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

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

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 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 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 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 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

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