS43
|
4.5
|
33.7
|
1.0
|
CA
|
M:CYS40
|
4.7
|
27.1
|
1.0
|
|
Zinc binding site 7 out
of 8 in 6rwn
Go back to
Zinc Binding Sites List in 6rwn
Zinc binding site 7 out
of 8 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn500
b:61.0
occ:1.00
|
NE2
|
C:HIS12
|
2.2
|
36.1
|
1.0
|
ND1
|
C:HIS16
|
2.2
|
29.7
|
1.0
|
SG
|
C:CYS40
|
2.4
|
45.6
|
1.0
|
SG
|
C:CYS43
|
2.4
|
40.2
|
1.0
|
CE1
|
C:HIS16
|
2.8
|
29.7
|
1.0
|
CE1
|
C:HIS12
|
2.9
|
36.1
|
1.0
|
CB
|
C:CYS40
|
3.0
|
45.6
|
1.0
|
CD2
|
C:HIS12
|
3.1
|
36.1
|
1.0
|
CG
|
C:HIS16
|
3.4
|
29.7
|
1.0
|
CB
|
C:CYS43
|
3.8
|
40.2
|
1.0
|
ND1
|
C:HIS12
|
4.0
|
36.1
|
1.0
|
CB
|
C:HIS16
|
4.0
|
29.7
|
1.0
|
NE2
|
C:HIS16
|
4.0
|
29.7
|
1.0
|
CG
|
C:HIS12
|
4.1
|
36.1
|
1.0
|
CD2
|
C:HIS16
|
4.3
|
29.7
|
1.0
|
N
|
C:CYS43
|
4.4
|
40.2
|
1.0
|
CA
|
C:HIS16
|
4.4
|
29.7
|
1.0
|
O
|
C:HIS12
|
4.5
|
36.1
|
1.0
|
CA
|
C:CYS40
|
4.5
|
45.6
|
1.0
|
CB
|
C:LYS42
|
4.7
|
36.7
|
1.0
|
CA
|
C:CYS43
|
4.7
|
40.2
|
1.0
|
C
|
C:LYS42
|
4.8
|
36.7
|
1.0
|
C
|
C:CYS40
|
5.0
|
45.6
|
1.0
|
|
Zinc binding site 8 out
of 8 in 6rwn
Go back to
Zinc Binding Sites List in 6rwn
Zinc binding site 8 out
of 8 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn500
b:56.6
occ:1.00
|
NE2
|
B:HIS12
|
2.2
|
25.1
|
1.0
|
ND1
|
B:HIS16
|
2.2
|
25.6
|
1.0
|
SG
|
B:CYS43
|
2.4
|
41.4
|
1.0
|
SG
|
B:CYS40
|
2.4
|
35.0
|
1.0
|
CE1
|
B:HIS16
|
2.9
|
25.6
|
1.0
|
CE1
|
B:HIS12
|
3.0
|
25.1
|
1.0
|
CB
|
B:CYS40
|
3.0
|
35.0
|
1.0
|
CD2
|
B:HIS12
|
3.2
|
25.1
|
1.0
|
CG
|
B:HIS16
|
3.4
|
25.6
|
1.0
|
CB
|
B:CYS43
|
3.7
|
41.4
|
1.0
|
CB
|
B:HIS16
|
4.0
|
25.6
|
1.0
|
NE2
|
B:HIS16
|
4.1
|
25.6
|
1.0
|
ND1
|
B:HIS12
|
4.1
|
25.1
|
1.0
|
CG
|
B:HIS12
|
4.2
|
25.1
|
1.0
|
N
|
B:CYS43
|
4.4
|
41.4
|
1.0
|
CD2
|
B:HIS16
|
4.4
|
25.6
|
1.0
|
CA
|
B:HIS16
|
4.4
|
25.6
|
1.0
|
CA
|
B:CYS40
|
4.5
|
35.0
|
1.0
|
CA
|
B:CYS43
|
4.6
|
41.4
|
1.0
|
O
|
B:HIS12
|
4.8
|
25.1
|
1.0
|
C
|
B:LYS42
|
4.8
|
38.1
|
1.0
|
|
Reference:
P.Cherepanov,
N.Nans,
N.J.Cook.
Structural Basis of Second-Generation Hiv Integrase Inhibitor Action and Viral Resistance Science 2020.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.AAY4919
Page generated: Tue Oct 29 06:49:54 2024
|