Magnesium in PDB 8aed: Broadly Neutralizing Darpin Bnd.9 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BG505)

The structure of Broadly Neutralizing Darpin Bnd.9 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BG505), PDB code: 8aed was solved by P.Mittl, M.Gloegl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.23 / 1.17
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.795, 55.233, 58.032, 90, 98.54, 90
R / Rfree (%)	15.4 / 18.4

The binding sites of Magnesium atom in the Broadly Neutralizing Darpin Bnd.9 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BG505) (pdb code 8aed). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Broadly Neutralizing Darpin Bnd.9 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BG505), PDB code: 8aed:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Broadly Neutralizing Darpin Bnd.9 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BG505)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Broadly Neutralizing Darpin Bnd.9 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BG505) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:12.8 occ:1.00 HO7 A:CIT206 1.5 14.0 1.0 OE2 A:GLU117 2.0 18.1 1.0 O B:HOH324 2.0 16.4 1.0 O4 A:CIT206 2.1 14.7 1.0 O A:HOH395 2.1 14.7 1.0 O7 A:CIT206 2.1 11.6 1.0 O6 A:CIT206 2.2 13.2 1.0 C6 A:CIT206 2.9 12.1 1.0 C3 A:CIT206 2.9 9.0 1.0 C5 A:CIT206 3.0 13.4 1.0 CD A:GLU117 3.1 18.5 1.0 HB2 A:GLU117 3.2 15.8 1.0 HG3 A:GLU117 3.3 18.9 1.0 C4 A:CIT206 3.5 10.8 1.0 CG A:GLU117 3.5 15.7 1.0 CB A:GLU117 3.8 13.1 1.0 H A:GLU117 3.9 12.3 1.0 O B:HOH330 4.0 21.8 1.0 O5 A:CIT206 4.0 11.2 1.0 O3 A:CIT206 4.1 15.9 1.0 OE1 A:GLU117 4.1 21.1 1.0 O A:HOH482 4.2 43.5 1.0 OD2 B:ASP18 4.2 15.1 1.0 O A:HOH483 4.2 27.2 1.0 H42 A:CIT206 4.2 13.0 1.0 O2 A:CIT206 4.2 11.2 1.0 H41 A:CIT206 4.3 13.0 1.0 C2 A:CIT206 4.3 10.4 1.0 HD23 B:LEU17 4.3 14.5 1.0 HB3 A:GLU117 4.4 15.8 1.0 HG2 A:GLU117 4.5 18.9 1.0 O A:HOH492 4.5 35.7 1.0 HD22 A:LEU83 4.6 11.8 0.2 OD1 B:ASP18 4.6 18.0 1.0 C1 A:CIT206 4.7 9.2 1.0 N A:GLU117 4.7 10.2 1.0 CG B:ASP18 4.8 15.9 1.0 H22 A:CIT206 4.8 12.5 1.0 CA A:GLU117 4.9 10.6 1.0 H21 A:CIT206 4.9 12.5 1.0

Magnesium binding site 2 out of 3 in the Broadly Neutralizing Darpin Bnd.9 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BG505)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Broadly Neutralizing Darpin Bnd.9 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BG505) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:9.7 occ:1.00 HO7 B:CIT204 1.6 10.1 1.0 OE1 B:GLU117 2.0 11.0 1.0 O A:HOH353 2.1 11.0 1.0 O B:HOH398 2.1 11.0 1.0 O4 B:CIT204 2.1 8.9 1.0 O7 B:CIT204 2.1 8.4 1.0 O6 B:CIT204 2.2 9.3 1.0 C6 B:CIT204 2.8 9.8 1.0 C3 B:CIT204 2.9 7.8 1.0 C5 B:CIT204 3.1 8.8 1.0 CD B:GLU117 3.1 11.1 1.0 HB2 B:GLU117 3.1 11.8 1.0 HG3 B:GLU117 3.2 12.6 1.0 C4 B:CIT204 3.5 7.6 1.0 CG B:GLU117 3.5 10.5 1.0 CB B:GLU117 3.8 9.9 1.0 H B:GLU117 3.9 10.1 0.3 H B:GLU117 3.9 10.1 0.7 O5 B:CIT204 4.0 8.4 1.0 O A:HOH385 4.0 16.6 1.0 O3 B:CIT204 4.1 11.0 1.0 H42 B:CIT204 4.2 9.2 1.0 OE2 B:GLU117 4.2 12.3 1.0 O2 B:CIT204 4.2 9.3 1.0 OD2 A:ASP18 4.3 11.9 1.0 C2 B:CIT204 4.3 8.3 1.0 HD23 A:LEU17 4.3 14.2 1.0 H41 B:CIT204 4.3 9.2 1.0 HB3 B:GLU117 4.4 11.8 1.0 HG2 B:GLU117 4.5 12.6 1.0 N B:GLU117 4.7 8.4 1.0 C1 B:CIT204 4.7 7.4 1.0 HD13 B:LEU83 4.7 14.2 1.0 O B:HOH321 4.8 24.1 1.0 H22 B:CIT204 4.8 10.0 1.0 OD1 A:ASP18 4.8 13.6 1.0 CA B:GLU117 4.9 8.5 1.0 CG A:ASP18 4.9 12.2 1.0 H21 B:CIT204 5.0 10.0 1.0 HB3 B:LEU116 5.0 11.1 0.3

Magnesium binding site 3 out of 3 in the Broadly Neutralizing Darpin Bnd.9 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BG505)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Broadly Neutralizing Darpin Bnd.9 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BG505) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:12.6 occ:1.00 OD1 C:ASP328 2.0 15.5 1.0 O C:HOH505 2.0 14.2 1.0 OD1 D:ASP328 2.0 13.0 1.0 O C:HOH507 2.0 18.5 1.0 O D:HOH405 2.1 14.2 1.0 O D:HOH404 2.1 18.3 1.0 CG C:ASP328 3.0 16.1 1.0 CG D:ASP328 3.0 14.4 1.0 OD2 C:ASP328 3.4 17.5 1.0 OD2 D:ASP328 3.4 15.9 1.0 OD1 D:ASP324 4.0 17.3 1.0 OD1 C:ASP324 4.0 15.9 0.4 O D:GLY327 4.1 13.4 1.0 O C:HOH501 4.1 37.1 1.0 O D:HOH419 4.1 38.4 1.0 HA C:ASP328 4.1 19.1 1.0 O D:ASP324 4.2 11.7 1.0 HA D:ASP328 4.2 18.3 1.0 O C:ASP324 4.2 9.5 0.4 C D:GLY327 4.2 12.6 1.0 HA3 D:GLY327 4.3 13.6 1.0 O C:ASP324 4.3 9.5 0.6 CB D:ASP328 4.3 15.1 1.0 CB C:ASP328 4.3 15.8 1.0 O C:GLY327 4.3 12.9 1.0 C C:GLY327 4.4 12.8 1.0 HA3 C:GLY327 4.4 12.1 1.0 O D:HOH420 4.4 28.3 1.0 N C:ASP328 4.4 13.8 1.0 N D:ASP328 4.5 13.1 1.0 CA C:ASP328 4.5 15.9 1.0 O D:HOH402 4.6 37.2 1.0 CA D:ASP328 4.6 15.2 1.0 HH11 D:ARG308 4.7 47.2 1.0 H C:ASP328 4.8 16.6 1.0 CA D:GLY327 4.8 11.3 1.0 HB2 D:ASP328 4.9 18.2 1.0 HB3 C:ASP328 4.9 19.0 1.0 HB2 C:ASP328 4.9 19.0 1.0 HB3 D:ASP328 4.9 18.2 1.0 HA D:ASP324 4.9 12.6 1.0 CG D:ASP324 4.9 15.9 1.0 CA C:GLY327 4.9 10.1 1.0 H D:ASP328 4.9 15.8 1.0 CG C:ASP324 5.0 14.4 0.4 HA C:ASP324 5.0 12.3 0.4 HA C:ASP324 5.0 12.1 0.6

M.Gloegl, P.R.Mittl. Broadly Neutralizing Darpin Bnd.8 in Complex with the Hiv-1 Envelope Variable Loop 3 Peptide V3 (BF520) To Be Published.