Atomistry » Magnesium » PDB 8ae7-8aq1 » 8aed
Atomistry »
  Magnesium »
    PDB 8ae7-8aq1 »
      8aed »

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

Go back to Magnesium Binding Sites List in 8aed
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

Go back to Magnesium Binding Sites List in 8aed
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

Go back to Magnesium Binding Sites List in 8aed
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

Last articles

Sr in 1SFC
Sr in 1OQ7
Sr in 1U3E
Sr in 1VC0
Sr in 1F1T
Sr in 1J8G
Sr in 1NVY
Sr in 1TJM
Sr in 1NUV
Sr in 1M6G
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy