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Magnesium in PDB 8u8i: CDC48-SHP1 Unfolding Native Substrate, Class 4

Enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 4

All present enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 4:
3.6.4.6;

Other elements in 8u8i:

The structure of CDC48-SHP1 Unfolding Native Substrate, Class 4 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 4 (pdb code 8u8i). 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 4, PDB code: 8u8i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8u8i

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Magnesium binding site 1 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 4


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

b:99.5
occ:1.00
 F1 A:08T901 2.0 97.7 1.0
O2B A:08T901 2.0 93.8 1.0
OG1 A:THR262 2.3 92.7 1.0
PB A:08T901 2.9 93.8 1.0
BE A:08T901 3.0 97.7 1.0
O3B A:08T901 3.1 93.8 1.0
CB A:THR262 3.2 92.7 1.0
O2A A:08T901 3.4 93.8 1.0
O3A A:08T901 3.5 93.8 1.0
PA A:08T901 4.0 93.8 1.0
N A:THR262 4.0 92.7 1.0
NH2 B:ARG372 4.1 102.8 1.0
F2 A:08T901 4.1 97.7 1.0
F3 A:08T901 4.2 97.7 1.0
CA A:THR262 4.2 92.7 1.0
CG2 A:THR262 4.2 92.7 1.0
O1B A:08T901 4.3 93.8 1.0
O1A A:08T901 4.4 93.8 1.0
OD1 B:ASP343 4.9 127.0 1.0
CG B:ASP343 4.9 127.0 1.0
OD2 B:ASP343 5.0 127.0 1.0

Magnesium binding site 2 out of 8 in 8u8i

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Magnesium binding site 2 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 4


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

b:70.3
occ:1.00
 F1 A:08T903 1.9 76.3 1.0
O2B A:08T903 2.0 77.3 1.0
OG1 A:THR535 2.2 68.5 1.0
PB A:08T903 2.8 77.3 1.0
O2A A:08T903 2.9 77.3 1.0
BE A:08T903 3.0 76.3 1.0
O3B A:08T903 3.1 77.3 1.0
CB A:THR535 3.1 68.5 1.0
O3A A:08T903 3.2 77.3 1.0
PA A:08T903 3.5 77.3 1.0
N A:THR535 3.7 68.5 1.0
O1A A:08T903 3.8 77.3 1.0
F3 A:08T903 3.9 76.3 1.0
CA A:THR535 4.1 68.5 1.0
F2 A:08T903 4.2 76.3 1.0
CG2 A:THR535 4.3 68.5 1.0
O1B A:08T903 4.3 77.3 1.0
NH2 B:ARG648 4.4 85.5 1.0
OD2 B:ASP619 4.9 97.4 1.0
C A:LYS534 4.9 68.1 1.0
O5' A:08T903 4.9 77.3 1.0
CB A:LYS534 4.9 68.1 1.0

Magnesium binding site 3 out of 8 in 8u8i

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


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

b:96.5
occ:1.00
 O1B B:08T901 1.9 83.2 1.0
F1 B:08T901 1.9 87.4 1.0
OG1 B:THR262 2.3 80.5 1.0
PB B:08T901 2.5 83.2 1.0
O3B B:08T901 2.7 83.2 1.0
O3A B:08T901 2.7 83.2 1.0
BE B:08T901 2.8 87.4 1.0
CB B:THR262 2.9 80.5 1.0
O2A B:08T901 3.2 83.2 1.0
PA B:08T901 3.4 83.2 1.0
O1A B:08T901 3.7 83.2 1.0
F3 B:08T901 3.7 87.4 1.0
N B:THR262 3.9 80.5 1.0
O2B B:08T901 4.0 83.2 1.0
CG2 B:THR262 4.0 80.5 1.0
CA B:THR262 4.0 80.5 1.0
F2 B:08T901 4.1 87.4 1.0
CG B:LYS261 4.4 76.0 1.0
NH2 C:ARG372 4.6 93.6 1.0
OD2 C:ASP343 4.6 103.2 1.0
NH2 C:ARG369 4.7 91.0 1.0
CG C:ASP343 4.7 103.2 1.0
O5' B:08T901 4.8 83.2 1.0
OD1 C:ASP343 4.9 103.2 1.0

Magnesium binding site 4 out of 8 in 8u8i

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


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

b:88.3
occ:1.00
 O2B B:08T903 2.0 81.5 1.0
F1 B:08T903 2.0 83.7 1.0
O3A B:08T903 2.2 81.5 1.0
OG1 B:THR535 2.3 80.5 1.0
PB B:08T903 2.3 81.5 1.0
O3B B:08T903 2.8 81.5 1.0
BE B:08T903 2.9 83.7 1.0
CB B:THR535 3.2 80.5 1.0
PA B:08T903 3.2 81.5 1.0
O1A B:08T903 3.3 81.5 1.0
O2A B:08T903 3.6 81.5 1.0
N B:THR535 3.7 80.5 1.0
F3 B:08T903 3.7 83.7 1.0
O1B B:08T903 3.8 81.5 1.0
CA B:THR535 4.1 80.5 1.0
F2 B:08T903 4.2 83.7 1.0
CG2 B:THR535 4.3 80.5 1.0
O5' B:08T903 4.5 81.5 1.0
OD2 C:ASP619 4.6 92.0 1.0
NH2 C:ARG648 4.7 80.4 1.0
CG C:ASP619 4.8 92.0 1.0
OD1 C:ASP619 4.8 92.0 1.0
O C:ASP619 4.8 92.0 1.0
C B:LYS534 4.9 74.8 1.0
N B:LYS534 4.9 74.8 1.0
CB B:LYS534 4.9 74.8 1.0

Magnesium binding site 5 out of 8 in 8u8i

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Magnesium binding site 5 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 4


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

b:100.0
occ:1.00
 OD2 D:ASP343 2.0 103.3 1.0
OD1 D:ASP343 2.3 103.3 1.0
O2A C:08T901 2.3 81.8 1.0
CG D:ASP343 2.4 103.3 1.0
OG1 C:THR262 2.9 85.0 1.0
CB C:THR262 3.0 85.0 1.0
O3A C:08T901 3.1 81.8 1.0
PA C:08T901 3.2 81.8 1.0
O2B C:08T901 3.3 81.8 1.0
CG2 C:THR262 3.4 85.0 1.0
F1 C:08T901 3.5 86.3 1.0
PB C:08T901 3.6 81.8 1.0
O1A C:08T901 3.9 81.8 1.0
O3B C:08T901 3.9 81.8 1.0
CB D:ASP343 3.9 103.3 1.0
N D:GLY344 4.0 108.8 1.0
BE C:08T901 4.3 86.3 1.0
C D:ASP343 4.3 103.3 1.0
CA C:THR262 4.4 85.0 1.0
CA D:GLY344 4.4 108.8 1.0
NH2 D:ARG372 4.5 90.9 1.0
NH2 D:ARG369 4.5 92.2 1.0
O5' C:08T901 4.5 81.8 1.0
CA D:ASP343 4.7 103.3 1.0
N C:THR262 4.8 85.0 1.0
O D:ASP343 4.8 103.3 1.0

Magnesium binding site 6 out of 8 in 8u8i

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Magnesium binding site 6 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 4


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

b:75.6
occ:1.00
 OG1 C:THR535 1.9 79.2 1.0
F1 C:08T903 1.9 91.6 1.0
O2B C:08T903 2.0 83.5 1.0
BE C:08T903 3.2 91.6 1.0
PB C:08T903 3.3 83.5 1.0
CB C:THR535 3.3 79.2 1.0
O3B C:08T903 3.5 83.5 1.0
OD1 C:ASP587 3.7 86.3 1.0
OD2 C:ASP587 4.0 86.3 1.0
N C:THR535 4.0 79.2 1.0
CG2 C:THR535 4.1 79.2 1.0
CA C:THR535 4.2 79.2 1.0
F2 C:08T903 4.2 91.6 1.0
OE2 C:GLU588 4.2 88.4 1.0
CG C:ASP587 4.2 86.3 1.0
F3 C:08T903 4.3 91.6 1.0
O1B C:08T903 4.3 83.5 1.0
O3A C:08T903 4.3 83.5 1.0
O D:ASP619 4.5 97.2 1.0
O2A C:08T903 4.8 83.5 1.0
NH2 D:ARG648 4.8 90.7 1.0
CB C:LYS534 4.8 74.9 1.0

Magnesium binding site 7 out of 8 in 8u8i

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Magnesium binding site 7 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 4


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

b:122.1
occ:1.00
 O2B D:08T901 2.0 122.1 1.0
F1 D:08T901 2.1 142.3 1.0
OG1 D:THR262 2.2 103.1 1.0
PB D:08T901 3.1 122.1 1.0
CB D:THR262 3.3 103.1 1.0
BE D:08T901 3.3 142.3 1.0
O3B D:08T901 3.4 122.1 1.0
O2A D:08T901 3.6 122.1 1.0
O3A D:08T901 3.8 122.1 1.0
NH2 E:ARG372 4.0 226.2 1.0
CG2 D:THR262 4.1 103.1 1.0
F2 D:08T901 4.2 142.3 1.0
PA D:08T901 4.2 122.1 1.0
N D:THR262 4.3 103.1 1.0
CA D:THR262 4.4 103.1 1.0
F3 D:08T901 4.4 142.3 1.0
O1B D:08T901 4.4 122.1 1.0
O1A D:08T901 4.5 122.1 1.0

Magnesium binding site 8 out of 8 in 8u8i

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


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

b:130.0
occ:1.00
 O2B D:08T903 1.9 129.4 1.0
F1 D:08T903 2.1 137.2 1.0
O1A D:08T903 2.1 129.4 1.0
OG1 D:THR535 2.1 122.9 1.0
O3A D:08T903 2.6 129.4 1.0
PB D:08T903 2.6 129.4 1.0
PA D:08T903 2.6 129.4 1.0
CB D:THR535 2.7 122.9 1.0
O2A D:08T903 3.0 129.4 1.0
BE D:08T903 3.1 137.2 1.0
O3B D:08T903 3.2 129.4 1.0
N D:THR535 3.5 122.9 1.0
F3 D:08T903 3.7 137.2 1.0
CA D:THR535 3.7 122.9 1.0
CG2 D:THR535 3.9 122.9 1.0
O1B D:08T903 4.0 129.4 1.0
O5' D:08T903 4.1 129.4 1.0
F2 D:08T903 4.4 137.2 1.0
C D:LYS534 4.7 117.7 1.0
C D:THR535 4.7 122.9 1.0
O E:ASP619 4.7 182.5 1.0
N D:LYS534 4.8 117.7 1.0
N D:LEU536 4.8 122.0 1.0
C5' D:08T903 4.9 129.4 1.0
CB D:LYS534 5.0 117.7 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 11:58:11 2024

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