Magnesium in PDB 8u9z: CDC48-SHP1 Unfolding Native Substrate, Class 7

All present enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 7:
3.6.4.6;

The structure of CDC48-SHP1 Unfolding Native Substrate, Class 7 also contains other interesting chemical elements:

Fluorine

(F)

18 atoms

The binding sites of Magnesium atom in the CDC48-SHP1 Unfolding Native Substrate, Class 7 (pdb code 8u9z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the CDC48-SHP1 Unfolding Native Substrate, Class 7, PDB code: 8u9z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the CDC48-SHP1 Unfolding Native Substrate, Class 7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CDC48-SHP1 Unfolding Native Substrate, Class 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:144.0 occ:1.00 OG1 A:THR262 1.8 150.7 1.0 F1 A:08T901 1.9 145.8 1.0 O2B A:08T901 2.0 154.8 1.0 CB A:THR262 2.5 150.7 1.0 PB A:08T901 3.0 154.8 1.0 BE A:08T901 3.1 145.8 1.0 O2A A:08T901 3.1 154.8 1.0 O3B A:08T901 3.2 154.8 1.0 CG2 A:THR262 3.5 150.7 1.0 O3A A:08T901 3.5 154.8 1.0 CA A:THR262 3.7 150.7 1.0 N A:THR262 3.7 150.7 1.0 PA A:08T901 3.8 154.8 1.0 F3 A:08T901 3.9 145.8 1.0 O1A A:08T901 4.3 154.8 1.0 F2 A:08T901 4.3 145.8 1.0 NH2 B:ARG372 4.3 148.9 1.0 O1B A:08T901 4.4 154.8 1.0 CG A:LYS261 4.4 141.0 1.0 OD2 A:ASP314 4.5 172.8 1.0 C A:THR262 4.8 150.7 1.0 CG B:ASP343 4.9 179.5 1.0 OD1 B:ASP343 4.9 179.5 1.0

Magnesium binding site 2 out of 6 in the CDC48-SHP1 Unfolding Native Substrate, Class 7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CDC48-SHP1 Unfolding Native Substrate, Class 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:124.5 occ:1.00 O2B A:08T903 2.0 125.2 1.0 F1 A:08T903 2.2 124.3 1.0 OG1 A:THR535 2.3 117.0 1.0 PB A:08T903 2.8 125.2 1.0 O1A A:08T903 2.9 125.2 1.0 O3B A:08T903 2.9 125.2 1.0 BE A:08T903 3.1 124.3 1.0 O3A A:08T903 3.1 125.2 1.0 CB A:THR535 3.2 117.0 1.0 PA A:08T903 3.5 125.2 1.0 N A:THR535 3.9 117.0 1.0 O2A A:08T903 4.0 125.2 1.0 F2 A:08T903 4.1 124.3 1.0 NH2 B:ARG648 4.2 137.2 1.0 CA A:THR535 4.2 117.0 1.0 O1B A:08T903 4.2 125.2 1.0 F3 A:08T903 4.3 124.3 1.0 CG2 A:THR535 4.3 117.0 1.0 NH1 B:ARG645 4.5 128.8 1.0 CB A:LYS534 5.0 128.1 1.0 O5' A:08T903 5.0 125.2 1.0

Magnesium binding site 3 out of 6 in the CDC48-SHP1 Unfolding Native Substrate, Class 7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CDC48-SHP1 Unfolding Native Substrate, Class 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:123.4 occ:1.00 O2B B:08T901 2.1 145.5 1.0 F1 B:08T901 2.1 128.4 1.0 O1A B:08T901 2.2 145.5 1.0 OG1 B:THR262 2.4 113.0 1.0 O2A B:08T901 2.5 145.5 1.0 PA B:08T901 2.5 145.5 1.0 O3A B:08T901 2.7 145.5 1.0 PB B:08T901 2.7 145.5 1.0 CB B:THR262 2.9 113.0 1.0 BE B:08T901 3.2 128.4 1.0 N B:THR262 3.2 113.0 1.0 O3B B:08T901 3.3 145.5 1.0 CA B:THR262 3.7 113.0 1.0 O5' B:08T901 4.1 145.5 1.0 O1B B:08T901 4.2 145.5 1.0 CG2 B:THR262 4.2 113.0 1.0 F3 B:08T901 4.3 128.4 1.0 F2 B:08T901 4.3 128.4 1.0 C B:LYS261 4.4 119.1 1.0 OD2 C:ASP343 4.4 132.7 1.0 N B:LYS261 4.4 119.1 1.0 CB B:LYS261 4.5 119.1 1.0 CA B:LYS261 4.7 119.1 1.0 NH2 C:ARG369 4.7 132.2 1.0 C B:THR262 4.7 113.0 1.0 N B:LEU263 4.8 123.7 1.0 CG C:ASP343 4.8 132.7 1.0 C5' B:08T901 4.9 145.5 1.0 OD1 C:ASP343 5.0 132.7 1.0

Magnesium binding site 4 out of 6 in the CDC48-SHP1 Unfolding Native Substrate, Class 7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of CDC48-SHP1 Unfolding Native Substrate, Class 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:119.6 occ:1.00 OG1 B:THR535 1.8 120.8 1.0 O2B B:08T903 2.0 109.9 1.0 F1 B:08T903 2.0 119.1 1.0 CB B:THR535 2.8 120.8 1.0 PB B:08T903 2.9 109.9 1.0 O3A B:08T903 3.1 109.9 1.0 BE B:08T903 3.2 119.1 1.0 O3B B:08T903 3.4 109.9 1.0 CG2 B:THR535 3.6 120.8 1.0 PA B:08T903 3.9 109.9 1.0 O1A B:08T903 3.9 109.9 1.0 O2A B:08T903 3.9 109.9 1.0 CA B:THR535 4.0 120.8 1.0 F3 B:08T903 4.1 119.1 1.0 N B:THR535 4.1 120.8 1.0 O1B B:08T903 4.3 109.9 1.0 OD1 C:ASP619 4.4 141.2 1.0 F2 B:08T903 4.4 119.1 1.0 NH1 C:ARG645 4.5 120.2 1.0 CG B:LYS534 4.6 123.7 1.0 NH1 C:ARG648 4.7 125.2 1.0 OD2 B:ASP587 4.8 142.7 1.0

Magnesium binding site 5 out of 6 in the CDC48-SHP1 Unfolding Native Substrate, Class 7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of CDC48-SHP1 Unfolding Native Substrate, Class 7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg902 b:135.5 occ:1.00 F1 C:08T901 1.9 147.9 1.0 OG1 C:THR262 1.9 124.0 1.0 O2B C:08T901 1.9 164.7 1.0 CB C:THR262 2.6 124.0 1.0 PB C:08T901 2.9 164.7 1.0 BE C:08T901 3.0 147.9 1.0 O3B C:08T901 3.1 164.7 1.0 O3A C:08T901 3.5 164.7 1.0 O1A C:08T901 3.6 164.7 1.0 CG2 C:THR262 3.7 124.0 1.0 N C:THR262 3.7 124.0 1.0 CA C:THR262 3.7 124.0 1.0 PA C:08T901 3.9 164.7 1.0 O2A C:08T901 4.1 164.7 1.0 F2 C:08T901 4.1 147.9 1.0 F3 C:08T901 4.1 147.9 1.0 CG C:LYS261 4.2 121.5 1.0 O1B C:08T901 4.3 164.7 1.0 NH2 D:ARG369 4.5 129.7 1.0 NH2 D:ARG372 4.8 132.9 1.0 C C:THR262 4.9 124.0 1.0 C C:LYS261 4.9 121.5 1.0

Magnesium binding site 6 out of 6 in the CDC48-SHP1 Unfolding Native Substrate, Class 7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of CDC48-SHP1 Unfolding Native Substrate, Class 7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg904 b:113.2 occ:1.00 OG1 C:THR535 1.8 108.4 1.0 O2B C:08T903 1.9 128.9 1.0 F1 C:08T903 2.0 127.9 1.0 CB C:THR535 2.7 108.4 1.0 PB C:08T903 2.8 128.9 1.0 BE C:08T903 3.1 127.9 1.0 O3A C:08T903 3.2 128.9 1.0 O3B C:08T903 3.2 128.9 1.0 CG2 C:THR535 3.6 108.4 1.0 CA C:THR535 3.9 108.4 1.0 N C:THR535 3.9 108.4 1.0 F3 C:08T903 4.0 127.9 1.0 PA C:08T903 4.1 128.9 1.0 O2A C:08T903 4.1 128.9 1.0 O D:ASP619 4.1 148.8 1.0 O1B C:08T903 4.3 128.9 1.0 F2 C:08T903 4.3 127.9 1.0 O1A C:08T903 4.3 128.9 1.0 OD2 D:ASP619 4.4 148.8 1.0 CG C:LYS534 4.5 115.0 1.0 CG D:ASP619 4.8 148.8 1.0

I.Cooney, H.L.Schubert, K.Cedeno, O.N.Fisher, R.Carson, J.C.Price, C.P.Hill, P.S.Shen. Visualization of the CDC48 Aaa+ Atpase Protein Unfolding Pathway. Nat Commun V. 15 7505 2024.
ISSN: ESSN 2041-1723
PubMed: 39209885
DOI: 10.1038/S41467-024-51835-3