Potassium 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:

Zinc

(Zn)

4 atoms

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of Hiv-1 Integrase with Native Amino-Terminal Sequence, PDB code: 6vrg:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium 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 Potassium with other atoms in the K 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:K302 b:46.7 occ:1.00 O A:CYS43 2.7 46.6 1.0 O A:ALA38 2.8 36.6 1.0 O A:CYS40 2.8 26.4 1.0 HA A:ALA38 2.9 25.7 1.0 HA A:GLN44 2.9 51.3 1.0 O A:VAL37 3.4 25.3 1.0 C A:ALA38 3.4 26.2 1.0 C A:CYS43 3.6 36.8 1.0 CA A:ALA38 3.6 21.4 1.0 HB3 A:GLN44 3.7 63.7 1.0 CA A:GLN44 3.8 42.7 1.0 O A:HOH462 3.8 44.5 1.0 C A:CYS40 4.0 26.7 1.0 N A:GLN44 4.1 32.6 1.0 CB A:GLN44 4.2 53.1 1.0 H A:CYS43 4.3 34.6 1.0 C A:VAL37 4.3 22.1 1.0 H A:CYS40 4.3 31.4 1.0 HA A:ASP41 4.4 38.6 1.0 N A:CYS40 4.4 26.2 1.0 N A:ALA38 4.4 25.3 1.0 HB2 A:GLN44 4.4 63.7 1.0 H A:LEU45 4.5 59.4 1.0 N A:SER39 4.6 22.4 1.0 HB2 A:CYS43 4.6 32.5 1.0 HB1 A:ALA38 4.6 25.2 1.0 HB3 A:CYS40 4.6 38.5 1.0 CA A:CYS43 4.7 33.0 1.0 CA A:CYS40 4.7 29.5 1.0 CB A:ALA38 4.7 21.0 1.0 C A:SER39 4.8 30.1 1.0 N A:CYS43 4.8 28.8 1.0 HG12 A:VAL37 4.8 29.5 1.0 H A:GLN44 4.8 39.1 1.0 N A:ASP41 4.9 26.3 1.0 C A:GLN44 5.0 45.3 1.0

Potassium 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 Potassium with other atoms in the K 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:K302 b:51.0 occ:1.00 O B:CYS43 2.6 39.4 1.0 O B:CYS40 2.7 32.7 1.0 O B:ALA38 2.9 22.4 1.0 HA B:ALA38 3.1 33.6 1.0 O B:VAL37 3.5 24.9 1.0 C B:ALA38 3.6 23.1 1.0 HA B:GLN44 3.6 56.1 1.0 O B:HOH429 3.7 32.3 1.0 C B:CYS43 3.8 32.4 1.0 CA B:ALA38 3.8 28.0 1.0 C B:CYS40 3.9 22.7 1.0 HG2 B:GLN44 3.9 75.8 1.0 H B:CYS43 4.1 36.4 1.0 O B:HOH432 4.2 30.5 1.0 HA B:ASP41 4.3 40.4 1.0 H B:CYS40 4.4 30.1 1.0 N B:CYS40 4.4 25.1 1.0 C B:VAL37 4.4 21.2 1.0 CA B:GLN44 4.4 46.7 1.0 N B:GLN44 4.6 38.4 1.0 N B:ALA38 4.6 28.9 1.0 HG3 B:GLN44 4.6 75.8 1.0 N B:SER39 4.6 21.7 1.0 CG B:GLN44 4.7 63.2 1.0 HB3 B:CYS40 4.7 28.0 1.0 C B:SER39 4.7 25.3 1.0 N B:CYS43 4.7 30.3 1.0 CA B:CYS40 4.7 24.8 1.0 HB1 B:ALA38 4.8 34.4 1.0 HB2 B:CYS43 4.8 38.4 1.0 CA B:CYS43 4.8 32.0 1.0 N B:ASP41 4.8 22.1 1.0 CA B:ASP41 4.9 33.7 1.0 CB B:ALA38 4.9 28.6 1.0

Potassium 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 Potassium with other atoms in the K 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:K302 b:60.2 occ:1.00 O C:ALA38 2.7 29.1 1.0 O C:CYS43 2.7 47.9 1.0 O C:HOH442 2.8 38.9 1.0 O C:CYS40 2.8 32.6 1.0 HA C:ALA38 3.2 29.6 1.0 HA C:GLN44 3.3 53.2 1.0 O C:HOH436 3.4 42.8 1.0 C C:ALA38 3.5 28.5 1.0 O C:VAL37 3.6 23.6 1.0 C C:CYS43 3.7 37.4 1.0 CA C:ALA38 3.8 24.7 1.0 C C:CYS40 4.0 31.8 1.0 CA C:GLN44 4.1 44.4 1.0 HB3 C:GLN44 4.1 59.5 1.0 H C:CYS43 4.1 42.5 1.0 N C:GLN44 4.3 46.3 1.0 HA C:ASP41 4.3 48.4 1.0 C C:VAL37 4.5 24.3 1.0 C C:SER39 4.5 36.0 1.0 N C:CYS40 4.6 35.4 1.0 N C:SER39 4.6 22.7 1.0 CB C:GLN44 4.6 49.6 1.0 O C:SER39 4.7 45.4 1.0 N C:ALA38 4.7 26.9 1.0 HB2 C:CYS43 4.7 33.4 1.0 H C:CYS40 4.7 42.5 1.0 HB3 C:CYS40 4.8 29.1 1.0 N C:CYS43 4.8 35.4 1.0 CA C:CYS43 4.8 32.2 1.0 HB1 C:ALA38 4.8 23.3 1.0 H C:LEU45 4.8 49.6 1.0 HB2 C:GLN44 4.8 59.5 1.0 CA C:CYS40 4.9 33.4 1.0 N C:ASP41 5.0 27.7 1.0 CB C:ALA38 5.0 19.4 1.0

Potassium 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 Potassium with other atoms in the K 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:K302 b:48.8 occ:1.00 O D:CYS40 2.6 37.5 1.0 O D:ALA38 2.7 33.6 1.0 O D:CYS43 2.8 51.9 1.0 HA D:ALA38 2.8 41.6 1.0 O D:HOH436 3.0 38.3 1.0 O D:VAL37 3.2 27.1 1.0 C D:ALA38 3.3 29.6 1.0 CA D:ALA38 3.5 34.7 1.0 HA D:GLN44 3.6 61.7 1.0 O D:HOH402 3.7 41.4 1.0 C D:CYS43 3.7 42.4 1.0 C D:CYS40 3.8 38.9 1.0 H D:CYS43 3.9 49.5 1.0 C D:VAL37 4.1 28.1 1.0 HA D:ASP41 4.1 52.3 1.0 N D:ALA38 4.3 33.9 1.0 H D:CYS40 4.3 39.2 1.0 N D:CYS40 4.3 32.6 1.0 CA D:GLN44 4.4 51.4 1.0 HG2 D:GLN44 4.4 76.9 1.0 N D:GLN44 4.5 48.3 1.0 N D:SER39 4.5 29.1 1.0 HB2 D:CYS43 4.5 56.0 1.0 HB3 D:CYS40 4.5 38.1 1.0 C D:SER39 4.6 35.5 1.0 CA D:CYS40 4.6 31.9 1.0 N D:CYS43 4.6 41.3 1.0 HB1 D:ALA38 4.6 41.7 1.0 HG12 D:VAL37 4.7 34.2 1.0 CA D:CYS43 4.7 45.2 1.0 CB D:ALA38 4.7 34.8 1.0 N D:ASP41 4.7 41.1 1.0 CA D:ASP41 4.8 43.6 1.0 HG3 D:GLN44 4.9 76.9 1.0 O D:SER39 5.0 45.5 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