Magnesium in PDB 8ooi: Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State

All present enzymatic activity of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State:
3.6.4.6;

The structure of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State also contains other interesting chemical elements:

Potassium

(K)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Magnesium atom in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State (pdb code 8ooi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 18 binding sites of Magnesium where determined in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State, PDB code: 8ooi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 18 in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:50.0 occ:1.00 OD1 A:ASP577 2.4 41.8 1.0 O1B A:ATP902 2.5 50.0 1.0 O A:HOH1018 2.9 50.0 1.0 CB A:ALA622 3.4 12.9 1.0 O2G A:ATP902 3.5 50.0 1.0 CB A:LYS524 3.6 24.9 1.0 CG A:ASP577 3.6 40.1 1.0 CE A:LYS524 3.6 27.3 1.0 PB A:ATP902 3.7 50.0 1.0 OG1 A:THR525 3.8 30.9 1.0 CD A:LYS524 4.0 24.5 1.0 O3B A:ATP902 4.1 50.0 1.0 CG A:LYS524 4.3 30.7 1.0 CZ A:PHE575 4.3 41.9 1.0 PG A:ATP902 4.3 50.0 1.0 O2B A:ATP902 4.3 50.0 1.0 N A:THR525 4.3 24.7 1.0 OD2 A:ASP577 4.3 41.5 1.0 CB A:ASP577 4.6 30.9 1.0 N A:GLU578 4.6 24.9 1.0 CA A:LYS524 4.7 23.7 1.0 NZ A:LYS524 4.8 34.2 1.0 CE2 A:PHE575 4.8 41.6 1.0 CA A:ASP577 4.8 21.8 1.0 O1G A:ATP902 4.8 50.0 1.0 C A:LYS524 4.8 27.8 1.0 CA A:ALA622 4.8 10.8 1.0 O3A A:ATP902 5.0 50.0 1.0 CB A:THR525 5.0 22.6 1.0

Magnesium binding site 2 out of 18 in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:50.0 occ:0.50 MG A:MG904 0.0 50.0 0.5 OD1 A:ASP304 2.1 50.0 1.0 O3 F:PO4901 2.4 50.0 0.5 O3B A:ADP901 3.1 50.0 1.0 CG A:ASP304 3.1 50.0 1.0 OG1 A:THR252 3.3 50.0 1.0 O A:HOH1022 3.3 50.0 1.0 OD2 A:ASP304 3.5 50.0 1.0 CB A:ALA346 3.6 41.6 1.0 P F:PO4901 3.7 50.0 0.5 NZ A:LYS251 3.7 50.0 1.0 MG A:MG904 3.7 50.0 0.5 O1 F:PO4901 3.8 50.0 0.5 PB A:ADP901 4.0 50.0 1.0 O2B A:ADP901 4.1 50.0 1.0 N A:GLU305 4.3 50.0 1.0 CB A:ASP304 4.5 50.0 1.0 O1B A:ADP901 4.5 50.0 1.0 O4 F:PO4901 4.6 50.0 0.5 N A:THR252 4.6 50.0 1.0 CB A:LYS251 4.6 50.0 1.0 CB A:THR252 4.6 50.0 1.0 O2 F:PO4901 4.6 50.0 0.5 O3 F:PO4901 4.7 50.0 0.5 CA A:ASP304 4.7 50.0 1.0 O A:ALA346 4.8 48.8 1.0 CZ A:PHE302 4.8 20.6 1.0 C A:ALA346 4.8 39.0 1.0 CA A:ALA346 4.8 37.5 1.0 CE A:LYS251 4.9 50.0 1.0 C A:ASP304 5.0 50.0 1.0

Magnesium binding site 3 out of 18 in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:50.0 occ:0.50 MG A:MG904 0.0 50.0 0.5 O3 F:PO4901 2.3 50.0 0.5 O3 F:PO4901 2.7 50.0 0.5 O1A A:ADP901 2.9 50.0 1.0 O3B A:ADP901 3.0 50.0 1.0 OD2 A:ASP304 3.4 50.0 1.0 OG1 A:THR252 3.5 50.0 1.0 O4 F:PO4901 3.5 50.0 0.5 P F:PO4901 3.7 50.0 0.5 MG A:MG904 3.7 50.0 0.5 P F:PO4901 3.8 50.0 0.5 PA A:ADP901 3.9 50.0 1.0 PB A:ADP901 4.1 50.0 1.0 O2A A:ADP901 4.2 50.0 1.0 O2B A:ADP901 4.2 50.0 1.0 CB A:THR252 4.3 50.0 1.0 CG A:ASP304 4.3 50.0 1.0 O4 F:PO4901 4.4 50.0 0.5 OD1 A:ASP304 4.4 50.0 1.0 O3A A:ADP901 4.4 50.0 1.0 O1 F:PO4901 4.5 50.0 0.5 O2 F:PO4901 4.5 50.0 0.5 K A:K905 4.5 50.0 1.0 O2 F:PO4901 4.6 50.0 0.5 O1 F:PO4901 4.9 50.0 0.5 CG2 A:THR252 4.9 50.0 1.0

Magnesium binding site 4 out of 18 in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg904 b:50.0 occ:1.00 OD1 F:ASP577 2.4 41.8 1.0 O1B F:ATP903 2.5 50.0 1.0 O F:HOH1018 2.9 50.0 1.0 CB F:ALA622 3.4 12.9 1.0 O2G F:ATP903 3.5 50.0 1.0 CB F:LYS524 3.6 24.9 1.0 CG F:ASP577 3.6 40.1 1.0 CE F:LYS524 3.6 27.3 1.0 PB F:ATP903 3.7 50.0 1.0 OG1 F:THR525 3.8 30.9 1.0 CD F:LYS524 4.0 24.5 1.0 O3B F:ATP903 4.1 50.0 1.0 CG F:LYS524 4.3 30.7 1.0 CZ F:PHE575 4.3 41.9 1.0 PG F:ATP903 4.3 50.0 1.0 O2B F:ATP903 4.3 50.0 1.0 N F:THR525 4.3 24.7 1.0 OD2 F:ASP577 4.3 41.5 1.0 CB F:ASP577 4.6 30.9 1.0 N F:GLU578 4.6 24.9 1.0 CA F:LYS524 4.7 23.7 1.0 NZ F:LYS524 4.8 34.2 1.0 CE2 F:PHE575 4.8 41.6 1.0 CA F:ASP577 4.8 21.8 1.0 O1G F:ATP903 4.8 50.0 1.0 C F:LYS524 4.8 27.8 1.0 CA F:ALA622 4.8 10.8 1.0 O3A F:ATP903 5.0 50.0 1.0 CB F:THR525 5.0 22.6 1.0

Magnesium binding site 5 out of 18 in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg905 b:50.0 occ:0.50 MG F:MG905 0.0 50.0 0.5 OD1 F:ASP304 2.1 50.0 1.0 O3 E:PO4901 2.4 50.0 0.5 O3B F:ADP902 3.1 50.0 1.0 CG F:ASP304 3.1 50.0 1.0 OG1 F:THR252 3.3 50.0 1.0 O F:HOH1022 3.3 50.0 1.0 OD2 F:ASP304 3.5 50.0 1.0 CB F:ALA346 3.6 41.6 1.0 P E:PO4901 3.7 50.0 0.5 NZ F:LYS251 3.7 50.0 1.0 MG F:MG905 3.7 50.0 0.5 O1 E:PO4901 3.8 50.0 0.5 PB F:ADP902 4.0 50.0 1.0 O2B F:ADP902 4.1 50.0 1.0 N F:GLU305 4.3 50.0 1.0 CB F:ASP304 4.5 50.0 1.0 O1B F:ADP902 4.5 50.0 1.0 O4 E:PO4901 4.6 50.0 0.5 N F:THR252 4.6 50.0 1.0 CB F:LYS251 4.6 50.0 1.0 CB F:THR252 4.6 50.0 1.0 O2 E:PO4901 4.6 50.0 0.5 O3 E:PO4901 4.7 50.0 0.5 CA F:ASP304 4.7 50.0 1.0 O F:ALA346 4.8 48.8 1.0 CZ F:PHE302 4.8 20.6 1.0 C F:ALA346 4.8 39.0 1.0 CA F:ALA346 4.8 37.5 1.0 CE F:LYS251 4.9 50.0 1.0 C F:ASP304 5.0 50.0 1.0

Magnesium binding site 6 out of 18 in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg905 b:50.0 occ:0.50 MG F:MG905 0.0 50.0 0.5 O3 E:PO4901 2.3 50.0 0.5 O3 E:PO4901 2.7 50.0 0.5 O1A F:ADP902 2.9 50.0 1.0 O3B F:ADP902 3.0 50.0 1.0 OD2 F:ASP304 3.4 50.0 1.0 OG1 F:THR252 3.5 50.0 1.0 O4 E:PO4901 3.5 50.0 0.5 P E:PO4901 3.7 50.0 0.5 MG F:MG905 3.7 50.0 0.5 P E:PO4901 3.8 50.0 0.5 PA F:ADP902 3.9 50.0 1.0 PB F:ADP902 4.1 50.0 1.0 O2A F:ADP902 4.2 50.0 1.0 O2B F:ADP902 4.2 50.0 1.0 CB F:THR252 4.3 50.0 1.0 CG F:ASP304 4.3 50.0 1.0 O4 E:PO4901 4.4 50.0 0.5 OD1 F:ASP304 4.4 50.0 1.0 O3A F:ADP902 4.4 50.0 1.0 O1 E:PO4901 4.5 50.0 0.5 O2 E:PO4901 4.5 50.0 0.5 K F:K906 4.5 50.0 1.0 O2 E:PO4901 4.6 50.0 0.5 O1 E:PO4901 4.9 50.0 0.5 CG2 F:THR252 4.9 50.0 1.0

Magnesium binding site 7 out of 18 in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:50.0 occ:1.00 OD1 B:ASP577 2.3 41.8 1.0 O1B B:ATP902 2.5 50.0 1.0 O B:HOH1018 2.9 50.0 1.0 CB B:ALA622 3.4 12.9 1.0 O2G B:ATP902 3.5 50.0 1.0 CB B:LYS524 3.6 24.9 1.0 CG B:ASP577 3.6 40.1 1.0 CE B:LYS524 3.6 27.3 1.0 PB B:ATP902 3.7 50.0 1.0 OG1 B:THR525 3.8 30.9 1.0 CD B:LYS524 4.0 24.5 1.0 O3B B:ATP902 4.1 50.0 1.0 CG B:LYS524 4.3 30.7 1.0 CZ B:PHE575 4.3 41.9 1.0 PG B:ATP902 4.3 50.0 1.0 O2B B:ATP902 4.3 50.0 1.0 N B:THR525 4.3 24.7 1.0 OD2 B:ASP577 4.3 41.5 1.0 CB B:ASP577 4.6 30.9 1.0 N B:GLU578 4.6 24.9 1.0 CA B:LYS524 4.7 23.7 1.0 NZ B:LYS524 4.8 34.2 1.0 CE2 B:PHE575 4.8 41.6 1.0 CA B:ASP577 4.8 21.8 1.0 O1G B:ATP902 4.8 50.0 1.0 C B:LYS524 4.8 27.8 1.0 CA B:ALA622 4.8 10.8 1.0 O3A B:ATP902 5.0 50.0 1.0 CB B:THR525 5.0 22.6 1.0

Magnesium binding site 8 out of 18 in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:50.0 occ:0.50 MG B:MG904 0.0 50.0 0.5 OD1 B:ASP304 2.1 50.0 1.0 O3 A:PO4906 2.4 50.0 0.5 O3B B:ADP901 3.1 50.0 1.0 CG B:ASP304 3.1 50.0 1.0 OG1 B:THR252 3.3 50.0 1.0 O B:HOH1022 3.3 50.0 1.0 OD2 B:ASP304 3.5 50.0 1.0 CB B:ALA346 3.6 41.6 1.0 P A:PO4906 3.7 50.0 0.5 NZ B:LYS251 3.7 50.0 1.0 MG B:MG904 3.7 50.0 0.5 O1 A:PO4906 3.8 50.0 0.5 PB B:ADP901 4.0 50.0 1.0 O2B B:ADP901 4.1 50.0 1.0 N B:GLU305 4.3 50.0 1.0 CB B:ASP304 4.5 50.0 1.0 O1B B:ADP901 4.5 50.0 1.0 O4 A:PO4906 4.6 50.0 0.5 N B:THR252 4.6 50.0 1.0 CB B:LYS251 4.6 50.0 1.0 CB B:THR252 4.6 50.0 1.0 O2 A:PO4906 4.6 50.0 0.5 O3 A:PO4906 4.7 50.0 0.5 CA B:ASP304 4.7 50.0 1.0 O B:ALA346 4.8 48.8 1.0 CZ B:PHE302 4.8 20.6 1.0 C B:ALA346 4.8 39.0 1.0 CA B:ALA346 4.8 37.5 1.0 CE B:LYS251 4.9 50.0 1.0 C B:ASP304 5.0 50.0 1.0

Magnesium binding site 9 out of 18 in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:50.0 occ:0.50 MG B:MG904 0.0 50.0 0.5 O3 A:PO4906 2.3 50.0 0.5 O3 A:PO4906 2.7 50.0 0.5 O1A B:ADP901 2.9 50.0 1.0 O3B B:ADP901 3.0 50.0 1.0 OD2 B:ASP304 3.4 50.0 1.0 OG1 B:THR252 3.5 50.0 1.0 O4 A:PO4906 3.5 50.0 0.5 P A:PO4906 3.7 50.0 0.5 MG B:MG904 3.7 50.0 0.5 P A:PO4906 3.8 50.0 0.5 PA B:ADP901 3.9 50.0 1.0 PB B:ADP901 4.1 50.0 1.0 O2A B:ADP901 4.2 50.0 1.0 O2B B:ADP901 4.2 50.0 1.0 CB B:THR252 4.3 50.0 1.0 CG B:ASP304 4.3 50.0 1.0 O4 A:PO4906 4.4 50.0 0.5 OD1 B:ASP304 4.4 50.0 1.0 O3A B:ADP901 4.4 50.0 1.0 O1 A:PO4906 4.5 50.0 0.5 O2 A:PO4906 4.5 50.0 0.5 K B:K905 4.5 50.0 1.0 O2 A:PO4906 4.6 50.0 0.5 O1 A:PO4906 4.9 50.0 0.5 CG2 B:THR252 4.9 50.0 1.0

Magnesium binding site 10 out of 18 in the Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Full Composite Cryo-Em Map of P97/Vcp in Adp.Pi State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg903 b:50.0 occ:1.00 OD1 D:ASP577 2.4 41.8 1.0 O1B D:ATP902 2.5 50.0 1.0 O D:HOH1018 2.9 50.0 1.0 CB D:ALA622 3.4 12.9 1.0 O2G D:ATP902 3.5 50.0 1.0 CB D:LYS524 3.6 24.9 1.0 CG D:ASP577 3.6 40.1 1.0 CE D:LYS524 3.6 27.3 1.0 PB D:ATP902 3.7 50.0 1.0 OG1 D:THR525 3.8 30.9 1.0 CD D:LYS524 4.0 24.5 1.0 O3B D:ATP902 4.1 50.0 1.0 CG D:LYS524 4.3 30.7 1.0 CZ D:PHE575 4.3 41.9 1.0 PG D:ATP902 4.3 50.0 1.0 O2B D:ATP902 4.3 50.0 1.0 N D:THR525 4.3 24.7 1.0 OD2 D:ASP577 4.3 41.5 1.0 CB D:ASP577 4.6 30.9 1.0 N D:GLU578 4.6 24.9 1.0 CA D:LYS524 4.7 23.7 1.0 NZ D:LYS524 4.8 34.2 1.0 CE2 D:PHE575 4.8 41.6 1.0 CA D:ASP577 4.8 21.8 1.0 O1G D:ATP902 4.8 50.0 1.0 C D:LYS524 4.8 27.8 1.0 CA D:ALA622 4.8 10.8 1.0 O3A D:ATP902 5.0 50.0 1.0 CB D:THR525 5.0 22.6 1.0

M.Shein, M.Hitzenberger, Cheng T.C., Rout S.R., Leitl K.D., Sato Y., Zacharias M., Sakata E., Schuetz A.K.. Characterizing Atp Processing By the Aaa+ Protein P97 at the Atomic Level Nat.Chem. 2024.
ISSN: ESSN 1755-4349
DOI: 10.1038/S41557-024-01440-0