Magnesium in PDB 8ua0: CDC48-SHP1 Unfolding Native Substrate, Class 8

Enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 8

All present enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 8:
3.6.4.6;

Other elements in 8ua0:

The structure of CDC48-SHP1 Unfolding Native Substrate, Class 8 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 8 (pdb code 8ua0). 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 8, PDB code: 8ua0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8ua0

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Magnesium binding site 1 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 8


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

b:108.9
occ:1.00
 OG1 A:THR262 1.9 112.9 1.0
F1 A:08T901 2.1 114.7 1.0
O2B A:08T901 2.5 109.4 1.0
CB A:THR262 3.2 112.9 1.0
BE A:08T901 3.4 114.7 1.0
PB A:08T901 3.6 109.4 1.0
O3B A:08T901 3.7 109.4 1.0
N A:THR262 3.8 112.9 1.0
CA A:THR262 4.0 112.9 1.0
CG2 A:THR262 4.1 112.9 1.0
NH2 B:ARG372 4.4 112.8 1.0
O3A A:08T901 4.4 109.4 1.0
F2 A:08T901 4.4 114.7 1.0
F3 A:08T901 4.4 114.7 1.0
O2A A:08T901 4.4 109.4 1.0
OD2 A:ASP314 4.5 126.3 1.0
OD1 A:ASP314 4.5 126.3 1.0
CB A:LYS261 4.8 108.1 1.0
OD2 B:ASP343 4.9 123.7 1.0
CG A:ASP314 4.9 126.3 1.0
C A:LYS261 5.0 108.1 1.0
O1B A:08T901 5.0 109.4 1.0
PA A:08T901 5.0 109.4 1.0

Magnesium binding site 2 out of 7 in 8ua0

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Magnesium binding site 2 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 8


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

b:106.4
occ:1.00
 O2B A:08T903 2.0 98.8 1.0
F1 A:08T903 2.0 103.0 1.0
OG1 A:THR535 2.3 92.5 1.0
O1A A:08T903 2.5 98.8 1.0
PB A:08T903 2.5 98.8 1.0
O3A A:08T903 2.5 98.8 1.0
CB A:THR535 2.7 92.5 1.0
PA A:08T903 2.8 98.8 1.0
O3B A:08T903 2.8 98.8 1.0
BE A:08T903 2.9 103.0 1.0
O2A A:08T903 3.1 98.8 1.0
N A:THR535 3.3 92.5 1.0
CA A:THR535 3.6 92.5 1.0
CG2 A:THR535 3.9 92.5 1.0
F2 A:08T903 3.9 103.0 1.0
O1B A:08T903 4.0 98.8 1.0
F3 A:08T903 4.1 103.0 1.0
O5' A:08T903 4.3 98.8 1.0
C A:LYS534 4.6 92.6 1.0
C A:THR535 4.6 92.5 1.0
NH2 B:ARG645 4.7 97.7 1.0
N A:LYS534 4.7 92.6 1.0
N A:LEU536 4.7 93.3 1.0
CB A:LYS534 4.8 92.6 1.0
NH2 B:ARG648 4.9 102.1 1.0
CA A:LYS534 5.0 92.6 1.0

Magnesium binding site 3 out of 7 in 8ua0

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


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

b:113.2
occ:1.00
 O2B B:08T901 2.0 97.4 1.0
F1 B:08T901 2.0 101.3 1.0
OG1 B:THR262 2.1 95.4 1.0
O3B B:08T901 2.4 97.4 1.0
PB B:08T901 2.5 97.4 1.0
CB B:THR262 2.6 95.4 1.0
BE B:08T901 2.7 101.3 1.0
O3A B:08T901 3.0 97.4 1.0
O1A B:08T901 3.2 97.4 1.0
N B:THR262 3.4 95.4 1.0
PA B:08T901 3.6 97.4 1.0
CA B:THR262 3.6 95.4 1.0
F3 B:08T901 3.7 101.3 1.0
CG2 B:THR262 3.8 95.4 1.0
O2A B:08T901 3.9 97.4 1.0
F2 B:08T901 3.9 101.3 1.0
O1B B:08T901 4.0 97.4 1.0
NH2 C:ARG369 4.3 102.8 1.0
NH2 C:ARG372 4.6 98.0 1.0
C B:LYS261 4.6 92.9 1.0
C B:THR262 4.7 95.4 1.0
O C:ASP343 4.8 116.8 1.0
N B:LYS261 4.8 92.9 1.0
N B:LEU263 4.9 100.9 1.0
OD2 C:ASP343 4.9 116.8 1.0
CB B:LYS261 5.0 92.9 1.0

Magnesium binding site 4 out of 7 in 8ua0

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


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

b:102.5
occ:1.00
 O2B B:08T903 2.0 89.7 1.0
F1 B:08T903 2.1 102.9 1.0
OG1 B:THR535 2.1 90.3 1.0
PB B:08T903 3.0 89.7 1.0
BE B:08T903 3.1 102.9 1.0
O3B B:08T903 3.2 89.7 1.0
CB B:THR535 3.4 90.3 1.0
OD1 B:ASP587 3.9 113.8 1.0
O3A B:08T903 3.9 89.7 1.0
F2 B:08T903 4.2 102.9 1.0
CG2 B:THR535 4.2 90.3 1.0
N B:THR535 4.2 90.3 1.0
OE2 B:GLU588 4.2 112.1 1.0
F3 B:08T903 4.2 102.9 1.0
O1B B:08T903 4.3 89.7 1.0
NH2 C:ARG648 4.3 95.6 1.0
CA B:THR535 4.4 90.3 1.0
OD2 B:ASP587 4.5 113.8 1.0
CG B:ASP587 4.6 113.8 1.0
O C:ASP619 4.7 114.5 1.0
O1A B:08T903 4.8 89.7 1.0
PA B:08T903 4.8 89.7 1.0
O2A B:08T903 4.9 89.7 1.0

Magnesium binding site 5 out of 7 in 8ua0

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Magnesium binding site 5 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 8


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

b:99.2
occ:1.00
 OG1 C:THR262 1.8 89.9 1.0
F1 C:08T901 2.0 97.0 1.0
O2B C:08T901 2.0 92.8 1.0
CB C:THR262 2.4 89.9 1.0
PB C:08T901 2.9 92.8 1.0
BE C:08T901 3.1 97.0 1.0
O3B C:08T901 3.2 92.8 1.0
O3A C:08T901 3.3 92.8 1.0
CG2 C:THR262 3.4 89.9 1.0
CA C:THR262 3.7 89.9 1.0
O1A C:08T901 3.7 92.8 1.0
N C:THR262 3.7 89.9 1.0
PA C:08T901 4.0 92.8 1.0
F3 C:08T901 4.1 97.0 1.0
O2A C:08T901 4.2 92.8 1.0
F2 C:08T901 4.3 97.0 1.0
O1B C:08T901 4.4 92.8 1.0
CG C:LYS261 4.6 87.7 1.0
NH2 D:ARG372 4.6 102.1 1.0
OD2 C:ASP314 4.7 103.4 1.0
C C:THR262 4.8 89.9 1.0

Magnesium binding site 6 out of 7 in 8ua0

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Magnesium binding site 6 out of 7 in the CDC48-SHP1 Unfolding Native Substrate, Class 8


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

b:96.7
occ:1.00
 O2B C:08T903 2.0 102.2 1.0
OG1 C:THR535 2.0 92.9 1.0
F1 C:08T903 2.1 106.7 1.0
PB C:08T903 3.0 102.2 1.0
BE C:08T903 3.1 106.7 1.0
O3B C:08T903 3.1 102.2 1.0
CB C:THR535 3.2 92.9 1.0
O3A C:08T903 3.6 102.2 1.0
F2 C:08T903 4.0 106.7 1.0
N C:THR535 4.1 92.9 1.0
CG2 C:THR535 4.2 92.9 1.0
CA C:THR535 4.2 92.9 1.0
NH2 D:ARG648 4.3 105.4 1.0
OD1 C:ASP587 4.3 101.0 1.0
F3 C:08T903 4.3 106.7 1.0
O1B C:08T903 4.4 102.2 1.0
O D:ASP619 4.4 120.2 1.0
OE2 C:GLU588 4.5 109.1 1.0
OD2 C:ASP587 4.6 101.0 1.0
PA C:08T903 4.7 102.2 1.0
O2A C:08T903 4.8 102.2 1.0
O1A C:08T903 4.9 102.2 1.0
CG C:ASP587 4.9 101.0 1.0

Magnesium binding site 7 out of 7 in 8ua0

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


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

b:265.4
occ:1.00
 N F:THR535 1.9 267.6 1.0
O2B F:08T901 2.0 240.5 1.0
OG1 F:THR535 2.1 267.6 1.0
C F:LYS534 2.7 259.5 1.0
CB F:LYS534 2.8 259.5 1.0
CA F:THR535 2.8 267.6 1.0
CB F:THR535 2.9 267.6 1.0
F1 F:08T901 3.1 234.6 1.0
CA F:LYS534 3.1 259.5 1.0
N F:LYS534 3.5 259.5 1.0
PB F:08T901 3.5 240.5 1.0
O F:LYS534 3.7 259.5 1.0
O2A F:08T901 3.9 240.5 1.0
CG F:LYS534 4.0 259.5 1.0
C F:THR535 4.1 267.6 1.0
CG2 F:THR535 4.2 267.6 1.0
CE F:LYS534 4.2 259.5 1.0
BE F:08T901 4.2 234.6 1.0
O3B F:08T901 4.3 240.5 1.0
O3A F:08T901 4.3 240.5 1.0
C F:GLY533 4.5 255.8 1.0
N F:LEU536 4.5 270.4 1.0
O1B F:08T901 4.5 240.5 1.0
CD F:LYS534 4.5 259.5 1.0
PA F:08T901 4.5 240.5 1.0
O1A F:08T901 4.6 240.5 1.0
CB F:ALA632 4.7 302.8 1.0
F2 F:08T901 4.8 234.6 1.0
NZ F:LYS534 4.8 259.5 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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