Magnesium in PDB 6bmf: VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P

The structure of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P also contains other interesting chemical elements:

Fluorine

(F)

9 atoms

The binding sites of Magnesium atom in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P (pdb code 6bmf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P, PDB code: 6bmf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:37.8 occ:1.00 F1 A:BEF502 2.0 37.8 1.0 O2B A:ADP501 2.0 37.8 1.0 OG A:SER180 2.0 16.1 1.0 CB A:SER180 3.1 16.1 1.0 BE A:BEF502 3.3 37.8 1.0 PB A:ADP501 3.3 37.8 1.0 O3B A:ADP501 3.5 37.8 1.0 N A:SER180 4.0 16.1 1.0 CA A:SER180 4.1 16.1 1.0 O1B A:ADP501 4.2 37.8 1.0 O2A A:ADP501 4.2 37.8 1.0 F3 A:BEF502 4.2 37.8 1.0 O1A A:ADP501 4.3 37.8 1.0 F2 A:BEF502 4.3 37.8 1.0 O3A A:ADP501 4.4 37.8 1.0 PA A:ADP501 4.6 37.8 1.0 NH2 B:ARG289 4.8 27.4 1.0 OD1 B:ASN261 4.9 50.4 1.0 ND2 B:ASN261 5.0 50.4 1.0 OD2 A:ASP232 5.0 16.1 1.0

Magnesium binding site 2 out of 4 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:19.7 occ:1.00 OG B:SER180 2.0 20.8 1.0 F1 B:BEF502 2.0 19.7 1.0 O2B B:ADP501 2.0 19.7 1.0 CB B:SER180 3.1 20.8 1.0 BE B:BEF502 3.3 19.7 1.0 PB B:ADP501 3.3 19.7 1.0 O1B B:ADP501 3.5 19.7 1.0 F3 B:BEF502 3.8 19.7 1.0 O1A B:ADP501 4.1 19.7 1.0 O3B B:ADP501 4.1 19.7 1.0 N B:SER180 4.2 20.8 1.0 CA B:SER180 4.3 20.8 1.0 OD2 B:ASP232 4.3 30.7 1.0 O3A B:ADP501 4.4 19.7 1.0 F2 B:BEF502 4.5 19.7 1.0 NH2 C:ARG289 4.5 19.1 1.0 O2A B:ADP501 4.6 19.7 1.0 OD1 B:ASP232 4.7 30.7 1.0 PA B:ADP501 4.7 19.7 1.0 OD1 C:ASN261 4.8 28.2 1.0 CG B:ASP232 4.9 30.7 1.0 ND2 C:ASN261 5.0 28.2 1.0

Magnesium binding site 3 out of 4 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:17.2 occ:1.00 F1 C:BEF502 2.0 17.2 1.0 OG C:SER180 2.0 20.1 1.0 O2B C:ADP501 2.0 17.2 1.0 CB C:SER180 3.1 20.1 1.0 BE C:BEF502 3.2 17.2 1.0 PB C:ADP501 3.3 17.2 1.0 O1B C:ADP501 3.5 17.2 1.0 O3B C:ADP501 4.0 17.2 1.0 F3 C:BEF502 4.0 17.2 1.0 O1A C:ADP501 4.2 17.2 1.0 N C:SER180 4.2 20.1 1.0 CA C:SER180 4.3 20.1 1.0 OD2 C:ASP232 4.3 24.3 1.0 F2 C:BEF502 4.4 17.2 1.0 NH2 D:ARG289 4.5 18.8 1.0 OD1 D:ASN261 4.5 24.3 1.0 O3A C:ADP501 4.5 17.2 1.0 OD1 C:ASP232 4.6 24.3 1.0 ND2 D:ASN261 4.8 24.3 1.0 PA C:ADP501 4.9 17.2 1.0 CG C:ASP232 4.9 24.3 1.0

Magnesium binding site 4 out of 4 in the VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of VPS4P-VTA1P Complex with Peptide Binding to the Central Pore of VPS4P within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:0.1 occ:1.00 OG D:SER180 1.9 24.9 1.0 O2B D:ADP501 2.1 53.3 1.0 CB D:SER180 2.8 24.9 1.0 PB D:ADP501 3.6 53.3 1.0 OD2 D:ASP232 3.8 23.1 1.0 O2A D:ADP501 4.0 53.3 1.0 O3A D:ADP501 4.0 53.3 1.0 CA D:SER180 4.1 24.9 1.0 N D:SER180 4.2 24.9 1.0 O1B D:ADP501 4.4 53.3 1.0 NH2 E:ARG289 4.5 20.0 1.0 OD1 E:ASN261 4.5 18.7 1.0 OD1 D:ASP232 4.5 23.1 1.0 O3B D:ADP501 4.6 53.3 1.0 CG D:ASP232 4.6 23.1 1.0 PA D:ADP501 4.6 53.3 1.0 ND2 E:ASN261 4.9 18.7 1.0

H.Han, N.Monroe, W.I.Sundquist, P.S.Shen, C.P.Hill. The Aaa Atpase VPS4 Binds Escrt-III Substrates Through A Repeating Array of Dipeptide-Binding Pockets. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 29165244
DOI: 10.7554/ELIFE.31324