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

Protein crystallography data

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

Magnesium Binding Sites:

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 8aed

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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 8aed

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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 8aed

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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

Reference:

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.
Page generated: Thu Oct 3 18:06:04 2024

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