Zinc in PDB 6rwo: Sivrcm Intasome (Q148/G140S) in Complex with Bictegravir

Other elements in 6rwo:

The structure of Sivrcm Intasome (Q148/G140S) in Complex with Bictegravir also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Magnesium (Mg) 4 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sivrcm Intasome (Q148/G140S) in Complex with Bictegravir (pdb code 6rwo). 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 (Q148/G140S) in Complex with Bictegravir, PDB code: 6rwo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6rwo

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Zinc binding site 1 out of 8 in the Sivrcm Intasome (Q148/G140S) 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 (Q148/G140S) in Complex with Bictegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:57.6
occ:1.00
NE2 A:HIS12 2.0 26.7 1.0
ND1 A:HIS16 2.2 25.3 1.0
SG A:CYS40 2.4 30.6 1.0
SG A:CYS43 2.4 29.9 1.0
CE1 A:HIS16 2.9 25.3 1.0
CE1 A:HIS12 2.9 26.7 1.0
CD2 A:HIS12 3.1 26.7 1.0
CB A:CYS40 3.1 30.6 1.0
CG A:HIS16 3.4 25.3 1.0
CB A:CYS43 3.9 29.9 1.0
ND1 A:HIS12 4.0 26.7 1.0
CB A:HIS16 4.0 25.3 1.0
CG A:HIS12 4.1 26.7 1.0
NE2 A:HIS16 4.1 25.3 1.0
N A:CYS43 4.2 29.9 1.0
CA A:HIS16 4.4 25.3 1.0
CD2 A:HIS16 4.4 25.3 1.0
CA A:CYS40 4.6 30.6 1.0
CA A:CYS43 4.7 29.9 1.0
O A:HIS12 4.8 26.7 1.0
CB A:LYS42 4.9 27.2 1.0
C A:LYS42 5.0 27.2 1.0

Zinc binding site 2 out of 8 in 6rwo

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Zinc binding site 2 out of 8 in the Sivrcm Intasome (Q148/G140S) 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 (Q148/G140S) in Complex with Bictegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn500

b:86.7
occ:1.00
ND1 E:HIS16 2.2 61.6 1.0
NE2 E:HIS12 2.2 58.5 1.0
SG E:CYS43 2.4 64.5 1.0
SG E:CYS40 2.4 59.1 1.0
CE1 E:HIS12 2.9 58.5 1.0
CE1 E:HIS16 3.1 61.6 1.0
CB E:CYS40 3.2 59.1 1.0
CD2 E:HIS12 3.2 58.5 1.0
CG E:HIS16 3.3 61.6 1.0
CB E:CYS43 3.3 64.5 1.0
CB E:HIS16 3.6 61.6 1.0
ND1 E:HIS12 4.0 58.5 1.0
CA E:HIS16 4.1 61.6 1.0
N E:CYS43 4.1 64.5 1.0
CG E:HIS12 4.2 58.5 1.0
NE2 E:HIS16 4.3 61.6 1.0
CA E:CYS43 4.3 64.5 1.0
CD2 E:HIS16 4.4 61.6 1.0
O E:HIS12 4.6 58.5 1.0
CA E:CYS40 4.7 59.1 1.0
C E:HIS16 4.9 61.6 1.0
CB E:LYS42 4.9 62.7 1.0
C E:LYS42 4.9 62.7 1.0

Zinc binding site 3 out of 8 in 6rwo

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Zinc binding site 3 out of 8 in the Sivrcm Intasome (Q148/G140S) 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 (Q148/G140S) in Complex with Bictegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn500

b:0.1
occ:1.00
NE2 K:HIS12 2.2 63.8 1.0
ND1 K:HIS16 2.2 57.6 1.0
SG K:CYS40 2.4 82.8 1.0
SG K:CYS43 2.4 79.4 1.0
CE1 K:HIS16 2.8 57.6 1.0
CE1 K:HIS12 3.0 63.8 1.0
CB K:CYS40 3.1 82.8 1.0
CD2 K:HIS12 3.1 63.8 1.0
CG K:HIS16 3.4 57.6 1.0
CB K:CYS43 4.0 79.4 1.0
ND1 K:HIS12 4.0 63.8 1.0
CB K:HIS16 4.0 57.6 1.0
CG K:HIS12 4.1 63.8 1.0
NE2 K:HIS16 4.1 57.6 1.0
N K:CYS43 4.4 79.4 1.0
CD2 K:HIS16 4.4 57.6 1.0
O K:HIS12 4.4 63.8 1.0
CB K:LYS42 4.4 74.0 1.0
CA K:CYS40 4.5 82.8 1.0
CA K:HIS16 4.5 57.6 1.0
CA K:CYS43 4.8 79.4 1.0
C K:LYS42 4.8 74.0 1.0
C K:CYS40 4.9 82.8 1.0
N K:LYS42 4.9 74.0 1.0
O K:CYS40 4.9 82.8 1.0
CA K:LYS42 4.9 74.0 1.0

Zinc binding site 4 out of 8 in 6rwo

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Zinc binding site 4 out of 8 in the Sivrcm Intasome (Q148/G140S) 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 (Q148/G140S) in Complex with Bictegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn500

b:89.3
occ:1.00
NE2 J:HIS12 2.2 60.7 1.0
ND1 J:HIS16 2.2 60.5 1.0
SG J:CYS43 2.4 77.6 1.0
SG J:CYS40 2.4 70.6 1.0
CE1 J:HIS12 2.9 60.7 1.0
CE1 J:HIS16 3.0 60.5 1.0
CB J:CYS40 3.1 70.6 1.0
CD2 J:HIS12 3.2 60.7 1.0
CG J:HIS16 3.3 60.5 1.0
CB J:CYS43 3.7 77.6 1.0
CB J:HIS16 3.8 60.5 1.0
ND1 J:HIS12 4.0 60.7 1.0
NE2 J:HIS16 4.2 60.5 1.0
CG J:HIS12 4.2 60.7 1.0
CA J:HIS16 4.3 60.5 1.0
CD2 J:HIS16 4.4 60.5 1.0
N J:CYS43 4.4 77.6 1.0
CA J:CYS40 4.6 70.6 1.0
O J:HIS12 4.6 60.7 1.0
CA J:CYS43 4.6 77.6 1.0

Zinc binding site 5 out of 8 in 6rwo

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Zinc binding site 5 out of 8 in the Sivrcm Intasome (Q148/G140S) 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 (Q148/G140S) in Complex with Bictegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn301

b:61.4
occ:1.00
NE2 I:HIS12 2.1 28.2 1.0
ND1 I:HIS16 2.2 25.6 1.0
SG I:CYS40 2.4 31.1 1.0
SG I:CYS43 2.4 31.1 1.0
CE1 I:HIS16 2.9 25.6 1.0
CE1 I:HIS12 2.9 28.2 1.0
CD2 I:HIS12 3.1 28.2 1.0
CB I:CYS40 3.1 31.1 1.0
CG I:HIS16 3.4 25.6 1.0
CB I:CYS43 3.9 31.1 1.0
ND1 I:HIS12 4.0 28.2 1.0
CB I:HIS16 4.0 25.6 1.0
CG I:HIS12 4.1 28.2 1.0
NE2 I:HIS16 4.1 25.6 1.0
N I:CYS43 4.2 31.1 1.0
CA I:HIS16 4.4 25.6 1.0
CD2 I:HIS16 4.4 25.6 1.0
CA I:CYS40 4.6 31.1 1.0
CA I:CYS43 4.7 31.1 1.0
O I:HIS12 4.8 28.2 1.0
CB I:LYS42 4.9 27.9 1.0
C I:LYS42 5.0 27.9 1.0

Zinc binding site 6 out of 8 in 6rwo

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Zinc binding site 6 out of 8 in the Sivrcm Intasome (Q148/G140S) 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 (Q148/G140S) in Complex with Bictegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn500

b:93.1
occ:1.00
ND1 M:HIS16 2.2 62.2 1.0
NE2 M:HIS12 2.2 59.2 1.0
SG M:CYS43 2.4 64.5 1.0
SG M:CYS40 2.4 58.9 1.0
CE1 M:HIS12 2.9 59.2 1.0
CE1 M:HIS16 3.1 62.2 1.0
CB M:CYS40 3.2 58.9 1.0
CD2 M:HIS12 3.3 59.2 1.0
CG M:HIS16 3.3 62.2 1.0
CB M:CYS43 3.3 64.5 1.0
CB M:HIS16 3.6 62.2 1.0
ND1 M:HIS12 4.0 59.2 1.0
CA M:HIS16 4.1 62.2 1.0
N M:CYS43 4.1 64.5 1.0
CG M:HIS12 4.2 59.2 1.0
NE2 M:HIS16 4.3 62.2 1.0
CA M:CYS43 4.3 64.5 1.0
CD2 M:HIS16 4.3 62.2 1.0
O M:HIS12 4.6 59.2 1.0
CA M:CYS40 4.7 58.9 1.0
C M:HIS16 4.9 62.2 1.0
CB M:LYS42 4.9 62.5 1.0
C M:LYS42 4.9 62.5 1.0

Zinc binding site 7 out of 8 in 6rwo

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Zinc binding site 7 out of 8 in the Sivrcm Intasome (Q148/G140S) 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 (Q148/G140S) in Complex with Bictegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:99.7
occ:1.00
NE2 C:HIS12 2.2 63.5 1.0
ND1 C:HIS16 2.2 57.5 1.0
SG C:CYS40 2.4 83.1 1.0
SG C:CYS43 2.4 78.2 1.0
CE1 C:HIS16 2.8 57.5 1.0
CE1 C:HIS12 3.0 63.5 1.0
CB C:CYS40 3.1 83.1 1.0
CD2 C:HIS12 3.1 63.5 1.0
CG C:HIS16 3.4 57.5 1.0
CB C:CYS43 4.0 78.2 1.0
ND1 C:HIS12 4.0 63.5 1.0
CB C:HIS16 4.0 57.5 1.0
CG C:HIS12 4.1 63.5 1.0
NE2 C:HIS16 4.1 57.5 1.0
N C:CYS43 4.4 78.2 1.0
CD2 C:HIS16 4.4 57.5 1.0
O C:HIS12 4.4 63.5 1.0
CB C:LYS42 4.4 74.0 1.0
CA C:CYS40 4.5 83.1 1.0
CA C:HIS16 4.5 57.5 1.0
CA C:CYS43 4.8 78.2 1.0
C C:LYS42 4.8 74.0 1.0
C C:CYS40 4.9 83.1 1.0
N C:LYS42 4.9 74.0 1.0
O C:CYS40 4.9 83.1 1.0
CA C:LYS42 4.9 74.0 1.0

Zinc binding site 8 out of 8 in 6rwo

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Zinc binding site 8 out of 8 in the Sivrcm Intasome (Q148/G140S) 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 (Q148/G140S) in Complex with Bictegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:87.6
occ:1.00
NE2 B:HIS12 2.2 60.8 1.0
ND1 B:HIS16 2.2 60.6 1.0
SG B:CYS43 2.4 78.4 1.0
SG B:CYS40 2.4 70.8 1.0
CE1 B:HIS12 2.9 60.8 1.0
CE1 B:HIS16 3.0 60.6 1.0
CB B:CYS40 3.1 70.8 1.0
CD2 B:HIS12 3.2 60.8 1.0
CG B:HIS16 3.3 60.6 1.0
CB B:CYS43 3.7 78.4 1.0
CB B:HIS16 3.8 60.6 1.0
ND1 B:HIS12 4.0 60.8 1.0
NE2 B:HIS16 4.2 60.6 1.0
CG B:HIS12 4.2 60.8 1.0
CA B:HIS16 4.3 60.6 1.0
CD2 B:HIS16 4.4 60.6 1.0
N B:CYS43 4.4 78.4 1.0
CA B:CYS40 4.6 70.8 1.0
O B:HIS12 4.6 60.8 1.0
CA B:CYS43 4.6 78.4 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: Wed Dec 16 12:42:59 2020

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