Zinc in PDB 6vrg: Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence

The structure of Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence, PDB code: 6vrg was solved by G.Eilers, K.Gupta, A.Allen, J.Zhou, Y.Hwang, M.Cory, F.D.Bushman, G.D.Vanduyne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.57 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.919, 102.919, 279.203, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 25.3

The structure of Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence (pdb code 6vrg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence, PDB code: 6vrg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.6 occ:1.00 NE2 A:HIS12 2.0 15.9 1.0 ND1 A:HIS16 2.0 20.1 1.0 SG A:CYS43 2.3 21.2 1.0 SG A:CYS40 2.3 28.1 1.0 CD2 A:HIS12 2.9 13.6 1.0 CE1 A:HIS16 3.0 24.9 1.0 HD2 A:HIS12 3.0 16.3 1.0 CE1 A:HIS12 3.0 16.9 1.0 HB3 A:HIS16 3.1 17.2 1.0 HE1 A:HIS16 3.1 29.8 1.0 CG A:HIS16 3.1 19.8 1.0 HB3 A:CYS40 3.1 38.5 1.0 CB A:CYS40 3.2 32.1 1.0 HB2 A:CYS43 3.2 32.5 1.0 HE1 A:HIS12 3.3 20.3 1.0 HB2 A:CYS40 3.3 38.5 1.0 CB A:CYS43 3.4 27.1 1.0 HA A:HIS16 3.4 17.4 1.0 CB A:HIS16 3.5 14.3 1.0 HB2 A:LYS42 3.6 33.4 1.0 H A:CYS43 3.9 34.6 1.0 CA A:HIS16 4.0 14.5 1.0 CG A:HIS12 4.0 13.2 1.0 N A:CYS43 4.0 28.8 1.0 ND1 A:HIS12 4.0 16.3 1.0 HB3 A:CYS43 4.1 32.5 1.0 NE2 A:HIS16 4.1 31.1 1.0 CD2 A:HIS16 4.2 20.8 1.0 H A:LYS42 4.2 33.4 1.0 CA A:CYS43 4.3 33.0 1.0 HB2 A:HIS16 4.4 17.2 1.0 HE22 A:GLN164 4.4 31.0 1.0 C A:LYS42 4.4 27.7 1.0 O A:HIS12 4.5 18.1 1.0 CB A:LYS42 4.5 27.8 1.0 HE21 A:GLN164 4.5 31.0 1.0 CA A:CYS40 4.6 29.5 1.0 NE2 A:GLN164 4.7 25.8 1.0 O A:HOH428 4.7 21.0 1.0 HA A:VAL37 4.8 24.8 1.0 HA A:CYS43 4.8 39.6 1.0 HB3 A:LYS42 4.8 33.4 1.0 CA A:LYS42 4.8 29.1 1.0 N A:LYS42 4.8 27.8 1.0 C A:HIS16 4.8 15.6 1.0 HD1 A:HIS12 4.8 19.5 1.0 HG13 A:VAL37 4.9 29.5 1.0 HE2 A:HIS16 4.9 37.4 1.0 HA A:CYS40 5.0 35.4 1.0

Zinc binding site 2 out of 4 in the Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:18.8 occ:1.00 NE2 B:HIS12 2.0 14.3 1.0 ND1 B:HIS16 2.1 22.6 1.0 SG B:CYS43 2.3 16.5 1.0 SG B:CYS40 2.3 19.4 1.0 CD2 B:HIS12 2.9 15.6 1.0 CE1 B:HIS12 3.0 17.1 1.0 CE1 B:HIS16 3.0 25.2 1.0 HD2 B:HIS12 3.1 18.8 1.0 HB3 B:HIS16 3.1 14.7 1.0 HE1 B:HIS16 3.1 30.2 1.0 CG B:HIS16 3.1 16.8 1.0 HB2 B:CYS43 3.1 38.4 1.0 HB3 B:CYS40 3.1 28.0 1.0 HE1 B:HIS12 3.2 20.5 1.0 CB B:CYS40 3.2 23.3 1.0 CB B:CYS43 3.4 32.0 1.0 HB2 B:CYS40 3.4 28.0 1.0 HA B:HIS16 3.4 19.2 1.0 HB2 B:LYS42 3.4 38.5 1.0 CB B:HIS16 3.5 12.3 1.0 CG B:HIS12 4.0 14.0 1.0 ND1 B:HIS12 4.0 14.5 1.0 CA B:HIS16 4.0 16.0 1.0 HB3 B:CYS43 4.0 38.4 1.0 N B:CYS43 4.1 30.3 1.0 H B:LYS42 4.1 43.0 1.0 H B:CYS43 4.1 36.4 1.0 NE2 B:HIS16 4.1 20.9 1.0 CD2 B:HIS16 4.2 19.5 1.0 CA B:CYS43 4.3 32.0 1.0 CB B:LYS42 4.4 32.1 1.0 HE21 B:GLN164 4.4 53.5 1.0 HB2 B:HIS16 4.4 14.7 1.0 C B:LYS42 4.4 29.1 1.0 O B:HIS12 4.5 16.2 1.0 CA B:CYS40 4.7 24.8 1.0 HA B:VAL37 4.7 25.4 1.0 N B:LYS42 4.7 35.9 1.0 CA B:LYS42 4.7 32.0 1.0 HD1 B:HIS12 4.7 17.4 1.0 HB3 B:LYS42 4.7 38.5 1.0 NE2 B:GLN164 4.8 44.6 1.0 HE22 B:GLN164 4.8 53.5 1.0 HA B:CYS43 4.8 38.4 1.0 C B:HIS16 4.8 16.5 1.0 HE2 B:HIS16 4.9 25.1 1.0 O B:HIS16 4.9 16.7 1.0 HB3 B:GLN164 4.9 23.4 1.0 HG13 B:VAL37 5.0 33.8 1.0

Zinc binding site 3 out of 4 in the Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:26.0 occ:1.00 NE2 C:HIS12 2.0 19.0 1.0 ND1 C:HIS16 2.0 20.9 1.0 SG C:CYS43 2.2 22.2 1.0 SG C:CYS40 2.4 25.8 1.0 CD2 C:HIS12 2.8 18.2 1.0 CE1 C:HIS16 2.9 18.8 1.0 CE1 C:HIS12 3.0 19.7 1.0 HD2 C:HIS12 3.0 21.9 1.0 HB3 C:HIS16 3.1 21.8 1.0 HE1 C:HIS16 3.1 22.6 1.0 CG C:HIS16 3.1 21.9 1.0 HB2 C:CYS43 3.1 33.4 1.0 HB3 C:CYS40 3.2 29.1 1.0 CB C:CYS40 3.2 24.2 1.0 HE1 C:HIS12 3.3 23.7 1.0 HB2 C:CYS40 3.3 29.1 1.0 CB C:CYS43 3.3 27.8 1.0 HA C:HIS16 3.4 19.1 1.0 CB C:HIS16 3.5 18.1 1.0 HB2 C:LYS42 3.6 39.3 1.0 CG C:HIS12 3.9 15.9 1.0 HB3 C:CYS43 4.0 33.4 1.0 CA C:HIS16 4.0 15.9 1.0 ND1 C:HIS12 4.0 16.7 1.0 NE2 C:HIS16 4.1 25.6 1.0 CD2 C:HIS16 4.2 23.7 1.0 N C:CYS43 4.2 35.4 1.0 H C:LYS42 4.2 47.2 1.0 H C:CYS43 4.3 42.5 1.0 CA C:CYS43 4.4 32.2 1.0 HB2 C:HIS16 4.4 21.8 1.0 O C:HIS12 4.4 20.6 1.0 C C:LYS42 4.5 32.8 1.0 CB C:LYS42 4.6 32.7 1.0 O C:HOH409 4.6 29.7 1.0 CA C:CYS40 4.7 33.4 1.0 HA C:VAL37 4.7 29.0 1.0 HD1 C:HIS12 4.7 20.1 1.0 HA C:CYS43 4.8 38.7 1.0 C C:HIS16 4.8 18.9 1.0 HE2 C:HIS16 4.9 30.7 1.0 CA C:LYS42 4.9 37.3 1.0 N C:LYS42 4.9 39.3 1.0 HB3 C:GLN164 4.9 23.1 1.0 HG13 C:VAL37 4.9 25.8 1.0 O C:HIS16 4.9 17.9 1.0 O C:LYS42 5.0 31.6 1.0

Zinc binding site 4 out of 4 in the Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:30.4 occ:1.00 NE2 D:HIS12 2.0 17.4 1.0 ND1 D:HIS16 2.0 27.6 1.0 SG D:CYS40 2.3 33.0 1.0 SG D:CYS43 2.3 30.7 1.0 CD2 D:HIS12 2.9 15.3 1.0 CE1 D:HIS16 2.9 26.9 1.0 HB3 D:HIS16 3.0 23.3 1.0 CE1 D:HIS12 3.0 20.9 1.0 CG D:HIS16 3.0 27.6 1.0 HD2 D:HIS12 3.1 18.4 1.0 HE1 D:HIS16 3.1 32.3 1.0 HB2 D:CYS43 3.1 56.0 1.0 HB3 D:CYS40 3.2 38.1 1.0 HE1 D:HIS12 3.2 25.1 1.0 CB D:CYS40 3.3 31.8 1.0 CB D:CYS43 3.3 46.6 1.0 CB D:HIS16 3.4 19.4 1.0 HB2 D:LYS42 3.5 55.5 1.0 HA D:HIS16 3.5 22.2 1.0 HB2 D:CYS40 3.5 38.1 1.0 H D:LYS42 4.0 57.1 1.0 CG D:HIS12 4.0 17.2 1.0 ND1 D:HIS12 4.0 15.3 1.0 CA D:HIS16 4.0 18.5 1.0 HB3 D:CYS43 4.0 56.0 1.0 NE2 D:HIS16 4.0 31.6 1.0 N D:CYS43 4.1 41.3 1.0 CD2 D:HIS16 4.1 30.3 1.0 C D:LYS42 4.2 44.2 1.0 HB2 D:HIS16 4.3 23.3 1.0 H D:CYS43 4.3 49.5 1.0 CA D:CYS43 4.3 45.2 1.0 CB D:LYS42 4.4 46.3 1.0 O D:HIS12 4.4 22.1 1.0 HE21 D:GLN164 4.5 61.1 1.0 O D:LYS42 4.5 50.2 1.0 CA D:LYS42 4.6 46.5 1.0 N D:LYS42 4.7 47.6 1.0 CA D:CYS40 4.7 31.9 1.0 HA D:CYS43 4.7 54.2 1.0 HE22 D:GLN164 4.7 61.1 1.0 HB3 D:LYS42 4.7 55.5 1.0 HD1 D:HIS12 4.8 18.4 1.0 HA D:VAL37 4.8 30.0 1.0 HE2 D:HIS16 4.8 38.0 1.0 NE2 D:GLN164 4.8 50.9 1.0 C D:HIS16 4.9 20.4 1.0 HD2 D:HIS16 5.0 36.3 1.0 O D:HIS16 5.0 18.6 1.0 HG13 D:VAL37 5.0 34.2 1.0

G.Eilers, K.Gupta, A.Allen, J.Zhou, Y.Hwang, M.B.Cory, F.D.Bushman, G.Van Duyne. Influence of the Amino-Terminal Sequence on the Structure and Function of Hiv Integrase. Retrovirology V. 17 28 2020.
ISSN: ESSN 1742-4690
PubMed: 32867805
DOI: 10.1186/S12977-020-00537-X