Zinc in PDB 6rwm: Sivrcm Intasome in Complex with Bictegravir
Other elements in 6rwm:
The structure of Sivrcm Intasome in Complex with Bictegravir also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Sivrcm Intasome in Complex with Bictegravir
(pdb code 6rwm). 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 Bictegravir, PDB code: 6rwm:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 6rwm
Go back to
Zinc Binding Sites List in 6rwm
Zinc binding site 1 out
of 8 in the Sivrcm Intasome in Complex with Bictegravir
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 Bictegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:52.4
occ:1.00
|
NE2
|
A:HIS12
|
2.1
|
17.8
|
1.0
|
ND1
|
A:HIS16
|
2.2
|
16.8
|
1.0
|
SG
|
A:CYS40
|
2.4
|
17.4
|
1.0
|
SG
|
A:CYS43
|
2.4
|
17.3
|
1.0
|
CE1
|
A:HIS12
|
2.9
|
17.8
|
1.0
|
CE1
|
A:HIS16
|
2.9
|
16.8
|
1.0
|
CD2
|
A:HIS12
|
3.1
|
17.8
|
1.0
|
CB
|
A:CYS40
|
3.2
|
17.4
|
1.0
|
CG
|
A:HIS16
|
3.4
|
16.8
|
1.0
|
CB
|
A:CYS43
|
3.9
|
17.3
|
1.0
|
ND1
|
A:HIS12
|
4.0
|
17.8
|
1.0
|
CB
|
A:HIS16
|
4.0
|
16.8
|
1.0
|
NE2
|
A:HIS16
|
4.1
|
16.8
|
1.0
|
CG
|
A:HIS12
|
4.1
|
17.8
|
1.0
|
N
|
A:CYS43
|
4.2
|
17.3
|
1.0
|
CD2
|
A:HIS16
|
4.4
|
16.8
|
1.0
|
CA
|
A:HIS16
|
4.4
|
16.8
|
1.0
|
CA
|
A:CYS43
|
4.7
|
17.3
|
1.0
|
CA
|
A:CYS40
|
4.7
|
17.4
|
1.0
|
CB
|
A:LYS42
|
4.8
|
17.6
|
1.0
|
O
|
A:HIS12
|
4.8
|
17.8
|
1.0
|
C
|
A:LYS42
|
4.9
|
17.6
|
1.0
|
|
Zinc binding site 2 out
of 8 in 6rwm
Go back to
Zinc Binding Sites List in 6rwm
Zinc binding site 2 out
of 8 in the Sivrcm Intasome in Complex with Bictegravir
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 Bictegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn500
b:66.5
occ:1.00
|
NE2
|
B:HIS12
|
2.2
|
38.6
|
1.0
|
ND1
|
B:HIS16
|
2.2
|
37.6
|
1.0
|
SG
|
B:CYS43
|
2.4
|
50.0
|
1.0
|
SG
|
B:CYS40
|
2.4
|
47.6
|
1.0
|
CE1
|
B:HIS16
|
3.0
|
37.6
|
1.0
|
CE1
|
B:HIS12
|
3.0
|
38.6
|
1.0
|
CB
|
B:CYS40
|
3.1
|
47.6
|
1.0
|
CD2
|
B:HIS12
|
3.1
|
38.6
|
1.0
|
CG
|
B:HIS16
|
3.3
|
37.6
|
1.0
|
CB
|
B:CYS43
|
3.7
|
50.0
|
1.0
|
CB
|
B:HIS16
|
3.8
|
37.6
|
1.0
|
ND1
|
B:HIS12
|
4.1
|
38.6
|
1.0
|
NE2
|
B:HIS16
|
4.2
|
37.6
|
1.0
|
CG
|
B:HIS12
|
4.2
|
38.6
|
1.0
|
CA
|
B:HIS16
|
4.3
|
37.6
|
1.0
|
N
|
B:CYS43
|
4.3
|
50.0
|
1.0
|
CD2
|
B:HIS16
|
4.4
|
37.6
|
1.0
|
CA
|
B:CYS43
|
4.6
|
50.0
|
1.0
|
CA
|
B:CYS40
|
4.6
|
47.6
|
1.0
|
O
|
B:HIS12
|
4.7
|
38.6
|
1.0
|
C
|
B:LYS42
|
4.8
|
48.6
|
1.0
|
|
Zinc binding site 3 out
of 8 in 6rwm
Go back to
Zinc Binding Sites List in 6rwm
Zinc binding site 3 out
of 8 in the Sivrcm Intasome in Complex with Bictegravir
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 Bictegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn500
b:80.5
occ:1.00
|
NE2
|
C:HIS12
|
2.2
|
43.4
|
1.0
|
ND1
|
C:HIS16
|
2.2
|
38.8
|
1.0
|
SG
|
C:CYS43
|
2.4
|
53.3
|
1.0
|
SG
|
C:CYS40
|
2.4
|
59.3
|
1.0
|
CE1
|
C:HIS16
|
3.0
|
38.8
|
1.0
|
CE1
|
C:HIS12
|
3.0
|
43.4
|
1.0
|
CD2
|
C:HIS12
|
3.1
|
43.4
|
1.0
|
CB
|
C:CYS40
|
3.2
|
59.3
|
1.0
|
CG
|
C:HIS16
|
3.3
|
38.8
|
1.0
|
CB
|
C:CYS43
|
3.7
|
53.3
|
1.0
|
CB
|
C:HIS16
|
3.8
|
38.8
|
1.0
|
ND1
|
C:HIS12
|
4.0
|
43.4
|
1.0
|
CG
|
C:HIS12
|
4.1
|
43.4
|
1.0
|
NE2
|
C:HIS16
|
4.2
|
38.8
|
1.0
|
CA
|
C:HIS16
|
4.3
|
38.8
|
1.0
|
N
|
C:CYS43
|
4.3
|
53.3
|
1.0
|
CD2
|
C:HIS16
|
4.4
|
38.8
|
1.0
|
O
|
C:HIS12
|
4.5
|
43.4
|
1.0
|
CA
|
C:CYS43
|
4.6
|
53.3
|
1.0
|
CA
|
C:CYS40
|
4.7
|
59.3
|
1.0
|
CB
|
C:LYS42
|
4.8
|
50.9
|
1.0
|
C
|
C:LYS42
|
4.8
|
50.9
|
1.0
|
NE2
|
B:GLN164
|
4.9
|
34.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 6rwm
Go back to
Zinc Binding Sites List in 6rwm
Zinc binding site 4 out
of 8 in the Sivrcm Intasome in Complex with Bictegravir
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 Bictegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Zn500
b:86.0
occ:1.00
|
ND1
|
M:HIS16
|
2.2
|
40.5
|
1.0
|
NE2
|
M:HIS12
|
2.2
|
39.3
|
1.0
|
SG
|
M:CYS43
|
2.4
|
44.5
|
1.0
|
SG
|
M:CYS40
|
2.4
|
39.1
|
1.0
|
CE1
|
M:HIS16
|
2.9
|
40.5
|
1.0
|
CD2
|
M:HIS12
|
3.0
|
39.3
|
1.0
|
CE1
|
M:HIS12
|
3.2
|
39.3
|
1.0
|
CG
|
M:HIS16
|
3.3
|
40.5
|
1.0
|
CB
|
M:CYS40
|
3.3
|
39.1
|
1.0
|
CB
|
M:CYS43
|
3.4
|
44.5
|
1.0
|
CB
|
M:HIS16
|
3.8
|
40.5
|
1.0
|
CG
|
M:HIS12
|
4.1
|
39.3
|
1.0
|
NE2
|
M:HIS16
|
4.1
|
40.5
|
1.0
|
ND1
|
M:HIS12
|
4.1
|
39.3
|
1.0
|
CA
|
M:HIS16
|
4.2
|
40.5
|
1.0
|
N
|
M:CYS43
|
4.3
|
44.5
|
1.0
|
CD2
|
M:HIS16
|
4.3
|
40.5
|
1.0
|
O
|
M:HIS12
|
4.4
|
39.3
|
1.0
|
CA
|
M:CYS43
|
4.4
|
44.5
|
1.0
|
CA
|
M:CYS40
|
4.8
|
39.1
|
1.0
|
CB
|
M:LYS42
|
5.0
|
44.1
|
1.0
|
|
Zinc binding site 5 out
of 8 in 6rwm
Go back to
Zinc Binding Sites List in 6rwm
Zinc binding site 5 out
of 8 in the Sivrcm Intasome in Complex with Bictegravir
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 Bictegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn301
b:54.2
occ:1.00
|
NE2
|
I:HIS12
|
2.1
|
17.8
|
1.0
|
ND1
|
I:HIS16
|
2.2
|
16.7
|
1.0
|
SG
|
I:CYS40
|
2.4
|
17.2
|
1.0
|
SG
|
I:CYS43
|
2.4
|
17.3
|
1.0
|
CE1
|
I:HIS12
|
2.9
|
17.8
|
1.0
|
CE1
|
I:HIS16
|
2.9
|
16.7
|
1.0
|
CD2
|
I:HIS12
|
3.1
|
17.8
|
1.0
|
CB
|
I:CYS40
|
3.2
|
17.2
|
1.0
|
CG
|
I:HIS16
|
3.4
|
16.7
|
1.0
|
CB
|
I:CYS43
|
3.9
|
17.3
|
1.0
|
ND1
|
I:HIS12
|
4.0
|
17.8
|
1.0
|
CB
|
I:HIS16
|
4.0
|
16.7
|
1.0
|
NE2
|
I:HIS16
|
4.1
|
16.7
|
1.0
|
CG
|
I:HIS12
|
4.1
|
17.8
|
1.0
|
N
|
I:CYS43
|
4.2
|
17.3
|
1.0
|
CD2
|
I:HIS16
|
4.4
|
16.7
|
1.0
|
CA
|
I:HIS16
|
4.4
|
16.7
|
1.0
|
CA
|
I:CYS43
|
4.7
|
17.3
|
1.0
|
CA
|
I:CYS40
|
4.7
|
17.2
|
1.0
|
CB
|
I:LYS42
|
4.8
|
17.8
|
1.0
|
O
|
I:HIS12
|
4.8
|
17.8
|
1.0
|
C
|
I:LYS42
|
4.9
|
17.8
|
1.0
|
|
Zinc binding site 6 out
of 8 in 6rwm
Go back to
Zinc Binding Sites List in 6rwm
Zinc binding site 6 out
of 8 in the Sivrcm Intasome in Complex with Bictegravir
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 Bictegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn500
b:67.8
occ:1.00
|
NE2
|
J:HIS12
|
2.2
|
38.7
|
1.0
|
ND1
|
J:HIS16
|
2.2
|
37.5
|
1.0
|
SG
|
J:CYS43
|
2.4
|
49.9
|
1.0
|
SG
|
J:CYS40
|
2.4
|
47.9
|
1.0
|
CE1
|
J:HIS16
|
3.0
|
37.5
|
1.0
|
CE1
|
J:HIS12
|
3.0
|
38.7
|
1.0
|
CB
|
J:CYS40
|
3.1
|
47.9
|
1.0
|
CD2
|
J:HIS12
|
3.1
|
38.7
|
1.0
|
CG
|
J:HIS16
|
3.3
|
37.5
|
1.0
|
CB
|
J:CYS43
|
3.7
|
49.9
|
1.0
|
CB
|
J:HIS16
|
3.8
|
37.5
|
1.0
|
ND1
|
J:HIS12
|
4.1
|
38.7
|
1.0
|
NE2
|
J:HIS16
|
4.2
|
37.5
|
1.0
|
CG
|
J:HIS12
|
4.2
|
38.7
|
1.0
|
CA
|
J:HIS16
|
4.3
|
37.5
|
1.0
|
N
|
J:CYS43
|
4.3
|
49.9
|
1.0
|
CD2
|
J:HIS16
|
4.4
|
37.5
|
1.0
|
CA
|
J:CYS43
|
4.6
|
49.9
|
1.0
|
CA
|
J:CYS40
|
4.6
|
47.9
|
1.0
|
O
|
J:HIS12
|
4.7
|
38.7
|
1.0
|
C
|
J:LYS42
|
4.8
|
48.8
|
1.0
|
|
Zinc binding site 7 out
of 8 in 6rwm
Go back to
Zinc Binding Sites List in 6rwm
Zinc binding site 7 out
of 8 in the Sivrcm Intasome in Complex with Bictegravir
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 Bictegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Zn500
b:79.8
occ:1.00
|
NE2
|
K:HIS12
|
2.2
|
43.5
|
1.0
|
ND1
|
K:HIS16
|
2.2
|
39.0
|
1.0
|
SG
|
K:CYS40
|
2.4
|
58.8
|
1.0
|
SG
|
K:CYS43
|
2.4
|
53.1
|
1.0
|
CE1
|
K:HIS16
|
3.0
|
39.0
|
1.0
|
CE1
|
K:HIS12
|
3.0
|
43.5
|
1.0
|
CD2
|
K:HIS12
|
3.1
|
43.5
|
1.0
|
CB
|
K:CYS40
|
3.2
|
58.8
|
1.0
|
CG
|
K:HIS16
|
3.3
|
39.0
|
1.0
|
CB
|
K:CYS43
|
3.7
|
53.1
|
1.0
|
CB
|
K:HIS16
|
3.8
|
39.0
|
1.0
|
ND1
|
K:HIS12
|
4.0
|
43.5
|
1.0
|
CG
|
K:HIS12
|
4.1
|
43.5
|
1.0
|
NE2
|
K:HIS16
|
4.2
|
39.0
|
1.0
|
CA
|
K:HIS16
|
4.3
|
39.0
|
1.0
|
N
|
K:CYS43
|
4.3
|
53.1
|
1.0
|
CD2
|
K:HIS16
|
4.4
|
39.0
|
1.0
|
O
|
K:HIS12
|
4.5
|
43.5
|
1.0
|
CA
|
K:CYS43
|
4.6
|
53.1
|
1.0
|
CA
|
K:CYS40
|
4.7
|
58.8
|
1.0
|
CB
|
K:LYS42
|
4.8
|
50.2
|
1.0
|
C
|
K:LYS42
|
4.8
|
50.2
|
1.0
|
NE2
|
J:GLN164
|
4.9
|
34.1
|
1.0
|
|
Zinc binding site 8 out
of 8 in 6rwm
Go back to
Zinc Binding Sites List in 6rwm
Zinc binding site 8 out
of 8 in the Sivrcm Intasome in Complex with Bictegravir
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 Bictegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn500
b:86.4
occ:1.00
|
ND1
|
E:HIS16
|
2.2
|
40.1
|
1.0
|
NE2
|
E:HIS12
|
2.2
|
39.5
|
1.0
|
SG
|
E:CYS43
|
2.4
|
44.3
|
1.0
|
SG
|
E:CYS40
|
2.4
|
39.2
|
1.0
|
CE1
|
E:HIS16
|
2.9
|
40.1
|
1.0
|
CD2
|
E:HIS12
|
3.0
|
39.5
|
1.0
|
CE1
|
E:HIS12
|
3.2
|
39.5
|
1.0
|
CG
|
E:HIS16
|
3.3
|
40.1
|
1.0
|
CB
|
E:CYS40
|
3.3
|
39.2
|
1.0
|
CB
|
E:CYS43
|
3.4
|
44.3
|
1.0
|
CB
|
E:HIS16
|
3.8
|
40.1
|
1.0
|
CG
|
E:HIS12
|
4.1
|
39.5
|
1.0
|
NE2
|
E:HIS16
|
4.1
|
40.1
|
1.0
|
ND1
|
E:HIS12
|
4.1
|
39.5
|
1.0
|
CA
|
E:HIS16
|
4.2
|
40.1
|
1.0
|
N
|
E:CYS43
|
4.3
|
44.3
|
1.0
|
CD2
|
E:HIS16
|
4.3
|
40.1
|
1.0
|
O
|
E:HIS12
|
4.4
|
39.5
|
1.0
|
CA
|
E:CYS43
|
4.4
|
44.3
|
1.0
|
CA
|
E:CYS40
|
4.8
|
39.2
|
1.0
|
CB
|
E:LYS42
|
5.0
|
44.1
|
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 06:49:53 2024
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