Magnesium in PDB 8uaa: CDC48-SHP1 Unfolding Native Substrate, Class 3

Enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 3

All present enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 3:
3.6.4.6;

Other elements in 8uaa:

The structure of CDC48-SHP1 Unfolding Native Substrate, Class 3 also contains other interesting chemical elements:

Fluorine (F) 24 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 8uaa

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Magnesium binding site 1 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 3


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

b:98.4
occ:1.00
 F1 A:08T901 2.0 92.4 1.0
O2B A:08T901 2.0 98.6 1.0
OG1 A:THR262 2.3 96.7 1.0
PB A:08T901 2.8 83.3 1.0
O3B A:08T901 2.9 83.8 1.0
BE A:08T901 3.0 91.0 1.0
CB A:THR262 3.3 93.9 1.0
O3A A:08T901 3.3 95.4 1.0
N A:THR262 3.7 94.7 1.0
F3 A:08T901 3.9 95.8 1.0
CA A:THR262 4.1 98.6 1.0
F2 A:08T901 4.2 95.3 1.0
O1B A:08T901 4.3 85.0 1.0
PA A:08T901 4.4 108.1 1.0
CG2 A:THR262 4.5 102.2 1.0
O1A A:08T901 4.5 107.7 1.0
CB A:LYS261 4.5 90.1 1.0
O2A A:08T901 4.6 108.5 1.0
NH2 B:ARG372 4.7 91.5 1.0
C A:LYS261 4.8 98.1 1.0

Magnesium binding site 2 out of 8 in 8uaa

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Magnesium binding site 2 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 3


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

b:69.6
occ:1.00
 OG1 A:THR535 1.8 68.8 1.0
F1 A:08T903 1.8 71.5 1.0
O2B A:08T903 2.6 72.4 1.0
CB A:THR535 3.0 61.0 1.0
BE A:08T903 3.3 77.5 1.0
O1A A:08T903 3.5 74.1 1.0
N A:THR535 3.6 60.9 1.0
PB A:08T903 3.7 67.9 1.0
CA A:THR535 3.8 60.4 1.0
O3B A:08T903 3.9 73.8 1.0
CG2 A:THR535 4.1 66.0 1.0
F2 A:08T903 4.1 76.8 1.0
OD2 A:ASP587 4.2 89.9 1.0
OD1 A:ASP587 4.2 96.7 1.0
O3A A:08T903 4.2 62.4 1.0
PA A:08T903 4.3 72.1 1.0
F3 A:08T903 4.3 84.0 1.0
OD2 B:ASP619 4.3 85.2 1.0
O2A A:08T903 4.4 68.8 1.0
CB A:LYS534 4.6 57.4 1.0
OE2 A:GLU588 4.6 95.3 1.0
C A:LYS534 4.6 64.7 1.0
CG A:ASP587 4.7 93.6 1.0
NH2 B:ARG648 5.0 80.1 1.0

Magnesium binding site 3 out of 8 in 8uaa

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Magnesium binding site 3 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 3


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

b:68.9
occ:1.00
 O2B B:08T901 1.9 65.2 1.0
F1 B:08T901 1.9 56.4 1.0
OG1 B:THR262 2.3 62.8 1.0
PB B:08T901 2.5 59.0 1.0
O3B B:08T901 2.8 52.0 1.0
O3A B:08T901 2.8 63.9 1.0
CB B:THR262 2.8 61.0 1.0
BE B:08T901 2.8 60.7 1.0
O1A B:08T901 3.2 73.2 1.0
PA B:08T901 3.4 70.3 1.0
O2A B:08T901 3.6 67.5 1.0
CG2 B:THR262 3.8 64.9 1.0
N B:THR262 3.9 60.0 1.0
F3 B:08T901 3.9 71.2 1.0
CA B:THR262 3.9 61.3 1.0
F2 B:08T901 4.0 70.7 1.0
O1B B:08T901 4.0 60.7 1.0
NH2 C:ARG372 4.4 59.3 1.0
O C:ASP343 4.5 69.4 1.0
CG B:LYS261 4.5 51.2 1.0
NH2 C:ARG369 4.8 66.6 1.0
OD2 C:ASP343 4.8 80.1 1.0
O5' B:08T901 4.9 69.4 1.0
C B:THR262 4.9 66.0 1.0

Magnesium binding site 4 out of 8 in 8uaa

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Magnesium binding site 4 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 3


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

b:62.9
occ:1.00
 OG1 B:THR535 1.8 65.2 1.0
F1 B:08T903 1.9 72.9 1.0
O2B B:08T903 2.0 66.7 1.0
CB B:THR535 3.2 59.7 1.0
PB B:08T903 3.2 58.9 1.0
BE B:08T903 3.3 65.6 1.0
O3B B:08T903 3.7 57.4 1.0
CG2 B:THR535 3.8 61.8 1.0
O3A B:08T903 3.9 56.1 1.0
OD1 B:ASP587 4.1 74.8 1.0
OD2 C:ASP619 4.1 68.3 1.0
F2 B:08T903 4.2 71.9 1.0
O C:ASP619 4.2 82.3 1.0
N B:THR535 4.2 54.9 1.0
CA B:THR535 4.2 57.6 1.0
NH2 C:ARG648 4.2 67.5 1.0
OD2 B:ASP587 4.3 69.8 1.0
F3 B:08T903 4.4 66.1 1.0
O1B B:08T903 4.5 62.5 1.0
CG B:ASP587 4.6 70.4 1.0
O1A B:08T903 4.7 67.5 1.0
PA B:08T903 4.8 63.4 1.0
OE2 B:GLU588 4.9 73.6 1.0
O2A B:08T903 4.9 62.3 1.0

Magnesium binding site 5 out of 8 in 8uaa

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Magnesium binding site 5 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 3


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

b:80.9
occ:1.00
 OD2 D:ASP343 2.1 83.4 1.0
OG1 C:THR262 2.3 62.1 1.0
O1A C:08T901 2.6 71.7 1.0
F1 C:08T901 2.6 64.0 1.0
O2B C:08T901 2.8 63.4 1.0
CB C:THR262 2.8 61.6 1.0
O3A C:08T901 3.1 69.6 1.0
PB C:08T901 3.3 56.0 1.0
CG D:ASP343 3.4 83.9 1.0
PA C:08T901 3.4 79.2 1.0
O3B C:08T901 3.5 55.8 1.0
BE C:08T901 3.6 64.8 1.0
CG2 C:THR262 3.7 69.9 1.0
CA C:THR262 4.1 56.0 1.0
O2A C:08T901 4.1 70.8 1.0
N C:THR262 4.2 59.4 1.0
F3 C:08T901 4.2 69.3 1.0
OD1 D:ASP343 4.2 86.5 1.0
CB D:ASP343 4.3 77.0 1.0
NH2 D:ARG369 4.6 65.3 1.0
NH2 D:ARG372 4.7 72.5 1.0
O5' C:08T901 4.7 73.8 1.0
C D:ASP343 4.7 88.2 1.0
O1B C:08T901 4.8 59.8 1.0
N D:GLY344 4.8 91.5 1.0
O D:ASP343 4.8 89.7 1.0
F2 C:08T901 4.9 74.4 1.0

Magnesium binding site 6 out of 8 in 8uaa

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Magnesium binding site 6 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 3


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

b:65.7
occ:1.00
 OG1 C:THR535 1.8 65.6 1.0
O2B C:08T903 2.0 69.1 1.0
F1 C:08T903 2.2 70.2 1.0
CB C:THR535 3.1 64.3 1.0
PB C:08T903 3.2 69.3 1.0
BE C:08T903 3.4 67.6 1.0
O3B C:08T903 3.6 68.5 1.0
O3A C:08T903 3.9 70.4 1.0
CG2 C:THR535 4.0 66.3 1.0
N C:THR535 4.1 63.8 1.0
CA C:THR535 4.1 62.5 1.0
OD1 C:ASP587 4.1 79.7 1.0
OD2 C:ASP587 4.1 76.6 1.0
F2 C:08T903 4.3 72.2 1.0
O1B C:08T903 4.5 63.6 1.0
F3 C:08T903 4.6 67.8 1.0
CG C:ASP587 4.6 75.4 1.0
O D:ASP619 4.6 79.3 1.0
OE2 C:GLU588 4.7 81.7 1.0
OD2 D:ASP619 4.9 80.0 1.0
PA C:08T903 5.0 77.2 1.0

Magnesium binding site 7 out of 8 in 8uaa

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Magnesium binding site 7 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 3


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

b:92.4
occ:1.00
 OG1 D:THR262 1.8 89.5 1.0
O2B D:08T901 1.9 82.3 1.0
F1 D:08T901 2.6 85.8 1.0
CB D:THR262 3.0 81.1 1.0
PB D:08T901 3.3 76.7 1.0
BE D:08T901 3.7 90.6 1.0
O3B D:08T901 3.8 88.6 1.0
CG2 D:THR262 3.9 90.8 1.0
O3A D:08T901 4.0 86.5 1.0
N D:THR262 4.0 76.0 1.0
OD2 D:ASP314 4.0 98.1 1.0
CA D:THR262 4.1 75.8 1.0
O2A D:08T901 4.4 99.8 1.0
OD1 D:ASP314 4.4 92.7 1.0
O1B D:08T901 4.5 80.7 1.0
F2 D:08T901 4.5 89.9 1.0
PA D:08T901 4.7 98.7 1.0
CG D:ASP314 4.7 91.6 1.0
NH2 E:ARG372 4.8 126.7 1.0
O1A D:08T901 4.8 91.5 1.0
F3 D:08T901 5.0 96.2 1.0

Magnesium binding site 8 out of 8 in 8uaa

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Magnesium binding site 8 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of CDC48-SHP1 Unfolding Native Substrate, Class 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:94.9
occ:1.00
 O2B D:08T903 1.9 93.1 1.0
F1 D:08T903 1.9 90.7 1.0
OG1 D:THR535 2.3 90.8 1.0
PB D:08T903 2.5 90.4 1.0
O3B D:08T903 2.7 93.4 1.0
BE D:08T903 2.8 94.0 1.0
O3A D:08T903 2.9 80.7 1.0
CB D:THR535 2.9 81.2 1.0
O2A D:08T903 2.9 86.5 1.0
PA D:08T903 3.4 83.2 1.0
F3 D:08T903 3.7 102.4 1.0
CG2 D:THR535 3.8 83.7 1.0
O1A D:08T903 4.0 81.9 1.0
O1B D:08T903 4.0 88.4 1.0
F2 D:08T903 4.1 84.2 1.0
N D:THR535 4.1 74.1 1.0
CA D:THR535 4.1 74.6 1.0
O E:ASP619 4.2 114.4 1.0
NH2 E:ARG648 4.5 105.9 1.0
O5' D:08T903 4.9 82.7 1.0
CG D:LYS534 4.9 73.7 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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