Atomistry » Magnesium » PDB 6oje-6oqw » 6omb
Atomistry »
  Magnesium »
    PDB 6oje-6oqw »
      6omb »

Magnesium in PDB 6omb: CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore

Enzymatic activity of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore

All present enzymatic activity of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore:
3.6.4.6;

Other elements in 6omb:

The structure of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore also contains other interesting chemical elements:

Fluorine (F) 24 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore (pdb code 6omb). 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 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore, PDB code: 6omb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6omb

Go back to Magnesium Binding Sites List in 6omb
Magnesium binding site 1 out of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:52.1
occ:1.00
 OG1 A:THR535 2.0 59.4 1.0
F1 A:BEF902 2.4 61.3 1.0
O3B A:ADP901 3.0 61.3 1.0
CB A:THR535 3.4 59.4 1.0
CG2 A:THR535 3.9 59.4 1.0
BE A:BEF902 3.9 61.3 1.0
OD2 A:ASP587 3.9 59.2 1.0
OD1 A:ASP587 4.0 59.2 1.0
CA A:THR535 4.4 59.4 1.0
CG A:ASP587 4.4 59.2 1.0
N A:THR535 4.4 59.4 1.0
PB A:ADP901 4.4 61.3 1.0
NH2 B:ARG648 4.5 51.4 1.0
O B:ASP619 4.5 58.4 1.0
O1B A:ADP901 4.6 61.3 1.0
OE2 A:GLU588 4.6 59.4 1.0
O1A A:ADP901 4.7 61.3 1.0
F2 A:BEF902 4.7 61.3 1.0
F3 A:BEF902 4.8 61.3 1.0

Magnesium binding site 2 out of 8 in 6omb

Go back to Magnesium Binding Sites List in 6omb
Magnesium binding site 2 out of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg906

b:85.0
occ:1.00
 OG1 A:THR262 2.0 96.0 1.0
O3B A:ADP904 2.2 89.7 1.0
F1 A:BEF905 2.8 89.7 1.0
CB A:THR262 3.4 96.0 1.0
PB A:ADP904 3.6 89.7 1.0
O2B A:ADP904 4.1 89.7 1.0
CG2 A:THR262 4.1 96.0 1.0
BE A:BEF905 4.1 89.7 1.0
O1B A:ADP904 4.3 89.7 1.0
OD2 A:ASP314 4.3 0.8 1.0
CA A:THR262 4.4 96.0 1.0
N A:THR262 4.4 96.0 1.0
NH2 B:ARG372 4.6 68.2 1.0
OD1 A:ASP314 4.6 0.8 1.0
CG A:LYS261 4.7 98.4 1.0
O3A A:ADP904 4.8 89.7 1.0
F3 A:BEF905 4.8 89.7 1.0
CG A:ASP314 4.9 0.8 1.0
O2A A:ADP904 5.0 89.7 1.0

Magnesium binding site 3 out of 8 in 6omb

Go back to Magnesium Binding Sites List in 6omb
Magnesium binding site 3 out of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:30.5
occ:1.00
 OG1 B:THR535 2.0 37.2 1.0
O3B B:ADP901 2.4 36.0 1.0
F1 C:BEF901 2.5 36.0 1.0
CB B:THR535 3.3 37.2 1.0
OD2 B:ASP587 3.6 38.2 1.0
CG2 B:THR535 3.7 37.2 1.0
BE C:BEF901 3.9 36.0 1.0
PB B:ADP901 3.9 36.0 1.0
OD1 B:ASP587 4.1 38.2 1.0
O C:ASP619 4.2 40.2 1.0
O1B B:ADP901 4.2 36.0 1.0
CG B:ASP587 4.3 38.2 1.0
NH2 C:ARG648 4.4 37.7 1.0
O1A B:ADP901 4.4 36.0 1.0
CA B:THR535 4.4 37.2 1.0
F3 C:BEF901 4.6 36.0 1.0
N B:THR535 4.6 37.2 1.0
O3A B:ADP901 4.6 36.0 1.0
OE2 B:GLU588 4.7 41.2 1.0
O2B B:ADP901 4.9 36.0 1.0
PA B:ADP901 5.0 36.0 1.0
F2 C:BEF901 5.0 36.0 1.0

Magnesium binding site 4 out of 8 in 6omb

Go back to Magnesium Binding Sites List in 6omb
Magnesium binding site 4 out of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg905

b:31.4
occ:1.00
 OG1 B:THR262 2.0 41.7 1.0
F1 B:BEF904 2.1 43.3 1.0
CB B:THR262 3.3 41.7 1.0
O3B B:ADP903 3.3 43.3 1.0
BE B:BEF904 3.6 43.3 1.0
CG2 B:THR262 3.8 41.7 1.0
OD1 B:ASP314 3.8 50.2 1.0
OD2 B:ASP314 3.9 50.2 1.0
CG B:ASP314 4.3 50.2 1.0
O1B B:ADP903 4.3 43.3 1.0
O C:ASP343 4.3 46.6 1.0
F2 B:BEF904 4.4 43.3 1.0
CA B:THR262 4.4 41.7 1.0
PB B:ADP903 4.5 43.3 1.0
NH2 C:ARG372 4.5 41.5 1.0
N B:THR262 4.6 41.7 1.0
F3 B:BEF904 4.6 43.3 1.0
O1A B:ADP903 4.9 43.3 1.0
CG B:LYS261 5.0 40.6 1.0

Magnesium binding site 5 out of 8 in 6omb

Go back to Magnesium Binding Sites List in 6omb
Magnesium binding site 5 out of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg904

b:34.1
occ:1.00
 OG1 C:THR535 2.0 37.4 1.0
F1 C:BEF903 2.1 41.3 1.0
CB C:THR535 3.4 37.4 1.0
O3B C:ADP902 3.5 41.3 1.0
BE C:BEF903 3.6 41.3 1.0
CG2 C:THR535 3.8 37.4 1.0
OD1 C:ASP587 4.0 39.7 1.0
OD2 C:ASP587 4.0 39.7 1.0
CA C:THR535 4.3 37.4 1.0
N C:THR535 4.4 37.4 1.0
CG C:ASP587 4.4 39.7 1.0
O1B C:ADP902 4.4 41.3 1.0
F3 C:BEF903 4.5 41.3 1.0
F2 C:BEF903 4.5 41.3 1.0
PB C:ADP902 4.6 41.3 1.0
O D:ASP619 4.6 39.0 1.0
NH2 D:ARG648 4.8 39.3 1.0

Magnesium binding site 6 out of 8 in 6omb

Go back to Magnesium Binding Sites List in 6omb
Magnesium binding site 6 out of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg907

b:27.8
occ:1.00
 OG1 C:THR262 2.0 38.4 1.0
F1 C:BEF906 2.2 38.8 1.0
O3B C:ADP905 3.3 38.8 1.0
CB C:THR262 3.4 38.4 1.0
OD2 C:ASP314 3.5 37.8 1.0
BE C:BEF906 3.7 38.8 1.0
CG2 C:THR262 3.9 38.4 1.0
OD1 C:ASP314 4.0 37.8 1.0
CG C:ASP314 4.2 37.8 1.0
O D:ASP343 4.3 45.8 1.0
CA C:THR262 4.4 38.4 1.0
O1B C:ADP905 4.4 38.8 1.0
N C:THR262 4.5 38.4 1.0
PB C:ADP905 4.5 38.8 1.0
F2 C:BEF906 4.5 38.8 1.0
NH2 D:ARG372 4.6 39.8 1.0
CG C:LYS261 4.6 34.5 1.0
F3 C:BEF906 4.7 38.8 1.0
O3A C:ADP905 5.0 38.8 1.0
CD C:LYS261 5.0 34.5 1.0

Magnesium binding site 7 out of 8 in 6omb

Go back to Magnesium Binding Sites List in 6omb
Magnesium binding site 7 out of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:38.9
occ:1.00
 OG1 D:THR535 2.0 46.7 1.0
F1 D:BEF902 2.1 51.7 1.0
O2B D:ADP901 3.1 51.7 1.0
CB D:THR535 3.4 46.7 1.0
BE D:BEF902 3.4 51.7 1.0
F3 D:BEF902 3.6 51.7 1.0
CG2 D:THR535 3.8 46.7 1.0
OD2 D:ASP587 4.1 44.9 1.0
O3B D:ADP901 4.2 51.7 1.0
O E:ASP619 4.2 56.2 1.0
PB D:ADP901 4.3 51.7 1.0
CA D:THR535 4.4 46.7 1.0
N D:THR535 4.4 46.7 1.0
OD1 D:ASP587 4.5 44.9 1.0
F2 D:BEF902 4.6 51.7 1.0
NH2 E:ARG648 4.6 54.1 1.0
CA E:GLY620 4.7 53.7 1.0
OE2 D:GLU588 4.7 49.2 1.0
CG D:ASP587 4.8 44.9 1.0
O2A D:ADP901 5.0 51.7 1.0

Magnesium binding site 8 out of 8 in 6omb

Go back to Magnesium Binding Sites List in 6omb
Magnesium binding site 8 out of 8 in the CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of CDC48 Hexamer (Subunits A to E) with Substrate Bound to the Central Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg906

b:41.6
occ:1.00
 OG1 D:THR262 2.0 46.8 1.0
O2B D:ADP904 2.3 49.7 1.0
F1 D:BEF905 3.1 49.7 1.0
CB D:THR262 3.4 46.8 1.0
PB D:ADP904 3.5 49.7 1.0
OD1 D:ASP314 3.7 42.8 1.0
O3B D:ADP904 3.9 49.7 1.0
CG2 D:THR262 4.0 46.8 1.0
BE D:BEF905 4.0 49.7 1.0
O1B D:ADP904 4.2 49.7 1.0
N D:THR262 4.3 46.8 1.0
CA D:THR262 4.4 46.8 1.0
OD2 D:ASP314 4.4 42.8 1.0
CG D:ASP314 4.5 42.8 1.0
CG D:LYS261 4.5 42.9 1.0
F3 D:BEF905 4.6 49.7 1.0
O3A D:ADP904 4.7 49.7 1.0
NH2 E:ARG372 4.8 57.3 1.0
O2A D:ADP904 4.9 49.7 1.0
CD D:LYS261 4.9 42.9 1.0

Reference:

I.Cooney, H.Han, M.G.Stewart, R.H.Carson, D.T.Hansen, J.H.Iwasa, J.C.Price, C.P.Hill, P.S.Shen. Structure of the CDC48 Segregase in the Act of Unfolding An Authentic Substrate. Science V. 365 502 2019.
ISSN: ESSN 1095-9203
PubMed: 31249134
DOI: 10.1126/SCIENCE.AAX0486
Page generated: Tue Oct 1 13:26:38 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy