Atomistry » Magnesium » PDB 8u37-8ucw » 8u9p
Atomistry »
  Magnesium »
    PDB 8u37-8ucw »
      8u9p »

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

Go back to Magnesium Binding Sites List in 8u9p
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

Go back to Magnesium Binding Sites List in 8u9p
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

Go back to Magnesium Binding Sites List in 8u9p
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

Go back to Magnesium Binding Sites List in 8u9p
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

Go back to Magnesium Binding Sites List in 8u9p
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

Go back to Magnesium Binding Sites List in 8u9p
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

Go back to Magnesium Binding Sites List in 8u9p
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

Go back to Magnesium Binding Sites List in 8u9p
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy