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Magnesium in PDB 8u9q: CDC48-SHP1 Unfolding Native Substrate, Class 6

Enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 6

All present enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 6:
3.6.4.6;

Other elements in 8u9q:

The structure of CDC48-SHP1 Unfolding Native Substrate, Class 6 also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the CDC48-SHP1 Unfolding Native Substrate, Class 6 (pdb code 8u9q). 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 6, PDB code: 8u9q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8u9q

Go back to Magnesium Binding Sites List in 8u9q
Magnesium binding site 1 out of 6 in the CDC48-SHP1 Unfolding Native Substrate, Class 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:185.6
occ:1.00
 OG1 A:THR262 1.9 183.6 1.0
OD2 B:ASP343 2.1 214.4 1.0
OD1 B:ASP343 2.1 214.4 1.0
CB A:THR262 2.1 183.6 1.0
CG B:ASP343 2.3 214.4 1.0
O2B A:08T901 2.7 197.3 1.0
CG2 A:THR262 2.7 183.6 1.0
O2A A:08T901 2.8 197.3 1.0
PA A:08T901 3.5 197.3 1.0
O1A A:08T901 3.5 197.3 1.0
CA A:THR262 3.5 183.6 1.0
PB A:08T901 3.7 197.3 1.0
CB B:ASP343 3.7 214.4 1.0
O3A A:08T901 3.8 197.3 1.0
N A:THR262 3.9 183.6 1.0
O3B A:08T901 4.2 197.3 1.0
C B:ASP343 4.3 214.4 1.0
F1 A:08T901 4.3 196.0 1.0
NH1 A:ARG266 4.4 197.2 1.0
NH2 A:ARG266 4.4 197.2 1.0
N B:GLY344 4.4 218.8 1.0
C A:THR262 4.4 183.6 1.0
O B:ASP343 4.4 214.4 1.0
CA B:ASP343 4.5 214.4 1.0
N A:LEU263 4.7 198.9 1.0
CZ A:ARG266 4.7 197.2 1.0
CA B:GLY344 4.8 218.8 1.0
BE A:08T901 5.0 196.0 1.0

Magnesium binding site 2 out of 6 in 8u9q

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


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:181.9
occ:1.00
 OG1 A:THR535 1.7 183.3 1.0
O2B A:08T903 1.9 192.4 1.0
F1 A:08T903 1.9 196.0 1.0
CB A:THR535 2.5 183.3 1.0
O1A A:08T903 2.6 192.4 1.0
N A:THR535 2.8 183.3 1.0
PB A:08T903 2.9 192.4 1.0
BE A:08T903 3.0 196.0 1.0
CA A:THR535 3.2 183.3 1.0
PA A:08T903 3.2 192.4 1.0
O3A A:08T903 3.2 192.4 1.0
O3B A:08T903 3.3 192.4 1.0
O2A A:08T903 3.3 192.4 1.0
F2 A:08T903 3.6 196.0 1.0
CG2 A:THR535 3.8 183.3 1.0
C A:LYS534 3.9 185.7 1.0
OD1 B:ASP619 4.1 230.4 1.0
OD2 B:ASP619 4.2 230.4 1.0
O1B A:08T903 4.3 192.4 1.0
CB A:LYS534 4.3 185.7 1.0
N A:LYS534 4.3 185.7 1.0
F3 A:08T903 4.3 196.0 1.0
CG B:ASP619 4.4 230.4 1.0
C A:THR535 4.4 183.3 1.0
CA A:LYS534 4.4 185.7 1.0
N A:LEU536 4.7 188.5 1.0
O5' A:08T903 4.7 192.4 1.0
O A:LYS534 5.0 185.7 1.0
C A:GLY533 5.0 187.1 1.0

Magnesium binding site 3 out of 6 in 8u9q

Go back to Magnesium Binding Sites List in 8u9q
Magnesium binding site 3 out of 6 in the CDC48-SHP1 Unfolding Native Substrate, Class 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:201.3
occ:1.00
 OG1 B:THR262 1.9 192.1 1.0
O2B B:08T901 1.9 201.6 1.0
F1 B:08T901 2.2 210.2 1.0
CB B:THR262 2.6 192.1 1.0
PB B:08T901 2.9 201.6 1.0
O3B B:08T901 3.2 201.6 1.0
BE B:08T901 3.2 210.2 1.0
O3A B:08T901 3.4 201.6 1.0
O1A B:08T901 3.4 201.6 1.0
CG2 B:THR262 3.6 192.1 1.0
NH2 C:ARG369 3.7 236.2 1.0
N B:THR262 3.8 192.1 1.0
PA B:08T901 3.8 201.6 1.0
CA B:THR262 3.8 192.1 1.0
O2A B:08T901 3.8 201.6 1.0
F3 B:08T901 4.2 210.2 1.0
O1B B:08T901 4.3 201.6 1.0
NH2 C:ARG372 4.3 232.6 1.0
F2 B:08T901 4.4 210.2 1.0
CG B:LYS261 4.5 192.5 1.0
CB C:ASP343 4.8 226.4 1.0
C B:THR262 4.9 192.1 1.0
CZ C:ARG369 4.9 236.2 1.0

Magnesium binding site 4 out of 6 in 8u9q

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


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg904

b:202.0
occ:1.00
 O3A B:08T903 2.0 199.8 1.0
O2B B:08T903 2.0 199.8 1.0
OG1 B:THR535 2.1 189.2 1.0
F1 B:08T903 2.2 211.7 1.0
PB B:08T903 2.4 199.8 1.0
CB B:THR535 2.6 189.2 1.0
PA B:08T903 2.6 199.8 1.0
O1A B:08T903 2.7 199.8 1.0
O2A B:08T903 3.0 199.8 1.0
O3B B:08T903 3.1 199.8 1.0
BE B:08T903 3.2 211.7 1.0
N B:THR535 3.3 189.2 1.0
CA B:THR535 3.5 189.2 1.0
O1B B:08T903 3.7 199.8 1.0
CG2 B:THR535 3.8 189.2 1.0
O5' B:08T903 4.1 199.8 1.0
F3 B:08T903 4.2 211.7 1.0
F2 B:08T903 4.4 211.7 1.0
C B:THR535 4.5 189.2 1.0
N B:LEU536 4.5 191.1 1.0
C B:LYS534 4.5 190.6 1.0
N B:LYS534 4.6 190.6 1.0
NH2 C:ARG648 4.7 218.8 1.0
C5' B:08T903 4.9 199.8 1.0
CA B:LYS534 5.0 190.6 1.0

Magnesium binding site 5 out of 6 in 8u9q

Go back to Magnesium Binding Sites List in 8u9q
Magnesium binding site 5 out of 6 in the CDC48-SHP1 Unfolding Native Substrate, Class 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:200.9
occ:1.00
 OD2 D:ASP343 2.1 241.2 1.0
OG1 C:THR262 2.4 195.3 1.0
O1A C:08T901 2.6 205.7 1.0
O2B C:08T901 2.6 205.7 1.0
CB C:THR262 2.7 195.3 1.0
F1 C:08T901 2.8 211.8 1.0
PB C:08T901 3.2 205.7 1.0
O3A C:08T901 3.2 205.7 1.0
PA C:08T901 3.3 205.7 1.0
CG D:ASP343 3.3 241.2 1.0
CG2 C:THR262 3.4 195.3 1.0
O3B C:08T901 3.4 205.7 1.0
O2A C:08T901 3.7 205.7 1.0
BE C:08T901 3.7 211.8 1.0
CA C:THR262 4.0 195.3 1.0
OD1 D:ASP343 4.1 241.2 1.0
N C:THR262 4.2 195.3 1.0
CB D:ASP343 4.3 241.2 1.0
NH2 D:ARG372 4.3 232.4 1.0
F3 C:08T901 4.5 211.8 1.0
NH2 D:ARG369 4.6 237.9 1.0
O1B C:08T901 4.7 205.7 1.0
O5' C:08T901 4.7 205.7 1.0
C C:THR262 4.9 195.3 1.0
F2 C:08T901 5.0 211.8 1.0

Magnesium binding site 6 out of 6 in 8u9q

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


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg904

b:210.4
occ:1.00
 OG1 C:THR535 1.8 190.8 1.0
F1 C:08T903 2.0 209.1 1.0
O2B C:08T903 2.0 197.2 1.0
CB C:THR535 3.1 190.8 1.0
N C:THR535 3.1 190.8 1.0
BE C:08T903 3.2 209.1 1.0
PB C:08T903 3.3 197.2 1.0
CA C:THR535 3.5 190.8 1.0
O3B C:08T903 3.6 197.2 1.0
F2 C:08T903 3.8 209.1 1.0
CB C:LYS534 4.0 194.6 1.0
C C:LYS534 4.1 194.6 1.0
CG2 C:THR535 4.2 190.8 1.0
O3A C:08T903 4.3 197.2 1.0
O1B C:08T903 4.3 197.2 1.0
F3 C:08T903 4.4 209.1 1.0
CA C:LYS534 4.5 194.6 1.0
O1A C:08T903 4.5 197.2 1.0
CE C:LYS534 4.6 194.6 1.0
O2A C:08T903 4.6 197.2 1.0
OE1 C:GLU588 4.7 246.5 1.0
PA C:08T903 4.8 197.2 1.0
OD2 C:ASP587 4.8 233.8 1.0
OD1 C:ASP587 4.8 233.8 1.0
N C:LYS534 4.8 194.6 1.0
C C:THR535 5.0 190.8 1.0

Reference:

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
Page generated: Wed Nov 13 11:58:13 2024

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