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Magnesium in PDB 8u9c: CDC48-SHP1 Unfolding Native Substrate, Class 5

Enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 5

All present enzymatic activity of CDC48-SHP1 Unfolding Native Substrate, Class 5:
3.6.4.6;

Other elements in 8u9c:

The structure of CDC48-SHP1 Unfolding Native Substrate, Class 5 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 5 (pdb code 8u9c). 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 5, PDB code: 8u9c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8u9c

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Magnesium binding site 1 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


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

b:136.7
occ:1.00
 OG1 A:THR262 1.8 128.3 1.0
F1 A:08T901 2.0 140.4 1.0
O2B A:08T901 2.0 131.5 1.0
CB A:THR262 3.0 128.3 1.0
PB A:08T901 3.1 131.5 1.0
BE A:08T901 3.2 140.4 1.0
O3B A:08T901 3.5 131.5 1.0
O2A A:08T901 3.8 131.5 1.0
O3A A:08T901 3.8 131.5 1.0
CG2 A:THR262 3.8 128.3 1.0
N A:THR262 4.0 128.3 1.0
CA A:THR262 4.0 128.3 1.0
F3 A:08T901 4.1 140.4 1.0
CG A:LYS261 4.2 132.3 1.0
F2 A:08T901 4.4 140.4 1.0
PA A:08T901 4.4 131.5 1.0
O1B A:08T901 4.5 131.5 1.0
OD2 A:ASP314 4.5 177.8 1.0
NH2 B:ARG372 4.6 133.3 1.0
CD A:LYS261 4.8 132.3 1.0
O1A A:08T901 4.9 131.5 1.0
NH2 B:ARG369 5.0 142.1 1.0

Magnesium binding site 2 out of 8 in 8u9c

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


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

b:114.5
occ:1.00
 OG1 A:THR535 1.9 110.5 1.0
F1 A:08T903 2.0 110.9 1.0
O1A A:08T903 2.0 117.4 1.0
O2B A:08T903 2.3 117.4 1.0
CB A:THR535 2.5 110.5 1.0
PA A:08T903 2.6 117.4 1.0
O2A A:08T903 2.8 117.4 1.0
O3A A:08T903 2.9 117.4 1.0
PB A:08T903 3.0 117.4 1.0
N A:THR535 3.1 110.5 1.0
BE A:08T903 3.2 110.9 1.0
CA A:THR535 3.4 110.5 1.0
O3B A:08T903 3.5 117.4 1.0
CG2 A:THR535 3.8 110.5 1.0
F2 A:08T903 4.0 110.9 1.0
O5' A:08T903 4.1 117.4 1.0
C A:LYS534 4.3 109.5 1.0
F3 A:08T903 4.4 110.9 1.0
O1B A:08T903 4.4 117.4 1.0
C A:THR535 4.5 110.5 1.0
N A:LYS534 4.5 109.5 1.0
CB A:LYS534 4.6 109.5 1.0
N A:LEU536 4.7 115.6 1.0
CA A:LYS534 4.7 109.5 1.0
C5' A:08T903 4.8 117.4 1.0

Magnesium binding site 3 out of 8 in 8u9c

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


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

b:123.1
occ:1.00
 OG1 B:THR262 1.8 112.0 1.0
O2B B:08T901 1.9 121.4 1.0
F1 B:08T901 2.1 125.0 1.0
CB B:THR262 2.5 112.0 1.0
PB B:08T901 2.8 121.4 1.0
O3A B:08T901 3.0 121.4 1.0
BE B:08T901 3.1 125.0 1.0
O1A B:08T901 3.1 121.4 1.0
O3B B:08T901 3.2 121.4 1.0
CG2 B:THR262 3.4 112.0 1.0
PA B:08T901 3.5 121.4 1.0
CA B:THR262 3.7 112.0 1.0
O2A B:08T901 3.7 121.4 1.0
N B:THR262 3.7 112.0 1.0
F3 B:08T901 4.0 125.0 1.0
OD1 C:ASP343 4.1 138.8 1.0
O1B B:08T901 4.2 121.4 1.0
F2 B:08T901 4.4 125.0 1.0
NH2 C:ARG372 4.6 131.3 1.0
CG B:LYS261 4.7 109.4 1.0
C B:THR262 4.7 112.0 1.0
NH2 C:ARG369 4.8 133.8 1.0
CG C:ASP343 5.0 138.8 1.0
O5' B:08T901 5.0 121.4 1.0
C B:LYS261 5.0 109.4 1.0
N B:LEU263 5.0 120.6 1.0

Magnesium binding site 4 out of 8 in 8u9c

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


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

b:123.6
occ:1.00
 O2B B:08T903 2.0 119.0 1.0
O3A B:08T903 2.0 119.0 1.0
F1 B:08T903 2.2 125.5 1.0
OG1 B:THR535 2.3 113.8 1.0
PB B:08T903 2.3 119.0 1.0
PA B:08T903 2.9 119.0 1.0
O1A B:08T903 2.9 119.0 1.0
O3B B:08T903 2.9 119.0 1.0
BE B:08T903 3.0 125.5 1.0
CB B:THR535 3.2 113.8 1.0
O2A B:08T903 3.4 119.0 1.0
F3 B:08T903 3.5 125.5 1.0
O1B B:08T903 3.8 119.0 1.0
N B:THR535 3.9 113.8 1.0
CA B:THR535 4.2 113.8 1.0
NH2 C:ARG648 4.2 114.1 1.0
O5' B:08T903 4.2 119.0 1.0
CG2 B:THR535 4.3 113.8 1.0
F2 B:08T903 4.4 125.5 1.0
C5' B:08T903 5.0 119.0 1.0

Magnesium binding site 5 out of 8 in 8u9c

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


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

b:142.4
occ:1.00
 OD2 D:ASP343 2.1 156.5 1.0
O2B C:08T901 2.2 121.7 1.0
F1 C:08T901 2.3 127.5 1.0
OG1 C:THR262 2.3 118.6 1.0
CB C:THR262 3.0 118.6 1.0
PB C:08T901 3.0 121.7 1.0
O3B C:08T901 3.3 121.7 1.0
CG D:ASP343 3.3 156.5 1.0
BE C:08T901 3.3 127.5 1.0
O3A C:08T901 3.3 121.7 1.0
O1A C:08T901 3.7 121.7 1.0
CG2 C:THR262 3.8 118.6 1.0
OD1 D:ASP343 3.9 156.5 1.0
NH2 D:ARG372 4.0 133.3 1.0
PA C:08T901 4.1 121.7 1.0
CA C:THR262 4.2 118.6 1.0
F3 C:08T901 4.3 127.5 1.0
N C:THR262 4.3 118.6 1.0
CB D:ASP343 4.4 156.5 1.0
O2A C:08T901 4.5 121.7 1.0
O1B C:08T901 4.5 121.7 1.0
F2 C:08T901 4.5 127.5 1.0
NH2 D:ARG369 4.6 129.7 1.0
O D:ASP343 4.8 156.5 1.0
OD2 C:ASP314 4.9 135.9 1.0
C D:ASP343 5.0 156.5 1.0
CG C:LYS261 5.0 118.5 1.0

Magnesium binding site 6 out of 8 in 8u9c

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Magnesium binding site 6 out of 8 in the CDC48-SHP1 Unfolding Native Substrate, Class 5


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

b:124.8
occ:1.00
 O2B C:08T903 2.0 126.6 1.0
F1 C:08T903 2.0 131.1 1.0
OG1 C:THR535 2.3 121.0 1.0
PB C:08T903 3.3 126.6 1.0
BE C:08T903 3.3 131.1 1.0
OD2 C:ASP587 3.6 134.3 1.0
O3B C:08T903 3.7 126.6 1.0
CB C:THR535 3.7 121.0 1.0
OD1 C:ASP587 3.8 134.3 1.0
CG C:ASP587 4.1 134.3 1.0
F2 C:08T903 4.2 131.1 1.0
O3A C:08T903 4.2 126.6 1.0
O D:ASP619 4.4 147.0 1.0
O1B C:08T903 4.4 126.6 1.0
N C:THR535 4.4 121.0 1.0
F3 C:08T903 4.4 131.1 1.0
CG2 C:THR535 4.5 121.0 1.0
CA C:THR535 4.5 121.0 1.0
OE2 C:GLU588 4.6 137.5 1.0
NH2 D:ARG648 4.6 133.2 1.0

Magnesium binding site 7 out of 8 in 8u9c

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


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

b:150.4
occ:1.00
 O2B D:08T901 1.9 154.4 1.0
OG1 D:THR262 2.3 150.2 1.0
O3A D:08T901 2.6 154.4 1.0
PB D:08T901 2.6 154.4 1.0
F1 D:08T901 2.7 150.2 1.0
CB D:THR262 2.8 150.2 1.0
O2A D:08T901 3.1 154.4 1.0
PA D:08T901 3.2 154.4 1.0
O3B D:08T901 3.3 154.4 1.0
O1A D:08T901 3.6 154.4 1.0
BE D:08T901 3.6 150.2 1.0
CG2 D:THR262 3.6 150.2 1.0
O1B D:08T901 4.0 154.4 1.0
CA D:THR262 4.1 150.2 1.0
N D:THR262 4.2 150.2 1.0
F3 D:08T901 4.6 150.2 1.0
O5' D:08T901 4.7 154.4 1.0
F2 D:08T901 4.7 150.2 1.0
NH1 D:ARG266 4.8 170.8 1.0
C D:THR262 5.0 150.2 1.0

Magnesium binding site 8 out of 8 in 8u9c

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


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

b:180.8
occ:1.00
 O2B D:08T903 2.0 180.7 1.0
F1 D:08T903 2.1 190.8 1.0
O2A D:08T903 2.1 180.7 1.0
OG1 D:THR535 2.3 178.6 1.0
PB D:08T903 2.5 180.7 1.0
O3A D:08T903 2.5 180.7 1.0
BE D:08T903 2.7 190.8 1.0
PA D:08T903 2.7 180.7 1.0
CB D:THR535 2.8 178.6 1.0
O3B D:08T903 2.9 180.7 1.0
F3 D:08T903 2.9 190.8 1.0
O1A D:08T903 3.3 180.7 1.0
N D:THR535 3.6 178.6 1.0
CA D:THR535 3.8 178.6 1.0
CG2 D:THR535 4.0 178.6 1.0
O1B D:08T903 4.0 180.7 1.0
O5' D:08T903 4.2 180.7 1.0
F2 D:08T903 4.2 190.8 1.0
O E:ASP619 4.6 256.9 1.0
C5' D:08T903 4.8 180.7 1.0
C D:THR535 4.8 178.6 1.0
NH2 E:ARG648 4.8 231.0 1.0
C D:LYS534 4.8 164.6 1.0
N D:LEU536 4.9 179.5 1.0
N D:LYS534 4.9 164.6 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 11:58:13 2024

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