Magnesium in PDB 8ua1: CDC48-SHP1 Unfolding Native Substrate, Class 9

Enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 9

All present enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 9:
3.6.4.6;

Other elements in 8ua1:

The structure of CDC48-SHP1 Unfolding Native Substrate, Class 9 also contains other interesting chemical elements:

Fluorine (F) 21 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the CDC48-SHP1 Unfolding Native Substrate, Class 9 (pdb code 8ua1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the CDC48-SHP1 Unfolding Native Substrate, Class 9, PDB code: 8ua1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8ua1

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Magnesium binding site 1 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 9


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

b:86.3
occ:1.00
 OG1 A:THR262 1.9 83.8 1.0
F1 A:08T901 2.0 91.0 1.0
O2B A:08T901 2.6 83.8 1.0
CB A:THR262 3.1 80.3 1.0
BE A:08T901 3.5 86.3 1.0
PB A:08T901 3.7 77.5 1.0
O3B A:08T901 3.9 81.2 1.0
CG2 A:THR262 4.0 87.1 1.0
N A:THR262 4.0 78.5 1.0
CA A:THR262 4.1 76.5 1.0
O2A A:08T901 4.1 86.3 1.0
O3A A:08T901 4.3 80.4 1.0
F3 A:08T901 4.4 87.4 1.0
F2 A:08T901 4.4 89.7 1.0
NH2 B:ARG372 4.5 82.8 1.0
OD1 A:ASP314 4.5 102.6 1.0
OD2 A:ASP314 4.7 95.3 1.0
PA A:08T901 4.8 89.7 1.0

Magnesium binding site 2 out of 7 in 8ua1

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Magnesium binding site 2 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 9


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

b:76.8
occ:1.00
 F1 A:08T903 1.8 75.2 1.0
O2B A:08T903 2.0 75.0 1.0
OG1 A:THR535 2.3 76.2 1.0
O1A A:08T903 2.7 76.1 1.0
PB A:08T903 2.8 79.0 1.0
BE A:08T903 2.9 78.7 1.0
O3B A:08T903 3.1 75.6 1.0
O3A A:08T903 3.1 74.5 1.0
CB A:THR535 3.2 71.7 1.0
PA A:08T903 3.3 69.6 1.0
N A:THR535 3.7 62.8 1.0
O2A A:08T903 3.7 66.0 1.0
F3 A:08T903 4.0 83.3 1.0
F2 A:08T903 4.0 85.3 1.0
CA A:THR535 4.1 63.8 1.0
O1B A:08T903 4.2 75.3 1.0
NH2 B:ARG648 4.3 81.5 1.0
CG2 A:THR535 4.4 80.6 1.0
CB A:LYS534 4.6 63.7 1.0
OD2 B:ASP619 4.7 94.8 1.0
O5' A:08T903 4.7 64.2 1.0
C A:LYS534 4.8 63.5 1.0
CG B:ASP619 5.0 98.7 1.0
N A:LYS534 5.0 63.5 1.0

Magnesium binding site 3 out of 7 in 8ua1

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Magnesium binding site 3 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 9


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

b:80.2
occ:1.00
 F1 B:08T901 1.8 76.2 1.0
OG1 B:THR262 2.2 71.3 1.0
O2B B:08T901 2.2 71.4 1.0
CB B:THR262 2.9 66.8 1.0
PB B:08T901 3.0 65.2 1.0
BE B:08T901 3.0 74.2 1.0
O3B B:08T901 3.1 69.9 1.0
O3A B:08T901 3.3 73.8 1.0
O1A B:08T901 3.7 77.3 1.0
N B:THR262 3.7 61.9 1.0
PA B:08T901 3.9 80.4 1.0
CA B:THR262 3.9 61.0 1.0
F2 B:08T901 4.0 77.4 1.0
CG2 B:THR262 4.0 71.3 1.0
F3 B:08T901 4.1 73.5 1.0
O2A B:08T901 4.2 72.4 1.0
OD2 C:ASP343 4.3 89.2 1.0
NH2 C:ARG372 4.4 72.0 1.0
O1B B:08T901 4.4 62.9 1.0
NH2 C:ARG369 4.7 73.7 1.0
O C:ASP343 4.8 83.5 1.0
CB B:LYS261 4.9 54.3 1.0
C B:LYS261 4.9 63.0 1.0
OD1 B:ASP314 5.0 88.9 1.0

Magnesium binding site 4 out of 7 in 8ua1

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Magnesium binding site 4 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 9


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

b:82.3
occ:1.00
 OG1 B:THR535 1.8 78.2 1.0
F1 B:08T903 1.9 82.4 1.0
O2B B:08T903 1.9 75.9 1.0
PB B:08T903 2.9 72.2 1.0
CB B:THR535 3.1 73.1 1.0
BE B:08T903 3.1 75.1 1.0
O3A B:08T903 3.2 76.3 1.0
O3B B:08T903 3.3 70.2 1.0
N B:THR535 3.8 65.1 1.0
CG2 B:THR535 4.0 79.2 1.0
CA B:THR535 4.0 67.7 1.0
F3 B:08T903 4.1 73.8 1.0
F2 B:08T903 4.2 77.8 1.0
OD1 C:ASP619 4.2 78.2 1.0
OD1 B:ASP587 4.2 88.3 1.0
PA B:08T903 4.2 84.0 1.0
O1A B:08T903 4.3 79.6 1.0
O1B B:08T903 4.3 65.8 1.0
NH2 C:ARG648 4.4 72.0 1.0
O2A B:08T903 4.5 73.7 1.0
O C:ASP619 4.6 92.7 1.0
OD2 B:ASP587 4.8 88.9 1.0
CG B:ASP587 4.9 85.6 1.0
CB B:LYS534 4.9 61.7 1.0
NH2 C:ARG645 5.0 78.5 1.0
C B:LYS534 5.0 61.9 1.0

Magnesium binding site 5 out of 7 in 8ua1

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Magnesium binding site 5 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 9


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

b:79.4
occ:1.00
 OG1 C:THR262 1.9 77.2 1.0
F1 C:08T901 1.9 80.1 1.0
O2B C:08T901 2.0 73.2 1.0
CB C:THR262 2.5 72.6 1.0
PB C:08T901 3.1 68.0 1.0
BE C:08T901 3.1 79.6 1.0
N C:THR262 3.3 60.8 1.0
O1A C:08T901 3.4 75.2 1.0
O3B C:08T901 3.4 71.4 1.0
CA C:THR262 3.5 61.5 1.0
O3A C:08T901 3.6 74.8 1.0
CG2 C:THR262 3.7 81.6 1.0
F3 C:08T901 3.8 84.9 1.0
PA C:08T901 3.9 81.1 1.0
O2A C:08T901 4.2 78.0 1.0
F2 C:08T901 4.4 88.2 1.0
O1B C:08T901 4.4 70.3 1.0
C C:LYS261 4.5 60.2 1.0
C C:THR262 4.6 61.8 1.0
CB C:LYS261 4.7 50.8 1.0
OD1 C:ASP314 4.9 83.2 1.0
N C:LEU263 4.9 62.7 1.0
N C:LYS261 5.0 57.8 1.0
CA C:LYS261 5.0 55.9 1.0

Magnesium binding site 6 out of 7 in 8ua1

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Magnesium binding site 6 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 9


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

b:81.6
occ:1.00
 OG1 C:THR535 1.8 78.7 1.0
O2B C:08T903 1.9 82.3 1.0
F1 C:08T903 1.9 89.2 1.0
CB C:THR535 3.0 74.9 1.0
PB C:08T903 3.0 78.9 1.0
BE C:08T903 3.2 84.5 1.0
O3B C:08T903 3.4 82.6 1.0
O3A C:08T903 3.7 73.7 1.0
N C:THR535 3.9 66.0 1.0
CG2 C:THR535 4.0 80.5 1.0
CA C:THR535 4.0 66.5 1.0
OD1 C:ASP587 4.0 84.7 1.0
F3 C:08T903 4.2 90.1 1.0
F2 C:08T903 4.3 80.9 1.0
OD2 C:ASP587 4.3 84.8 1.0
O1B C:08T903 4.4 71.2 1.0
NH2 D:ARG648 4.4 85.2 1.0
CG C:ASP587 4.6 80.8 1.0
PA C:08T903 4.6 83.5 1.0
O2A C:08T903 4.6 72.8 1.0
OD2 D:ASP619 4.7 95.0 1.0
O D:ASP619 4.8 98.3 1.0
O1A C:08T903 4.8 81.7 1.0
OE2 C:GLU588 4.8 91.0 1.0

Magnesium binding site 7 out of 7 in 8ua1

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Magnesium binding site 7 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of CDC48-SHP1 Unfolding Native Substrate, Class 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg902

b:175.2
occ:1.00
 F1 F:08T901 1.8 172.1 1.0
OG1 F:THR535 2.1 190.7 1.0
O2B F:08T901 2.1 184.5 1.0
BE F:08T901 3.1 173.6 1.0
PB F:08T901 3.1 181.6 1.0
O1A F:08T901 3.2 183.2 1.0
CB F:THR535 3.2 193.9 1.0
O3B F:08T901 3.5 172.9 1.0
O3A F:08T901 3.6 173.8 1.0
N F:THR535 3.7 192.6 1.0
F2 F:08T901 3.7 185.1 1.0
PA F:08T901 3.8 183.1 1.0
CA F:THR535 4.0 197.5 1.0
O2A F:08T901 4.1 192.1 1.0
F3 F:08T901 4.3 166.3 1.0
CG2 F:THR535 4.3 196.6 1.0
O1B F:08T901 4.5 174.2 1.0
CB F:LYS534 4.6 180.3 1.0
C F:LYS534 4.7 191.4 1.0
NH2 A:ARG648 4.8 133.6 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 11:58:14 2024

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