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:

Fluorine (F) 4 atoms
Magnesium (Mg) 4 atoms
Chlorine (Cl) 2 atoms

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

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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

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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

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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

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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

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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

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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

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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

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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: Wed Dec 16 12:42:57 2020

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