Zinc in PDB 6rwl: Sivrcm Intasome

Zinc Binding Sites:

The binding sites of Zinc atom in the Sivrcm Intasome (pdb code 6rwl). 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, PDB code: 6rwl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6rwl

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Zinc binding site 1 out of 8 in the Sivrcm Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sivrcm Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:77.8
occ:1.00
 NE2 A:HIS12 2.0 35.3 1.0
ND1 A:HIS16 2.2 31.6 1.0
SG A:CYS43 2.4 39.6 1.0
SG A:CYS40 2.4 37.5 1.0
CE1 A:HIS16 2.7 31.6 1.0
CE1 A:HIS12 2.7 35.3 1.0
CB A:CYS40 3.0 37.5 1.0
CD2 A:HIS12 3.1 35.3 1.0
CG A:HIS16 3.5 31.6 1.0
CB A:CYS43 3.8 39.6 1.0
ND1 A:HIS12 3.8 35.3 1.0
NE2 A:HIS16 4.0 31.6 1.0
CG A:HIS12 4.1 35.3 1.0
CB A:HIS16 4.2 31.6 1.0
N A:CYS43 4.2 39.6 1.0
CD2 A:HIS16 4.4 31.6 1.0
CA A:HIS16 4.5 31.6 1.0
CA A:CYS40 4.5 37.5 1.0
CA A:CYS43 4.6 39.6 1.0
O A:HIS12 4.6 35.3 1.0
CB A:LYS42 5.0 40.0 1.0

Zinc binding site 2 out of 8 in 6rwl

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Zinc binding site 2 out of 8 in the Sivrcm Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sivrcm Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:0.9
occ:1.00
 ND1 B:HIS16 2.2 73.1 1.0
NE2 B:HIS12 2.2 73.6 1.0
SG B:CYS43 2.4 83.4 1.0
SG B:CYS40 2.4 80.2 1.0
CE1 B:HIS12 2.9 73.6 1.0
CE1 B:HIS16 2.9 73.1 1.0
CB B:CYS40 3.1 80.2 1.0
CD2 B:HIS12 3.2 73.6 1.0
CB B:CYS43 3.2 83.4 1.0
CG B:HIS16 3.3 73.1 1.0
CB B:HIS16 3.9 73.1 1.0
ND1 B:HIS12 3.9 73.6 1.0
N B:CYS43 4.0 83.4 1.0
NE2 B:HIS16 4.0 73.1 1.0
CG B:HIS12 4.1 73.6 1.0
CA B:CYS43 4.2 83.4 1.0
CA B:HIS16 4.3 73.1 1.0
CD2 B:HIS16 4.3 73.1 1.0
O B:HIS12 4.5 73.6 1.0
CA B:CYS40 4.6 80.2 1.0
C B:LYS42 4.7 81.4 1.0

Zinc binding site 3 out of 8 in 6rwl

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Zinc binding site 3 out of 8 in the Sivrcm Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sivrcm Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:0.6
occ:1.00
 ND1 C:HIS16 2.2 90.0 1.0
NE2 C:HIS12 2.2 0.7 1.0
SG C:CYS40 2.4 0.2 1.0
SG C:CYS43 2.4 0.9 1.0
CE1 C:HIS12 2.7 0.7 1.0
CB C:CYS40 3.0 0.2 1.0
CE1 C:HIS16 3.0 90.0 1.0
CD2 C:HIS12 3.3 0.7 1.0
CG C:HIS16 3.4 90.0 1.0
CB C:CYS43 3.6 0.9 1.0
ND1 C:HIS12 3.8 0.7 1.0
CB C:HIS16 3.8 90.0 1.0
CG C:HIS12 4.1 0.7 1.0
NE2 C:HIS16 4.2 90.0 1.0
N C:CYS43 4.3 0.9 1.0
CD2 C:HIS16 4.4 90.0 1.0
CA C:HIS16 4.4 90.0 1.0
CA C:CYS40 4.5 0.2 1.0
CA C:CYS43 4.5 0.9 1.0
O C:HIS12 4.6 0.7 1.0

Zinc binding site 4 out of 8 in 6rwl

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Zinc binding site 4 out of 8 in the Sivrcm Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sivrcm Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn500

b:88.4
occ:1.00
 ND1 M:HIS16 2.2 66.0 1.0
NE2 M:HIS12 2.2 62.3 1.0
SG M:CYS43 2.4 72.9 1.0
SG M:CYS40 2.4 65.4 1.0
CE1 M:HIS12 2.9 62.3 1.0
CE1 M:HIS16 3.0 66.0 1.0
CB M:CYS43 3.1 72.9 1.0
CD2 M:HIS12 3.2 62.3 1.0
CB M:CYS40 3.2 65.4 1.0
CG M:HIS16 3.3 66.0 1.0
CB M:HIS16 3.8 66.0 1.0
ND1 M:HIS12 3.9 62.3 1.0
N M:CYS43 4.0 72.9 1.0
CG M:HIS12 4.1 62.3 1.0
CA M:CYS43 4.1 72.9 1.0
NE2 M:HIS16 4.1 66.0 1.0
CA M:HIS16 4.3 66.0 1.0
CD2 M:HIS16 4.3 66.0 1.0
O M:HIS12 4.4 62.3 1.0
CA M:CYS40 4.7 65.4 1.0
C M:LYS42 4.9 73.3 1.0
CB M:LYS42 5.0 73.3 1.0

Zinc binding site 5 out of 8 in 6rwl

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Zinc binding site 5 out of 8 in the Sivrcm Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sivrcm Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn500

b:78.6
occ:1.00
 NE2 I:HIS12 2.0 36.1 1.0
ND1 I:HIS16 2.2 33.9 1.0
SG I:CYS43 2.4 41.6 1.0
SG I:CYS40 2.4 38.7 1.0
CE1 I:HIS16 2.7 33.9 1.0
CE1 I:HIS12 2.7 36.1 1.0
CB I:CYS40 3.0 38.7 1.0
CD2 I:HIS12 3.1 36.1 1.0
CG I:HIS16 3.5 33.9 1.0
CB I:CYS43 3.8 41.6 1.0
ND1 I:HIS12 3.8 36.1 1.0
NE2 I:HIS16 4.0 33.9 1.0
CG I:HIS12 4.1 36.1 1.0
CB I:HIS16 4.2 33.9 1.0
N I:CYS43 4.2 41.6 1.0
CD2 I:HIS16 4.4 33.9 1.0
CA I:HIS16 4.5 33.9 1.0
CA I:CYS40 4.5 38.7 1.0
CA I:CYS43 4.6 41.6 1.0
O I:HIS12 4.6 36.1 1.0
CB I:LYS42 5.0 41.9 1.0

Zinc binding site 6 out of 8 in 6rwl

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Zinc binding site 6 out of 8 in the Sivrcm Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sivrcm Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn500

b:0.9
occ:1.00
 ND1 J:HIS16 2.2 71.6 1.0
NE2 J:HIS12 2.2 73.2 1.0
SG J:CYS43 2.4 84.6 1.0
SG J:CYS40 2.4 79.0 1.0
CE1 J:HIS12 2.8 73.2 1.0
CE1 J:HIS16 2.9 71.6 1.0
CB J:CYS40 3.1 79.0 1.0
CD2 J:HIS12 3.2 73.2 1.0
CB J:CYS43 3.2 84.6 1.0
CG J:HIS16 3.3 71.6 1.0
CB J:HIS16 3.9 71.6 1.0
ND1 J:HIS12 3.9 73.2 1.0
N J:CYS43 4.0 84.6 1.0
NE2 J:HIS16 4.0 71.6 1.0
CG J:HIS12 4.1 73.2 1.0
CA J:CYS43 4.2 84.6 1.0
CA J:HIS16 4.3 71.6 1.0
CD2 J:HIS16 4.3 71.6 1.0
O J:HIS12 4.5 73.2 1.0
CA J:CYS40 4.6 79.0 1.0
C J:LYS42 4.7 82.9 1.0

Zinc binding site 7 out of 8 in 6rwl

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Zinc binding site 7 out of 8 in the Sivrcm Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Sivrcm Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn500

b:0.8
occ:1.00
 ND1 K:HIS16 2.2 87.0 1.0
NE2 K:HIS12 2.2 99.4 1.0
SG K:CYS40 2.4 0.2 1.0
SG K:CYS43 2.4 98.3 1.0
CE1 K:HIS12 2.7 99.4 1.0
CB K:CYS40 3.0 0.2 1.0
CE1 K:HIS16 3.0 87.0 1.0
CD2 K:HIS12 3.3 99.4 1.0
CG K:HIS16 3.4 87.0 1.0
CB K:CYS43 3.6 98.3 1.0
ND1 K:HIS12 3.8 99.4 1.0
CB K:HIS16 3.8 87.0 1.0
CG K:HIS12 4.1 99.4 1.0
NE2 K:HIS16 4.2 87.0 1.0
N K:CYS43 4.3 98.3 1.0
CD2 K:HIS16 4.4 87.0 1.0
CA K:HIS16 4.4 87.0 1.0
CA K:CYS40 4.5 0.2 1.0
CA K:CYS43 4.5 98.3 1.0
O K:HIS12 4.6 99.4 1.0
NE2 J:GLN164 4.9 57.0 1.0

Zinc binding site 8 out of 8 in 6rwl

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Zinc binding site 8 out of 8 in the Sivrcm Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Sivrcm Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn500

b:91.0
occ:1.00
 ND1 E:HIS16 2.2 65.9 1.0
NE2 E:HIS12 2.2 63.0 1.0
SG E:CYS43 2.4 73.4 1.0
SG E:CYS40 2.4 65.5 1.0
CE1 E:HIS12 2.9 63.0 1.0
CE1 E:HIS16 3.0 65.9 1.0
CB E:CYS43 3.1 73.4 1.0
CD2 E:HIS12 3.2 63.0 1.0
CB E:CYS40 3.2 65.5 1.0
CG E:HIS16 3.3 65.9 1.0
CB E:HIS16 3.8 65.9 1.0
ND1 E:HIS12 3.9 63.0 1.0
N E:CYS43 4.0 73.4 1.0
CG E:HIS12 4.1 63.0 1.0
CA E:CYS43 4.1 73.4 1.0
NE2 E:HIS16 4.1 65.9 1.0
CA E:HIS16 4.3 65.9 1.0
CD2 E:HIS16 4.3 65.9 1.0
O E:HIS12 4.4 63.0 1.0
CA E:CYS40 4.7 65.5 1.0
C E:LYS42 4.9 72.8 1.0
CB E:LYS42 5.0 72.8 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 12:42:53 2020

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