Magnesium in PDB 8u9p: CDC48-SHP1 Unfolding Native Substrate, Class 2

Enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 2

All present enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 2:
3.6.4.6;

Other elements in 8u9p:

The structure of CDC48-SHP1 Unfolding Native Substrate, Class 2 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 2 (pdb code 8u9p). 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 2, PDB code: 8u9p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8u9p

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Magnesium binding site 1 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 2


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

b:146.4
occ:1.00
 F1 A:08T901 1.9 142.1 1.0
O2B A:08T901 2.0 142.1 1.0
OG1 A:THR262 2.4 147.9 1.0
BE A:08T901 2.9 146.1 1.0
PB A:08T901 2.9 133.8 1.0
O3B A:08T901 3.0 141.6 1.0
CB A:THR262 3.1 143.8 1.0
O2A A:08T901 3.4 145.6 1.0
O3A A:08T901 3.7 143.2 1.0
F3 A:08T901 3.7 148.9 1.0
N A:THR262 4.0 137.8 1.0
CG2 A:THR262 4.1 136.2 1.0
CA A:THR262 4.2 142.9 1.0
F2 A:08T901 4.2 151.7 1.0
PA A:08T901 4.2 157.1 1.0
CG A:LYS261 4.3 143.4 1.0
O1B A:08T901 4.3 138.8 1.0
OD1 B:ASP343 4.6 168.5 1.0
NH1 B:ARG369 4.9 133.4 1.0
CD A:LYS261 5.0 148.7 1.0

Magnesium binding site 2 out of 8 in 8u9p

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


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

b:88.3
occ:1.00
 OG1 A:THR535 1.8 105.6 1.0
F1 A:08T903 1.9 105.2 1.0
O2B A:08T903 2.6 103.6 1.0
CB A:THR535 2.7 104.0 1.0
O2A A:08T903 3.1 111.2 1.0
BE A:08T903 3.2 105.3 1.0
PB A:08T903 3.5 102.4 1.0
O3A A:08T903 3.6 96.7 1.0
F3 A:08T903 3.7 112.9 1.0
O3B A:08T903 3.7 103.5 1.0
CG2 A:THR535 3.7 114.0 1.0
PA A:08T903 3.7 109.1 1.0
N A:THR535 3.7 91.7 1.0
CA A:THR535 3.8 95.9 1.0
O1A A:08T903 3.9 109.0 1.0
F2 A:08T903 4.4 100.5 1.0
NH2 B:ARG648 4.6 114.7 1.0
OD2 B:ASP619 4.8 121.6 1.0
O1B A:08T903 4.9 103.3 1.0
C A:LYS534 5.0 95.7 1.0

Magnesium binding site 3 out of 8 in 8u9p

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


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

b:101.9
occ:1.00
 F1 B:08T901 1.8 98.0 1.0
O1B B:08T901 2.0 95.2 1.0
OG1 B:THR262 2.0 95.9 1.0
CB B:THR262 2.7 93.2 1.0
PB B:08T901 2.9 85.1 1.0
BE B:08T901 3.0 97.1 1.0
O2A B:08T901 3.0 99.7 1.0
O3B B:08T901 3.2 88.6 1.0
O3A B:08T901 3.3 86.6 1.0
N B:THR262 3.5 86.3 1.0
PA B:08T901 3.6 95.2 1.0
CA B:THR262 3.7 85.8 1.0
O1A B:08T901 3.8 93.0 1.0
CG2 B:THR262 3.9 98.2 1.0
F2 B:08T901 4.0 103.3 1.0
F3 B:08T901 4.1 106.7 1.0
O2B B:08T901 4.3 95.0 1.0
OD2 C:ASP343 4.4 118.8 1.0
NH2 C:ARG372 4.6 94.0 1.0
C B:LYS261 4.7 86.0 1.0
O C:ASP343 4.7 111.4 1.0
C B:THR262 4.8 92.4 1.0
CB B:LYS261 4.9 78.1 1.0
NH2 C:ARG369 4.9 91.6 1.0

Magnesium binding site 4 out of 8 in 8u9p

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


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

b:98.5
occ:1.00
 F1 B:08T903 1.9 99.4 1.0
O1B B:08T903 2.0 99.3 1.0
OG1 B:THR535 2.1 102.1 1.0
PB B:08T903 3.1 93.2 1.0
BE B:08T903 3.1 97.5 1.0
O3B B:08T903 3.2 92.9 1.0
CB B:THR535 3.5 88.5 1.0
O3A B:08T903 3.8 88.5 1.0
NH2 C:ARG648 4.0 100.3 1.0
F2 B:08T903 4.1 104.4 1.0
F3 B:08T903 4.1 101.3 1.0
N B:THR535 4.2 79.7 1.0
OD1 B:ASP587 4.2 108.9 1.0
O2B B:08T903 4.3 89.3 1.0
CG2 B:THR535 4.3 98.7 1.0
CA B:THR535 4.4 80.6 1.0
OD2 B:ASP587 4.5 111.6 1.0
O C:ASP619 4.7 124.6 1.0
CG B:ASP587 4.8 106.0 1.0
PA B:08T903 4.9 93.6 1.0
OE2 B:GLU588 4.9 113.4 1.0
O2A B:08T903 4.9 105.7 1.0
O1A B:08T903 5.0 91.5 1.0

Magnesium binding site 5 out of 8 in 8u9p

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Magnesium binding site 5 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 2


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

b:102.7
occ:1.00
 F1 C:08T901 1.9 105.5 1.0
O2B C:08T901 2.0 90.8 1.0
OG1 C:THR262 2.1 89.0 1.0
CB C:THR262 2.9 85.4 1.0
PB C:08T901 3.0 89.9 1.0
BE C:08T901 3.1 99.1 1.0
O3B C:08T901 3.2 90.4 1.0
O3A C:08T901 3.5 90.3 1.0
N C:THR262 3.6 83.2 1.0
O2A C:08T901 3.7 97.5 1.0
CA C:THR262 3.9 80.9 1.0
PA C:08T901 4.1 98.7 1.0
CG2 C:THR262 4.1 93.3 1.0
F3 C:08T901 4.1 99.3 1.0
F2 C:08T901 4.2 102.1 1.0
O1A C:08T901 4.4 94.5 1.0
O1B C:08T901 4.4 91.1 1.0
NH2 D:ARG372 4.6 96.4 1.0
OD2 C:ASP314 4.7 106.3 1.0
CB C:LYS261 4.7 73.1 1.0
O D:ASP343 4.7 109.5 1.0
OD1 C:ASP314 4.8 99.0 1.0
C C:LYS261 4.8 83.1 1.0

Magnesium binding site 6 out of 8 in 8u9p

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Magnesium binding site 6 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 2


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

b:100.3
occ:1.00
 F1 C:08T903 1.8 91.9 1.0
O2B C:08T903 1.8 90.5 1.0
PB C:08T903 2.3 89.0 1.0
OG1 C:THR535 2.4 87.2 1.0
O3A C:08T903 2.6 87.2 1.0
O3B C:08T903 2.6 89.4 1.0
BE C:08T903 2.7 94.9 1.0
CB C:THR535 3.0 85.4 1.0
O2A C:08T903 3.4 97.9 1.0
PA C:08T903 3.4 99.3 1.0
F3 C:08T903 3.7 95.9 1.0
N C:THR535 3.7 80.3 1.0
O1A C:08T903 3.8 91.2 1.0
O1B C:08T903 3.8 83.8 1.0
F2 C:08T903 3.9 105.2 1.0
CA C:THR535 4.0 81.2 1.0
CG2 C:THR535 4.1 92.4 1.0
OD2 D:ASP619 4.5 107.4 1.0
O D:ASP619 4.6 108.4 1.0
CG D:ASP619 4.7 106.8 1.0
NH1 D:ARG645 4.8 87.8 1.0
O5' C:08T903 4.8 85.5 1.0
OD1 D:ASP619 4.9 108.0 1.0
NH2 D:ARG648 4.9 86.5 1.0
C C:LYS534 4.9 77.7 1.0

Magnesium binding site 7 out of 8 in 8u9p

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


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

b:114.5
occ:1.00
 OG1 D:THR262 1.7 106.3 1.0
O2B D:08T901 1.9 110.8 1.0
F1 D:08T901 2.0 121.4 1.0
CB D:THR262 2.9 100.5 1.0
PB D:08T901 3.2 100.4 1.0
BE D:08T901 3.3 118.7 1.0
O3B D:08T901 3.5 112.0 1.0
N D:THR262 3.8 93.4 1.0
CG2 D:THR262 3.9 113.5 1.0
CA D:THR262 3.9 92.2 1.0
O3A D:08T901 3.9 109.8 1.0
F3 D:08T901 4.2 125.8 1.0
OD1 E:ASP343 4.2 137.6 1.0
F2 D:08T901 4.4 119.1 1.0
O1B D:08T901 4.4 99.6 1.0
NH2 E:ARG372 4.7 122.8 1.0
O1A D:08T901 4.8 114.5 1.0
PA D:08T901 4.8 121.7 1.0
O2A D:08T901 4.9 125.3 1.0
C D:LYS261 4.9 95.9 1.0
CB D:LYS261 4.9 82.1 1.0

Magnesium binding site 8 out of 8 in 8u9p

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


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

b:102.6
occ:1.00
 OG1 D:THR535 1.8 101.5 1.0
F1 D:08T903 1.9 108.3 1.0
O2B D:08T903 2.0 107.3 1.0
CB D:THR535 2.8 102.7 1.0
PB D:08T903 3.1 103.7 1.0
BE D:08T903 3.2 102.5 1.0
O1A D:08T903 3.5 111.0 1.0
O3B D:08T903 3.5 98.9 1.0
O3A D:08T903 3.6 104.2 1.0
N D:THR535 3.7 89.9 1.0
CG2 D:THR535 3.9 109.6 1.0
CA D:THR535 3.9 92.8 1.0
F3 D:08T903 3.9 107.2 1.0
PA D:08T903 3.9 112.8 1.0
O2A D:08T903 4.2 104.7 1.0
O E:ASP619 4.2 120.8 1.0
F2 D:08T903 4.4 97.8 1.0
O1B D:08T903 4.5 99.4 1.0
NH2 E:ARG648 4.8 116.5 1.0
CB D:LYS534 4.8 86.4 1.0
C D:LYS534 4.9 88.4 1.0
OD2 D:ASP587 4.9 101.8 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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