Magnesium in PDB 6chs: CDC48-NPL4 Complex in the Presence of Atp-Gamma-S

The structure of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S (pdb code 6chs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S, PDB code: 6chs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg903 b:17.7 occ:1.00 O3G H:AGS901 2.1 8.2 1.0 O2B H:AGS901 2.1 7.2 1.0 OG1 H:THR268 2.5 0.8 1.0 O3A H:AGS901 2.7 4.6 1.0 PB H:AGS901 2.8 6.9 1.0 PG H:AGS901 3.1 7.3 1.0 OD2 H:ASP320 3.1 0.9 1.0 O3B H:AGS901 3.3 3.8 1.0 S1G H:AGS901 3.6 21.3 1.0 OD1 H:ASP320 3.6 0.9 1.0 CG H:ASP320 3.8 0.9 1.0 CB H:THR268 3.8 0.8 1.0 PA H:AGS901 4.1 5.8 1.0 O1B H:AGS901 4.2 2.9 1.0 O2G H:AGS901 4.4 7.1 1.0 O1A H:AGS901 4.5 1.4 1.0 CG2 H:THR268 4.6 0.8 1.0 N H:THR268 4.6 0.8 1.0 O5' H:AGS901 4.8 1.9 1.0 CA H:THR268 4.8 0.8 1.0

Magnesium binding site 2 out of 12 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg904 b:17.7 occ:1.00 O2A H:AGS902 2.0 49.5 1.0 O2G H:AGS902 2.1 45.9 1.0 O2B H:AGS902 2.1 37.5 1.0 OG1 H:THR542 2.2 0.8 1.0 PA H:AGS902 2.9 60.8 1.0 O1A H:AGS902 3.1 60.0 1.0 PB H:AGS902 3.2 36.2 1.0 PG H:AGS902 3.4 39.6 1.0 O3A H:AGS902 3.5 40.1 1.0 CB H:THR542 3.6 0.8 1.0 O3B H:AGS902 3.7 38.5 1.0 OD1 H:ASP594 3.8 0.9 1.0 OD2 H:ASP594 3.8 0.9 1.0 CG H:ASP594 4.3 0.9 1.0 O5' H:AGS902 4.3 53.7 1.0 N H:THR542 4.3 0.8 1.0 CG2 H:THR542 4.4 0.8 1.0 CA H:THR542 4.5 0.8 1.0 S1G H:AGS902 4.5 22.8 1.0 O3G H:AGS902 4.5 40.2 1.0 O1B H:AGS902 4.5 35.2 1.0 C5' H:AGS902 4.8 51.7 1.0

Magnesium binding site 3 out of 12 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg903 b:17.7 occ:1.00 O3G I:AGS901 2.1 8.2 1.0 O2B I:AGS901 2.1 7.2 1.0 OG1 I:THR268 2.5 0.8 1.0 PB I:AGS901 2.9 6.9 1.0 O3A I:AGS901 2.9 4.6 1.0 OD2 I:ASP320 3.0 0.9 1.0 PG I:AGS901 3.0 7.3 1.0 OD1 I:ASP320 3.4 0.9 1.0 S1G I:AGS901 3.4 21.3 1.0 O3B I:AGS901 3.4 3.8 1.0 CG I:ASP320 3.6 0.9 1.0 CB I:THR268 3.8 0.8 1.0 PA I:AGS901 4.3 5.8 1.0 O1B I:AGS901 4.3 2.9 1.0 O2G I:AGS901 4.4 7.1 1.0 O1A I:AGS901 4.5 1.4 1.0 N I:THR268 4.6 0.8 1.0 CG2 I:THR268 4.7 0.8 1.0 CA I:THR268 4.8 0.8 1.0

Magnesium binding site 4 out of 12 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg904 b:17.7 occ:1.00 O2A I:AGS902 2.0 49.5 1.0 O2B I:AGS902 2.1 37.5 1.0 O2G I:AGS902 2.1 45.9 1.0 OG1 I:THR542 2.1 0.8 1.0 PA I:AGS902 2.7 60.8 1.0 O1A I:AGS902 2.8 60.0 1.0 PB I:AGS902 3.0 36.2 1.0 O3A I:AGS902 3.2 40.1 1.0 PG I:AGS902 3.4 39.6 1.0 CB I:THR542 3.5 0.8 1.0 O3B I:AGS902 3.6 38.5 1.0 OD1 I:ASP594 3.8 0.9 1.0 N I:THR542 3.9 0.8 1.0 OD2 I:ASP594 4.0 0.9 1.0 O5' I:AGS902 4.2 53.7 1.0 CA I:THR542 4.2 0.8 1.0 CG I:ASP594 4.3 0.9 1.0 O1B I:AGS902 4.4 35.2 1.0 O3G I:AGS902 4.5 40.2 1.0 CG2 I:THR542 4.5 0.8 1.0 S1G I:AGS902 4.7 22.8 1.0 C I:LYS541 4.9 0.8 1.0 N I:LYS541 5.0 0.8 1.0

Magnesium binding site 5 out of 12 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg903 b:17.7 occ:1.00 O3G J:AGS901 2.1 8.2 1.0 O2B J:AGS901 2.1 7.2 1.0 OG1 J:THR268 2.4 0.8 1.0 O3A J:AGS901 2.6 4.6 1.0 PB J:AGS901 2.7 6.9 1.0 OD2 J:ASP320 3.1 0.9 1.0 PG J:AGS901 3.2 7.3 1.0 O3B J:AGS901 3.4 3.8 1.0 OD1 J:ASP320 3.5 0.9 1.0 CB J:THR268 3.6 0.8 1.0 CG J:ASP320 3.7 0.9 1.0 S1G J:AGS901 3.8 21.3 1.0 PA J:AGS901 4.0 5.8 1.0 O1B J:AGS901 4.1 2.9 1.0 N J:THR268 4.3 0.8 1.0 O2A J:AGS901 4.4 1.4 1.0 O2G J:AGS901 4.5 7.1 1.0 CG2 J:THR268 4.5 0.8 1.0 CA J:THR268 4.6 0.8 1.0 O5' J:AGS901 4.7 1.9 1.0

Magnesium binding site 6 out of 12 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg904 b:17.7 occ:1.00 O1A J:AGS902 2.1 49.5 1.0 O2B J:AGS902 2.1 37.5 1.0 O2G J:AGS902 2.1 45.9 1.0 OG1 J:THR542 2.1 0.8 1.0 PA J:AGS902 2.7 60.8 1.0 O2A J:AGS902 2.8 60.0 1.0 PB J:AGS902 3.0 36.2 1.0 O3A J:AGS902 3.3 40.1 1.0 PG J:AGS902 3.4 39.6 1.0 CB J:THR542 3.5 0.8 1.0 O3B J:AGS902 3.6 38.5 1.0 OD1 J:ASP594 3.8 0.9 1.0 N J:THR542 3.9 0.8 1.0 OD2 J:ASP594 4.0 0.9 1.0 O5' J:AGS902 4.2 53.7 1.0 CA J:THR542 4.2 0.8 1.0 CG J:ASP594 4.4 0.9 1.0 O3G J:AGS902 4.4 40.2 1.0 O1B J:AGS902 4.4 35.2 1.0 CG2 J:THR542 4.5 0.8 1.0 S1G J:AGS902 4.7 22.8 1.0 C J:LYS541 4.9 0.8 1.0 N J:LYS541 5.0 0.8 1.0

Magnesium binding site 7 out of 12 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg903 b:17.7 occ:1.00 O1B D:AGS901 2.0 7.2 1.0 O3G D:AGS901 2.1 8.2 1.0 PG D:AGS901 2.8 7.3 1.0 OD1 D:ASP320 2.8 0.9 1.0 S1G D:AGS901 3.0 21.3 1.0 PB D:AGS901 3.0 6.9 1.0 OG1 D:THR268 3.0 0.8 1.0 O3B D:AGS901 3.2 3.8 1.0 OD2 D:ASP320 3.3 0.9 1.0 O1A D:AGS901 3.4 1.4 1.0 CG D:ASP320 3.4 0.9 1.0 O3A D:AGS901 3.7 4.6 1.0 PA D:AGS901 4.0 5.8 1.0 O2G D:AGS901 4.3 7.1 1.0 O2B D:AGS901 4.4 2.9 1.0 O2A D:AGS901 4.4 3.3 1.0 CB D:THR268 4.4 0.8 1.0 N D:THR268 4.7 0.8 1.0 CE D:LYS267 4.8 0.8 1.0 CB D:ASP320 4.9 0.9 1.0 N D:GLU321 4.9 0.8 1.0

Magnesium binding site 8 out of 12 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg904 b:17.7 occ:1.00 O1A D:AGS902 2.0 49.5 1.0 O1B D:AGS902 2.1 37.5 1.0 O2G D:AGS902 2.1 45.9 1.0 OG1 D:THR542 2.6 0.8 1.0 PA D:AGS902 2.9 60.8 1.0 PB D:AGS902 3.0 36.2 1.0 O3A D:AGS902 3.1 40.1 1.0 O2A D:AGS902 3.3 60.0 1.0 PG D:AGS902 3.4 39.6 1.0 O3B D:AGS902 3.5 38.5 1.0 OD1 D:ASP594 3.6 0.9 1.0 OD2 D:ASP594 3.9 0.9 1.0 CB D:THR542 4.1 0.8 1.0 CG D:ASP594 4.2 0.9 1.0 O5' D:AGS902 4.3 53.7 1.0 O2B D:AGS902 4.4 35.2 1.0 O3G D:AGS902 4.4 40.2 1.0 N D:THR542 4.5 0.8 1.0 S1G D:AGS902 4.7 22.8 1.0 CA D:THR542 4.8 0.8 1.0 CG2 D:THR542 4.9 0.8 1.0

Magnesium binding site 9 out of 12 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg903 b:17.7 occ:1.00 O1B E:AGS901 2.1 7.2 1.0 O3G E:AGS901 2.1 8.2 1.0 OG1 E:THR268 2.2 0.8 1.0 O3A E:AGS901 2.7 4.6 1.0 PB E:AGS901 2.8 6.9 1.0 OD2 E:ASP320 3.0 0.9 1.0 PG E:AGS901 3.3 7.3 1.0 OD1 E:ASP320 3.4 0.9 1.0 CB E:THR268 3.5 0.8 1.0 O3B E:AGS901 3.5 3.8 1.0 CG E:ASP320 3.6 0.9 1.0 S1G E:AGS901 3.9 21.3 1.0 PA E:AGS901 4.0 5.8 1.0 O2B E:AGS901 4.1 2.9 1.0 O2A E:AGS901 4.2 1.4 1.0 N E:THR268 4.2 0.8 1.0 CG2 E:THR268 4.4 0.8 1.0 CA E:THR268 4.5 0.8 1.0 O2G E:AGS901 4.6 7.1 1.0 O5' E:AGS901 4.7 1.9 1.0

Magnesium binding site 10 out of 12 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg904 b:17.7 occ:1.00 O1A E:AGS902 2.1 49.5 1.0 O1B E:AGS902 2.1 37.5 1.0 O2G E:AGS902 2.1 45.9 1.0 PA E:AGS902 2.5 60.8 1.0 OG1 E:THR542 2.5 0.8 1.0 O2A E:AGS902 2.6 60.0 1.0 PB E:AGS902 2.8 36.2 1.0 O3A E:AGS902 2.8 40.1 1.0 PG E:AGS902 3.3 39.6 1.0 O3B E:AGS902 3.4 38.5 1.0 CB E:THR542 3.8 0.8 1.0 O5' E:AGS902 4.0 53.7 1.0 OD1 E:ASP594 4.1 0.9 1.0 N E:THR542 4.2 0.8 1.0 S1G E:AGS902 4.2 22.8 1.0 O2B E:AGS902 4.2 35.2 1.0 OD2 E:ASP594 4.3 0.9 1.0 CA E:THR542 4.5 0.8 1.0 O3G E:AGS902 4.5 40.2 1.0 CG E:ASP594 4.6 0.9 1.0 CG2 E:THR542 4.8 0.8 1.0 C5' E:AGS902 4.9 51.7 1.0

N.O.Bodnar, K.H.Kim, Z.Ji, T.E.Wales, V.Svetlov, E.Nudler, J.R.Engen, T.Walz, T.A.Rapoport. Structure of the CDC48 Atpase with Its Ubiquitin-Binding Cofactor UFD1-NPL4. Nat. Struct. Mol. Biol. V. 25 616 2018.
ISSN: ESSN 1545-9985
PubMed: 29967539
DOI: 10.1038/S41594-018-0085-X