Magnesium in PDB 6ndy: VPS4 with Cyclic Peptide Bound in the Central Pore

The structure of VPS4 with Cyclic Peptide Bound in the Central Pore also contains other interesting chemical elements:

Fluorine

(F)

9 atoms

The binding sites of Magnesium atom in the VPS4 with Cyclic Peptide Bound in the Central Pore (pdb code 6ndy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the VPS4 with Cyclic Peptide Bound in the Central Pore, PDB code: 6ndy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the VPS4 with Cyclic Peptide Bound in the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of VPS4 with Cyclic Peptide Bound in the Central Pore within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:62.5 occ:1.00 OG A:SER180 2.0 68.3 1.0 O2B A:ADP501 2.0 62.5 1.0 F1 A:BEF502 2.0 62.5 1.0 CB A:SER180 3.0 68.3 1.0 PB A:ADP501 3.1 62.5 1.0 BE A:BEF502 3.2 62.5 1.0 O3B A:ADP501 3.4 62.5 1.0 O3A A:ADP501 3.8 62.5 1.0 OD2 A:ASP232 3.8 67.1 1.0 N A:SER180 3.8 68.3 1.0 CA A:SER180 4.0 68.3 1.0 F3 A:BEF502 4.0 62.5 1.0 OD1 A:ASP232 4.1 67.1 1.0 F2 A:BEF502 4.4 62.5 1.0 CG A:ASP232 4.4 67.1 1.0 O1B A:ADP501 4.4 62.5 1.0 NH2 B:ARG289 4.6 45.1 1.0 OE2 A:GLU233 4.8 69.4 1.0 O2A A:ADP501 4.8 62.5 1.0 CB A:LYS179 4.9 59.8 1.0 C A:LYS179 4.9 59.8 1.0 NH2 B:ARG288 5.0 49.2 1.0 PA A:ADP501 5.0 62.5 1.0

Magnesium binding site 2 out of 4 in the VPS4 with Cyclic Peptide Bound in the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of VPS4 with Cyclic Peptide Bound in the Central Pore within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:27.8 occ:1.00 OG B:SER180 2.0 35.9 1.0 F1 B:BEF502 2.0 27.8 1.0 O1B B:ADP501 2.0 27.8 1.0 O2B B:ADP501 2.5 27.8 1.0 PB B:ADP501 2.6 27.8 1.0 BE B:BEF502 3.2 27.8 1.0 O3B B:ADP501 3.3 27.8 1.0 CB B:SER180 3.4 35.9 1.0 N B:SER180 3.7 35.9 1.0 OD2 B:ASP232 4.1 35.8 1.0 CA B:SER180 4.1 35.9 1.0 O3A B:ADP501 4.1 27.8 1.0 OD1 B:ASP232 4.1 35.8 1.0 F3 B:BEF502 4.2 27.8 1.0 F2 B:BEF502 4.2 27.8 1.0 CB B:LYS179 4.5 31.4 1.0 CG B:ASP232 4.5 35.8 1.0 C B:LYS179 4.6 31.4 1.0 NH2 C:ARG288 4.7 26.7 1.0 NH2 C:ARG289 4.7 23.4 1.0 CE B:LYS179 4.8 31.4 1.0 OE2 B:GLU233 4.8 38.2 1.0 CB B:ALA275 4.9 34.1 1.0 CA B:LYS179 5.0 31.4 1.0

Magnesium binding site 3 out of 4 in the VPS4 with Cyclic Peptide Bound in the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of VPS4 with Cyclic Peptide Bound in the Central Pore within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:39.5 occ:1.00 OG C:SER180 2.0 36.2 1.0 F1 C:BEF502 2.0 39.5 1.0 O1B C:ADP501 2.0 39.5 1.0 O2B C:ADP501 2.5 39.5 1.0 PB C:ADP501 2.6 39.5 1.0 CB C:SER180 3.2 36.2 1.0 BE C:BEF502 3.2 39.5 1.0 O3B C:ADP501 3.3 39.5 1.0 N C:SER180 3.6 36.2 1.0 CA C:SER180 4.0 36.2 1.0 O3A C:ADP501 4.1 39.5 1.0 F2 C:BEF502 4.2 39.5 1.0 OD2 C:ASP232 4.2 41.1 1.0 F3 C:BEF502 4.2 39.5 1.0 OD1 C:ASP232 4.3 41.1 1.0 CB C:LYS179 4.5 32.5 1.0 C C:LYS179 4.6 32.5 1.0 CG C:ASP232 4.7 41.1 1.0 OE2 C:GLU233 4.9 42.8 1.0 CE C:LYS179 4.9 32.5 1.0 CA C:LYS179 5.0 32.5 1.0

Magnesium binding site 4 out of 4 in the VPS4 with Cyclic Peptide Bound in the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of VPS4 with Cyclic Peptide Bound in the Central Pore within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:43.8 occ:1.00 O1B D:ADP501 2.1 46.8 1.0 OG D:SER180 2.1 45.8 1.0 PB D:ADP501 3.3 46.8 1.0 CB D:SER180 3.4 45.8 1.0 O3B D:ADP501 3.6 46.8 1.0 OD1 D:ASP232 3.8 40.6 1.0 OD2 D:ASP232 3.9 40.6 1.0 O1A D:ADP501 3.9 46.8 1.0 N D:SER180 4.1 45.8 1.0 O2B D:ADP501 4.3 46.8 1.0 CG D:ASP232 4.3 40.6 1.0 CA D:SER180 4.3 45.8 1.0 O3A D:ADP501 4.3 46.8 1.0 PA D:ADP501 4.4 46.8 1.0 O2A D:ADP501 4.4 46.8 1.0 NH2 E:ARG289 4.4 63.0 1.0 OE1 D:GLU233 4.6 47.4 1.0

H.Han, J.M.Fulcher, V.P.Dandey, J.H.Iwasa, W.I.Sundquist, M.S.Kay, P.S.Shen, C.P.Hill. Structure of VPS4 with Circular Peptides and Implications For Translocation of Two Polypeptide Chains By Aaa+ Atpases. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31184588
DOI: 10.7554/ELIFE.44071