Yttrium in PDB 2r3c: Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1

The structure of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1, PDB code: 2r3c was solved by A.P.Vandemark, B.Welch, A.Heroux, C.P.Hill, M.S.Kay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.73
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	46.843, 46.843, 137.079, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 23

The structure of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Yttrium atom in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 (pdb code 2r3c). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 5 binding sites of Yttrium where determined in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1, PDB code: 2r3c:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5;

Yttrium binding site 1 out of 5 in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Y501 b:28.4 occ:1.00 O C:HOH113 2.3 26.6 1.0 OE2 C:DGL9 2.4 27.7 1.0 OE2 A:GLU10 2.4 17.9 1.0 OE1 A:GLU10 2.5 22.6 1.0 O C:HOH107 2.5 28.5 1.0 OE1 C:DGL9 2.5 26.0 1.0 O A:HOH633 2.5 30.2 1.0 OD2 A:ASP7 2.8 29.9 1.0 CD A:GLU10 2.8 19.0 1.0 CD C:DGL9 2.8 26.0 1.0 CG A:ASP7 3.9 30.9 1.0 CG C:DGL9 4.3 26.7 1.0 CG A:GLU10 4.3 18.9 1.0 O A:HOH637 4.6 30.7 1.0 OD1 A:ASP7 4.6 33.6 1.0 O C:HOH119 4.7 29.6 1.0 O A:HOH616 4.7 42.8 1.0 CA A:ASP7 4.8 26.6 1.0 CB A:ASP7 4.9 27.9 1.0

Yttrium binding site 2 out of 5 in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Y502 b:22.6 occ:0.33 OE1 A:GLN16 3.4 25.2 1.0 CG A:GLN16 3.8 21.7 1.0 CD A:GLN16 4.0 22.2 1.0 CD1 A:ILE19 4.2 19.6 1.0 CB A:GLN16 4.4 19.2 1.0 CA A:GLN16 4.5 19.1 1.0

Yttrium binding site 3 out of 5 in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Y101 b:35.3 occ:1.00 OD1 B:ASP7 2.1 42.2 1.0 OE2 D:DGL9 2.3 23.5 1.0 O B:HOH222 2.3 29.6 1.0 OE1 D:DGL9 2.4 20.6 1.0 OE1 B:GLU10 2.4 36.3 1.0 O B:HOH206 2.5 27.3 1.0 CD D:DGL9 2.7 21.6 1.0 O D:HOH112 2.7 25.8 1.0 OE2 B:GLU10 2.7 36.1 1.0 CD B:GLU10 2.9 35.9 1.0 CG B:ASP7 3.3 44.0 1.0 OD2 B:ASP7 3.9 45.7 1.0 CG D:DGL9 4.2 22.4 1.0 O B:HOH275 4.3 41.4 1.0 O B:HOH218 4.4 28.3 1.0 CB B:ASP7 4.4 43.2 1.0 CG B:GLU10 4.4 32.3 1.0 CA B:ASP7 4.5 42.4 1.0 O D:HOH116 4.5 19.6 1.0 O B:HOH235 4.6 43.0 1.0

Yttrium binding site 4 out of 5 in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Y102 b:25.6 occ:0.33 NE2 B:GLN16 3.2 22.7 1.0 CG B:GLN16 3.6 22.2 1.0 CD B:GLN16 3.9 22.7 1.0 CB B:GLN16 4.1 20.3 1.0 CD1 B:ILE19 4.4 19.4 1.0 CA B:GLN16 4.4 20.2 1.0

Yttrium binding site 5 out of 5 in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Y103 b:32.4 occ:0.33 OG1 B:THR33 2.8 21.8 1.0 CB B:THR33 3.3 20.1 1.0 CD1 B:LEU30 3.6 20.5 1.0 CG2 B:THR33 3.7 20.2 1.0 CA B:THR33 4.8 20.4 1.0 O B:LEU30 5.0 23.4 1.0

B.D.Welch, A.P.Vandemark, A.Heroux, C.P.Hill, M.S.Kay. Potent D-Peptide Inhibitors of Hiv-1 Entry Proc.Natl.Acad.Sci.Usa V. 104 16828 2007.
ISSN: ISSN 0027-8424
PubMed: 17942675
DOI: 10.1073/PNAS.0708109104