Arsenic in PDB 5krt: Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor

The structure of Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor, PDB code: 5krt was solved by D.Patel, J.D.Bauman, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.24 / 1.65
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.069, 72.069, 66.348, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 19.5

The structure of Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Arsenic atom in the Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor (pdb code 5krt). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor, PDB code: 5krt:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in the Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:As65 b:25.9 occ:1.00 AS A:CAF65 0.0 25.9 1.0 O1 A:CAF65 1.6 31.9 1.0 CE2 A:CAF65 2.0 30.4 1.0 CE1 A:CAF65 2.0 51.0 1.0 SG A:CAF65 2.2 20.4 1.0 HE23 A:CAF65 2.5 36.4 1.0 HE21 A:CAF65 2.5 36.4 1.0 HE22 A:CAF65 2.5 36.4 1.0 HE13 A:CAF65 2.5 61.2 1.0 HE11 A:CAF65 2.5 61.2 1.0 HE12 A:CAF65 2.5 61.2 1.0 HB2 A:CAF65 3.0 24.5 1.0 CB A:CAF65 3.2 20.4 1.0 HD21 A:ASN120 3.4 23.9 1.0 N A:CAF65 3.5 19.1 1.0 OD1 A:ASN120 3.5 28.5 1.0 ND2 A:ASN120 3.6 19.9 1.0 CG A:ASN120 3.7 24.6 1.0 HG2 A:GLU92 3.7 39.6 1.0 H A:CAF65 3.8 22.9 1.0 CA A:CAF65 3.9 18.7 1.0 HB3 A:CAF65 4.0 24.5 1.0 HD22 A:ASN120 4.0 23.9 1.0 HA A:ASP64 4.1 21.4 1.0 C A:ASP64 4.1 18.9 1.0 HG A:LEU74 4.1 37.6 1.0 CD A:GLU92 4.2 39.1 1.0 OE1 A:GLU92 4.2 50.5 1.0 HG1 A:THR97 4.2 25.5 1.0 HA A:CAF65 4.2 22.4 1.0 HB3 A:ASN120 4.3 28.8 1.0 CG A:GLU92 4.4 33.0 1.0 OG1 A:THR97 4.5 21.3 1.0 OE2 A:GLU92 4.5 38.4 1.0 CA A:ASP64 4.6 17.8 1.0 CB A:ASN120 4.6 24.0 1.0 O A:ASP64 4.8 21.4 1.0 HB3 A:GLU92 4.8 41.0 1.0 HD12 A:LEU74 4.8 38.0 1.0 O A:HOH450 4.9 35.8 1.0 O A:HOH411 5.0 32.3 1.0

Arsenic binding site 2 out of 2 in the Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:As130 b:32.7 occ:1.00 AS A:CAF130 0.0 32.7 1.0 O1 A:CAF130 1.5 20.3 1.0 CE1 A:CAF130 1.9 39.3 1.0 CE2 A:CAF130 2.0 51.2 1.0 SG A:CAF130 2.2 16.9 1.0 HE11 A:CAF130 2.4 47.1 1.0 HE13 A:CAF130 2.4 47.1 1.0 HE12 A:CAF130 2.4 47.1 1.0 HE23 A:CAF130 2.5 61.4 1.0 HE22 A:CAF130 2.5 61.4 1.0 HE21 A:CAF130 2.5 61.4 1.0 HB2 A:CAF130 3.1 22.4 1.0 CB A:CAF130 3.1 18.7 1.0 HB3 A:CAF130 3.2 22.4 1.0 HG21 A:VAL113 3.4 50.3 1.0 HG22 A:VAL113 3.6 50.3 1.0 HG22 A:ILE135 3.7 22.3 1.0 CG2 A:VAL113 3.8 41.9 1.0 HG23 A:VAL113 3.8 50.3 1.0 HG12 A:VAL126 4.0 21.6 1.0 HG21 A:ILE135 4.2 22.3 1.0 HB A:ILE135 4.2 21.7 1.0 CG2 A:ILE135 4.3 18.6 1.0 O A:ILE135 4.4 23.5 1.0 HD13 A:LEU101 4.4 24.6 1.0 HA A:CAF130 4.4 22.8 1.0 HB3 A:PHE121 4.4 27.7 1.0 HB2 A:GLN137 4.4 51.2 1.0 HA A:GLN137 4.5 38.9 1.0 CA A:CAF130 4.6 19.0 1.0 HG13 A:VAL126 4.6 21.6 1.0 CG1 A:VAL126 4.7 18.0 1.0 HA A:LYS127 4.7 20.6 1.0 C A:LYS136 4.8 27.6 1.0 N A:GLN137 4.8 28.9 1.0 O A:LYS136 4.8 26.9 1.0 HG11 A:VAL126 4.8 21.6 1.0 CB A:ILE135 4.8 18.1 1.0 HA A:LYS136 4.8 32.6 1.0 C A:ILE135 4.9 22.5 1.0 H A:CAF130 4.9 18.9 1.0 HD11 A:LEU101 4.9 24.6 1.0 CD2 A:PHE121 4.9 28.9 1.0 OE1 A:GLN137 4.9 48.5 1.0 O A:VAL126 5.0 15.7 1.0 CG A:PHE121 5.0 22.6 1.0 H A:GLN137 5.0 34.7 1.0 CA A:GLN137 5.0 32.4 1.0

D.Patel, J.Antwi, P.C.Koneru, E.Serrao, S.Forli, J.J.Kessl, L.Feng, N.Deng, R.M.Levy, J.R.Fuchs, A.J.Olson, A.N.Engelman, J.D.Bauman, M.Kvaratskhelia, E.Arnold. A New Class of Allosteric Hiv-1 Integrase Inhibitors Identified By Crystallographic Fragment Screening of the Catalytic Core Domain. J.Biol.Chem. V. 291 23569 2016.
ISSN: ESSN 1083-351X
PubMed: 27645997
DOI: 10.1074/JBC.M116.753384