Zinc in PDB 7oug: Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir

Other elements in 7oug:

The structure of Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir (pdb code 7oug). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir, PDB code: 7oug:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7oug

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Zinc binding site 1 out of 4 in the Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1000

b:83.5
occ:1.00
ND1 D:HIS12 2.0 33.5 1.0
NE2 D:HIS8 2.0 22.7 1.0
CD2 D:HIS8 2.3 22.7 1.0
SG D:CYS38 2.3 61.4 1.0
SG D:CYS35 2.3 64.4 1.0
CE1 D:HIS12 2.6 33.5 1.0
CG D:HIS12 3.2 33.5 1.0
CE1 D:HIS8 3.2 22.7 1.0
CB D:CYS35 3.3 64.4 1.0
CG D:HIS8 3.5 22.7 1.0
CB D:CYS38 3.5 61.4 1.0
NE2 D:HIS12 3.8 33.5 1.0
CB D:HIS12 3.8 33.5 1.0
CA D:HIS12 3.9 33.5 1.0
ND1 D:HIS8 3.9 22.7 1.0
CD2 D:HIS12 4.0 33.5 1.0
O D:HIS8 4.2 22.7 1.0
N D:CYS38 4.6 61.4 1.0
CA D:CYS38 4.7 61.4 1.0
CB D:HIS8 4.7 22.7 1.0
C D:HIS12 4.8 33.5 1.0
CA D:CYS35 4.8 64.4 1.0
C D:HIS8 4.8 22.7 1.0
N D:HIS12 4.9 33.5 1.0

Zinc binding site 2 out of 4 in 7oug

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Zinc binding site 2 out of 4 in the Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:39.6
occ:1.00
NE2 E:HIS8 2.0 11.6 1.0
ND1 E:HIS12 2.0 7.4 1.0
SG E:CYS35 2.3 18.2 1.0
SG E:CYS38 2.3 8.9 1.0
CE1 E:HIS12 2.7 7.4 1.0
CE1 E:HIS8 2.9 11.6 1.0
CD2 E:HIS8 3.0 11.6 1.0
CG E:HIS12 3.2 7.4 1.0
CB E:CYS35 3.3 18.2 1.0
CB E:CYS38 3.7 8.9 1.0
CB E:HIS12 3.8 7.4 1.0
ND1 E:HIS8 3.9 11.6 1.0
NE2 E:HIS12 3.9 7.4 1.0
CG E:HIS8 4.0 11.6 1.0
N E:CYS38 4.0 8.9 1.0
CA E:HIS12 4.2 7.4 1.0
CD2 E:HIS12 4.2 7.4 1.0
CA E:CYS38 4.3 8.9 1.0
O E:HIS8 4.6 11.6 1.0
CA E:CYS35 4.8 18.2 1.0
CB E:ALA37 4.8 11.4 1.0
C E:ALA37 4.9 11.4 1.0
C E:HIS12 5.0 7.4 1.0

Zinc binding site 3 out of 4 in 7oug

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Zinc binding site 3 out of 4 in the Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:82.1
occ:1.00
ND1 A:HIS12 2.0 34.6 1.0
NE2 A:HIS8 2.0 24.4 1.0
CD2 A:HIS8 2.3 24.4 1.0
SG A:CYS38 2.3 58.7 1.0
SG A:CYS35 2.3 64.0 1.0
CE1 A:HIS12 2.6 34.6 1.0
CG A:HIS12 3.2 34.6 1.0
CE1 A:HIS8 3.2 24.4 1.0
CB A:CYS35 3.3 64.0 1.0
CG A:HIS8 3.5 24.4 1.0
CB A:CYS38 3.5 58.7 1.0
NE2 A:HIS12 3.8 34.6 1.0
CB A:HIS12 3.8 34.6 1.0
CA A:HIS12 3.9 34.6 1.0
ND1 A:HIS8 3.9 24.4 1.0
CD2 A:HIS12 4.0 34.6 1.0
O A:HIS8 4.2 24.4 1.0
N A:CYS38 4.6 58.7 1.0
CA A:CYS38 4.7 58.7 1.0
CB A:HIS8 4.7 24.4 1.0
C A:HIS12 4.8 34.6 1.0
CA A:CYS35 4.8 64.0 1.0
C A:HIS8 4.8 24.4 1.0
N A:HIS12 4.9 34.6 1.0

Zinc binding site 4 out of 4 in 7oug

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Zinc binding site 4 out of 4 in the Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Stlv-1 Intasome:B56 in Complex with the Strand-Transfer Inhibitor Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:32.3
occ:1.00
NE2 B:HIS8 2.0 10.9 1.0
ND1 B:HIS12 2.0 11.7 1.0
SG B:CYS35 2.3 18.6 1.0
SG B:CYS38 2.3 9.3 1.0
CE1 B:HIS12 2.7 11.7 1.0
CE1 B:HIS8 2.9 10.9 1.0
CD2 B:HIS8 3.0 10.9 1.0
CG B:HIS12 3.2 11.7 1.0
CB B:CYS35 3.3 18.6 1.0
CB B:CYS38 3.7 9.3 1.0
CB B:HIS12 3.8 11.7 1.0
ND1 B:HIS8 3.9 10.9 1.0
NE2 B:HIS12 3.9 11.7 1.0
CG B:HIS8 4.0 10.9 1.0
N B:CYS38 4.0 9.3 1.0
CA B:HIS12 4.2 11.7 1.0
CD2 B:HIS12 4.2 11.7 1.0
CA B:CYS38 4.3 9.3 1.0
O B:HIS8 4.6 10.9 1.0
CA B:CYS35 4.8 18.6 1.0
CB B:ALA37 4.8 12.1 1.0
C B:ALA37 4.9 12.1 1.0
C B:HIS12 5.0 11.7 1.0

Reference:

M.S.Barski, T.Vanzo, X.Zhao, S.J.Smith, A.Ballandras-Colas, N.B.Cronin, V.E.Pye, S.H.Hughes, T.R.Burke, P.Cherepanov, G.N.Maertens. Structural Basis For the Inhibition of Htlv-1 Integration Inferred From Cryo-Em Deltaretroviral Intasome Structures Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Sun Aug 22 09:53:07 2021

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