Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Sivrcm Intasome in Complex with Dolutegravir
(pdb code 6rwn). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Sivrcm Intasome in Complex with Dolutegravir, PDB code: 6rwn:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6rwn
Go back to
Magnesium Binding Sites List in 6rwn
Magnesium binding site 1 out
of 4 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg304
b:9.6
occ:1.00
|
O
|
A:HOH402
|
2.0
|
11.4
|
1.0
|
OAC
|
A:DLU303
|
2.0
|
9.6
|
1.0
|
O
|
A:HOH401
|
2.0
|
13.7
|
1.0
|
OAE
|
A:DLU303
|
2.1
|
9.6
|
1.0
|
OD2
|
A:ASP116
|
2.1
|
7.8
|
1.0
|
OD1
|
A:ASP64
|
2.1
|
6.4
|
1.0
|
CG
|
A:ASP64
|
3.1
|
6.4
|
1.0
|
CAS
|
A:DLU303
|
3.1
|
9.6
|
1.0
|
CAW
|
A:DLU303
|
3.2
|
9.6
|
1.0
|
CG
|
A:ASP116
|
3.2
|
7.8
|
1.0
|
OD2
|
A:ASP64
|
3.4
|
6.4
|
1.0
|
MG
|
A:MG305
|
3.5
|
4.9
|
1.0
|
CAY
|
A:DLU303
|
3.6
|
9.6
|
1.0
|
OD1
|
A:ASP116
|
3.7
|
7.8
|
1.0
|
NBC
|
A:DLU303
|
4.2
|
9.6
|
1.0
|
O
|
A:HOH403
|
4.2
|
7.8
|
1.0
|
O
|
A:CYS65
|
4.4
|
12.1
|
1.0
|
CAZ
|
A:DLU303
|
4.4
|
9.6
|
1.0
|
CB
|
A:ASP116
|
4.5
|
7.8
|
1.0
|
CB
|
A:ASP64
|
4.5
|
6.4
|
1.0
|
N
|
A:CYS65
|
4.5
|
12.1
|
1.0
|
CBA
|
A:DLU303
|
4.5
|
9.6
|
1.0
|
OE2
|
A:GLU152
|
4.6
|
9.6
|
1.0
|
OAD
|
A:DLU303
|
4.7
|
9.6
|
1.0
|
CA
|
A:ASP64
|
4.8
|
6.4
|
1.0
|
N7
|
T:DA21
|
4.9
|
20.5
|
1.0
|
NBD
|
A:DLU303
|
5.0
|
9.6
|
1.0
|
O
|
A:HOH404
|
5.0
|
16.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6rwn
Go back to
Magnesium Binding Sites List in 6rwn
Magnesium binding site 2 out
of 4 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg305
b:4.9
occ:1.00
|
OAD
|
A:DLU303
|
2.0
|
9.6
|
1.0
|
O
|
A:HOH403
|
2.0
|
7.8
|
1.0
|
OE1
|
A:GLU152
|
2.0
|
9.6
|
1.0
|
OE2
|
A:GLU152
|
2.0
|
9.6
|
1.0
|
OD2
|
A:ASP64
|
2.1
|
6.4
|
1.0
|
OAE
|
A:DLU303
|
2.1
|
9.6
|
1.0
|
CD
|
A:GLU152
|
2.3
|
9.6
|
1.0
|
CAZ
|
A:DLU303
|
2.7
|
9.6
|
1.0
|
CAW
|
A:DLU303
|
2.8
|
9.6
|
1.0
|
CG
|
A:ASP64
|
3.1
|
6.4
|
1.0
|
OD1
|
A:ASP64
|
3.5
|
6.4
|
1.0
|
MG
|
A:MG304
|
3.5
|
9.6
|
1.0
|
CG
|
A:GLU152
|
3.8
|
9.6
|
1.0
|
O
|
A:HOH402
|
4.1
|
11.4
|
1.0
|
CAX
|
A:DLU303
|
4.1
|
9.6
|
1.0
|
CAY
|
A:DLU303
|
4.2
|
9.6
|
1.0
|
CB
|
A:ASP64
|
4.4
|
6.4
|
1.0
|
NAP
|
A:DLU303
|
4.4
|
9.6
|
1.0
|
OAC
|
A:DLU303
|
4.5
|
9.6
|
1.0
|
FAG
|
A:DLU303
|
4.6
|
9.6
|
1.0
|
O
|
A:CYS65
|
4.6
|
12.1
|
1.0
|
CB
|
A:GLU152
|
4.7
|
9.6
|
1.0
|
OD2
|
A:ASP116
|
4.7
|
7.8
|
1.0
|
ND2
|
A:ASN155
|
4.7
|
5.5
|
1.0
|
CAR
|
A:DLU303
|
4.8
|
9.6
|
1.0
|
OP1
|
T:DA21
|
4.9
|
20.5
|
1.0
|
CAS
|
A:DLU303
|
4.9
|
9.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6rwn
Go back to
Magnesium Binding Sites List in 6rwn
Magnesium binding site 3 out
of 4 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg304
b:9.1
occ:1.00
|
O
|
I:HOH403
|
2.0
|
10.8
|
1.0
|
O
|
I:HOH401
|
2.0
|
14.0
|
1.0
|
OAC
|
I:DLU303
|
2.0
|
11.0
|
1.0
|
OAE
|
I:DLU303
|
2.1
|
11.0
|
1.0
|
OD2
|
I:ASP116
|
2.1
|
8.0
|
1.0
|
OD1
|
I:ASP64
|
2.1
|
6.5
|
1.0
|
CG
|
I:ASP64
|
3.1
|
6.5
|
1.0
|
CAS
|
I:DLU303
|
3.1
|
11.0
|
1.0
|
CAW
|
I:DLU303
|
3.2
|
11.0
|
1.0
|
CG
|
I:ASP116
|
3.2
|
8.0
|
1.0
|
OD2
|
I:ASP64
|
3.4
|
6.5
|
1.0
|
MG
|
I:MG305
|
3.5
|
4.9
|
1.0
|
CAY
|
I:DLU303
|
3.6
|
11.0
|
1.0
|
OD1
|
I:ASP116
|
3.7
|
8.0
|
1.0
|
O
|
I:HOH402
|
4.1
|
6.4
|
1.0
|
NBC
|
I:DLU303
|
4.2
|
11.0
|
1.0
|
O
|
I:CYS65
|
4.4
|
12.3
|
1.0
|
CAZ
|
I:DLU303
|
4.4
|
11.0
|
1.0
|
CB
|
I:ASP116
|
4.5
|
8.0
|
1.0
|
CB
|
I:ASP64
|
4.5
|
6.5
|
1.0
|
N
|
I:CYS65
|
4.5
|
12.3
|
1.0
|
CBA
|
I:DLU303
|
4.5
|
11.0
|
1.0
|
OE2
|
I:GLU152
|
4.6
|
10.2
|
1.0
|
OAD
|
I:DLU303
|
4.7
|
11.0
|
1.0
|
CA
|
I:ASP64
|
4.8
|
6.5
|
1.0
|
N7
|
W:DA21
|
4.9
|
20.4
|
1.0
|
NBD
|
I:DLU303
|
5.0
|
11.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6rwn
Go back to
Magnesium Binding Sites List in 6rwn
Magnesium binding site 4 out
of 4 in the Sivrcm Intasome in Complex with Dolutegravir
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Sivrcm Intasome in Complex with Dolutegravir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg305
b:4.9
occ:1.00
|
OE2
|
I:GLU152
|
2.0
|
10.2
|
1.0
|
O
|
I:HOH402
|
2.0
|
6.4
|
1.0
|
OAD
|
I:DLU303
|
2.0
|
11.0
|
1.0
|
OD2
|
I:ASP64
|
2.1
|
6.5
|
1.0
|
OE1
|
I:GLU152
|
2.1
|
10.2
|
1.0
|
OAE
|
I:DLU303
|
2.1
|
11.0
|
1.0
|
CD
|
I:GLU152
|
2.3
|
10.2
|
1.0
|
CAZ
|
I:DLU303
|
2.8
|
11.0
|
1.0
|
CAW
|
I:DLU303
|
2.8
|
11.0
|
1.0
|
CG
|
I:ASP64
|
3.1
|
6.5
|
1.0
|
OD1
|
I:ASP64
|
3.5
|
6.5
|
1.0
|
MG
|
I:MG304
|
3.5
|
9.1
|
1.0
|
CG
|
I:GLU152
|
3.9
|
10.2
|
1.0
|
O
|
I:HOH403
|
4.1
|
10.8
|
1.0
|
CAX
|
I:DLU303
|
4.1
|
11.0
|
1.0
|
CAY
|
I:DLU303
|
4.2
|
11.0
|
1.0
|
CB
|
I:ASP64
|
4.4
|
6.5
|
1.0
|
NAP
|
I:DLU303
|
4.4
|
11.0
|
1.0
|
OAC
|
I:DLU303
|
4.5
|
11.0
|
1.0
|
FAG
|
I:DLU303
|
4.6
|
11.0
|
1.0
|
O
|
I:CYS65
|
4.6
|
12.3
|
1.0
|
OD2
|
I:ASP116
|
4.7
|
8.0
|
1.0
|
CB
|
I:GLU152
|
4.7
|
10.2
|
1.0
|
ND2
|
I:ASN155
|
4.8
|
8.6
|
1.0
|
CAR
|
I:DLU303
|
4.8
|
11.0
|
1.0
|
CAS
|
I:DLU303
|
4.8
|
11.0
|
1.0
|
OP1
|
W:DA21
|
4.9
|
20.4
|
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 1 17:32:49 2024
|