Atomistry » Magnesium » PDB 8p1m-8p5w » 8p4m
Atomistry »
  Magnesium »
    PDB 8p1m-8p5w »
      8p4m »

Magnesium in PDB 8p4m: Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx

Enzymatic activity of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx

All present enzymatic activity of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx:
5.6.1.7;

Other elements in 8p4m:

The structure of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx also contains other interesting chemical elements:

Potassium (K) 7 atoms
Fluorine (F) 21 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx (pdb code 8p4m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx, PDB code: 8p4m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8p4m

Go back to Magnesium Binding Sites List in 8p4m
Magnesium binding site 1 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:32.5
occ:1.00
 O A:HOH1705 1.8 30.0 1.0
O A:HOH1710 1.9 30.1 1.0
F1 A:BEF1602 2.0 34.0 1.0
O1B A:ADP1600 2.1 43.1 1.0
OD1 A:ASP87 2.1 31.7 1.0
O1A A:ADP1600 2.6 43.1 1.0
CG A:ASP87 2.8 31.7 1.0
OD2 A:ASP87 2.9 31.7 1.0
PB A:ADP1600 3.3 43.1 1.0
BE A:BEF1602 3.3 34.0 1.0
O3B A:ADP1600 3.6 43.1 1.0
PA A:ADP1600 3.7 43.1 1.0
O3A A:ADP1600 3.8 43.1 1.0
F2 A:BEF1602 4.0 34.0 1.0
O A:HOH1714 4.0 36.0 1.0
N A:GLY88 4.1 29.9 1.0
OD1 A:ASP398 4.1 35.6 1.0
CB A:ASP87 4.2 31.7 1.0
OG A:SER151 4.4 31.9 1.0
F3 A:BEF1602 4.4 34.0 1.0
O5' A:ADP1600 4.5 43.1 1.0
O2B A:ADP1600 4.5 43.1 1.0
O A:SER151 4.6 31.9 1.0
CA A:ASP87 4.6 31.7 1.0
O A:HOH1724 4.7 30.2 1.0
C5' A:ADP1600 4.8 43.1 1.0
CA A:GLY88 4.9 29.9 1.0
C A:ASP87 4.9 31.7 1.0
O A:HOH1728 4.9 34.9 1.0
O A:HOH1701 5.0 26.8 1.0

Magnesium binding site 2 out of 7 in 8p4m

Go back to Magnesium Binding Sites List in 8p4m
Magnesium binding site 2 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1601

b:32.5
occ:1.00
 O B:HOH1706 1.9 29.7 1.0
F1 B:BEF1602 2.0 34.7 1.0
O B:HOH1710 2.0 31.0 1.0
O1B B:ADP1600 2.2 43.1 1.0
OD1 B:ASP87 2.4 32.0 1.0
O1A B:ADP1600 2.5 43.1 1.0
OD2 B:ASP87 2.9 32.0 1.0
CG B:ASP87 2.9 32.0 1.0
BE B:BEF1602 3.3 34.7 1.0
PB B:ADP1600 3.4 43.1 1.0
O3B B:ADP1600 3.6 43.1 1.0
PA B:ADP1600 3.7 43.1 1.0
O B:HOH1707 3.9 33.8 1.0
O3A B:ADP1600 3.9 43.1 1.0
F2 B:BEF1602 4.0 34.7 1.0
N B:GLY88 4.1 29.2 1.0
CB B:ASP87 4.3 32.0 1.0
F3 B:BEF1602 4.5 34.7 1.0
O5' B:ADP1600 4.6 43.1 1.0
C5' B:ADP1600 4.7 43.1 1.0
O2B B:ADP1600 4.7 43.1 1.0
O B:SER151 4.7 30.6 1.0
O B:HOH1718 4.7 29.7 1.0
CA B:ASP87 4.7 32.0 1.0
OG B:SER151 4.8 30.6 1.0
O B:HOH1730 4.8 32.2 1.0
O B:HOH1709 4.9 26.9 1.0
O2A B:ADP1600 4.9 43.1 1.0
CA B:GLY88 4.9 29.2 1.0
C B:ASP87 5.0 32.0 1.0

Magnesium binding site 3 out of 7 in 8p4m

Go back to Magnesium Binding Sites List in 8p4m
Magnesium binding site 3 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1601

b:32.8
occ:1.00
 O C:HOH1706 1.9 30.3 1.0
O C:HOH1711 2.0 32.3 1.0
F1 C:BEF1602 2.0 33.1 1.0
OD1 C:ASP87 2.2 32.7 1.0
O1B C:ADP1600 2.2 43.1 1.0
O1A C:ADP1600 2.4 43.1 1.0
CG C:ASP87 2.8 32.7 1.0
OD2 C:ASP87 2.9 32.7 1.0
PB C:ADP1600 3.3 43.1 1.0
BE C:BEF1602 3.4 33.1 1.0
O3B C:ADP1600 3.6 43.1 1.0
PA C:ADP1600 3.7 43.1 1.0
O3A C:ADP1600 3.9 43.1 1.0
O C:HOH1709 4.0 33.5 1.0
N C:GLY88 4.1 29.5 1.0
F2 C:BEF1602 4.1 33.1 1.0
CB C:ASP87 4.2 32.7 1.0
F3 C:BEF1602 4.5 33.1 1.0
O5' C:ADP1600 4.5 43.1 1.0
O C:HOH1727 4.6 27.5 1.0
O2B C:ADP1600 4.7 43.1 1.0
CA C:ASP87 4.7 32.7 1.0
O C:SER151 4.7 31.6 1.0
C5' C:ADP1600 4.7 43.1 1.0
O C:HOH1707 4.8 26.7 1.0
CA C:GLY88 4.9 29.5 1.0
O2A C:ADP1600 4.9 43.1 1.0
O C:HOH1729 4.9 34.5 1.0
C C:ASP87 4.9 32.7 1.0

Magnesium binding site 4 out of 7 in 8p4m

Go back to Magnesium Binding Sites List in 8p4m
Magnesium binding site 4 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1601

b:32.7
occ:1.00
 O D:HOH1705 1.8 30.4 1.0
O D:HOH1707 1.9 29.8 1.0
F1 D:BEF1602 1.9 33.3 1.0
OD1 D:ASP87 2.1 31.6 1.0
O1B D:ADP1600 2.3 43.1 1.0
O1A D:ADP1600 2.4 43.1 1.0
CG D:ASP87 2.9 31.6 1.0
OD2 D:ASP87 3.0 31.6 1.0
BE D:BEF1602 3.2 33.3 1.0
PB D:ADP1600 3.3 43.1 1.0
O3B D:ADP1600 3.5 43.1 1.0
PA D:ADP1600 3.6 43.1 1.0
O3A D:ADP1600 3.8 43.1 1.0
F2 D:BEF1602 3.9 33.3 1.0
O D:HOH1710 4.1 31.8 1.0
N D:GLY88 4.1 28.9 1.0
CB D:ASP87 4.3 31.6 1.0
F3 D:BEF1602 4.4 33.3 1.0
O5' D:ADP1600 4.5 43.1 1.0
OG D:SER151 4.5 30.9 1.0
O D:SER151 4.6 30.9 1.0
O D:HOH1724 4.6 29.4 1.0
O2B D:ADP1600 4.7 43.1 1.0
O D:HOH1729 4.7 31.2 1.0
CA D:ASP87 4.7 31.6 1.0
O D:HOH1709 4.8 26.3 1.0
O2A D:ADP1600 4.8 43.1 1.0
C5' D:ADP1600 4.9 43.1 1.0
CA D:GLY88 4.9 28.9 1.0
C D:ASP87 4.9 31.6 1.0

Magnesium binding site 5 out of 7 in 8p4m

Go back to Magnesium Binding Sites List in 8p4m
Magnesium binding site 5 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1601

b:32.4
occ:1.00
 O E:HOH1705 1.9 29.9 1.0
F1 E:BEF1602 1.9 32.9 1.0
O E:HOH1706 1.9 31.1 1.0
OD1 E:ASP87 2.1 31.6 1.0
O1B E:ADP1600 2.3 43.1 1.0
O1A E:ADP1600 2.5 43.1 1.0
CG E:ASP87 2.9 31.6 1.0
OD2 E:ASP87 3.1 31.6 1.0
PB E:ADP1600 3.3 43.1 1.0
BE E:BEF1602 3.3 32.9 1.0
O3B E:ADP1600 3.4 43.1 1.0
PA E:ADP1600 3.7 43.1 1.0
O3A E:ADP1600 3.8 43.1 1.0
F2 E:BEF1602 3.9 32.9 1.0
O E:HOH1708 4.0 34.7 1.0
N E:GLY88 4.1 28.5 1.0
CB E:ASP87 4.3 31.6 1.0
F3 E:BEF1602 4.4 32.9 1.0
OG E:SER151 4.5 31.2 1.0
O E:HOH1724 4.6 30.3 1.0
O E:HOH1709 4.6 27.0 1.0
O2B E:ADP1600 4.6 43.1 1.0
O E:SER151 4.6 31.2 1.0
O5' E:ADP1600 4.6 43.1 1.0
CA E:ASP87 4.7 31.6 1.0
O E:HOH1729 4.7 31.6 1.0
C5' E:ADP1600 4.8 43.1 1.0
O2A E:ADP1600 4.8 43.1 1.0
CA E:GLY88 4.9 28.5 1.0
C E:ASP87 4.9 31.6 1.0

Magnesium binding site 6 out of 7 in 8p4m

Go back to Magnesium Binding Sites List in 8p4m
Magnesium binding site 6 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1601

b:31.7
occ:1.00
 O F:HOH1704 1.9 31.6 1.0
O F:HOH1708 1.9 30.4 1.0
F1 F:BEF1602 1.9 33.9 1.0
OD1 F:ASP87 2.2 32.0 1.0
O1B F:ADP1600 2.5 43.1 1.0
O1A F:ADP1600 2.6 43.1 1.0
CG F:ASP87 2.8 32.0 1.0
OD2 F:ASP87 2.8 32.0 1.0
BE F:BEF1602 3.1 33.9 1.0
PB F:ADP1600 3.4 43.1 1.0
O3B F:ADP1600 3.4 43.1 1.0
F2 F:BEF1602 3.7 33.9 1.0
PA F:ADP1600 3.8 43.1 1.0
O3A F:ADP1600 3.9 43.1 1.0
N F:GLY88 4.1 28.9 1.0
O F:HOH1706 4.1 34.7 1.0
CB F:ASP87 4.1 32.0 1.0
F3 F:BEF1602 4.4 33.9 1.0
O F:HOH1710 4.5 27.3 1.0
CA F:ASP87 4.5 32.0 1.0
O F:HOH1724 4.5 30.0 1.0
O5' F:ADP1600 4.6 43.1 1.0
O F:SER151 4.7 31.3 1.0
O2B F:ADP1600 4.8 43.1 1.0
C F:ASP87 4.8 32.0 1.0
O F:HOH1728 4.9 30.8 1.0
CA F:GLY88 4.9 28.9 1.0

Magnesium binding site 7 out of 7 in 8p4m

Go back to Magnesium Binding Sites List in 8p4m
Magnesium binding site 7 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1601

b:31.6
occ:1.00
 O G:HOH1703 1.9 30.3 1.0
O G:HOH1709 2.0 29.4 1.0
F1 G:BEF1602 2.0 32.7 1.0
O1B G:ADP1600 2.2 43.1 1.0
OD1 G:ASP87 2.3 31.4 1.0
O1A G:ADP1600 2.5 43.1 1.0
CG G:ASP87 2.9 31.4 1.0
OD2 G:ASP87 2.9 31.4 1.0
PB G:ADP1600 3.3 43.1 1.0
BE G:BEF1602 3.5 32.7 1.0
O3B G:ADP1600 3.5 43.1 1.0
PA G:ADP1600 3.7 43.1 1.0
O3A G:ADP1600 3.8 43.1 1.0
O G:HOH1708 4.0 32.2 1.0
N G:GLY88 4.1 28.0 1.0
F2 G:BEF1602 4.2 32.7 1.0
OD2 G:ASP398 4.2 35.8 1.0
CB G:ASP87 4.3 31.4 1.0
F3 G:BEF1602 4.5 32.7 1.0
O5' G:ADP1600 4.6 43.1 1.0
O G:HOH1725 4.6 28.2 1.0
O2B G:ADP1600 4.6 43.1 1.0
O G:SER151 4.6 30.8 1.0
C5' G:ADP1600 4.7 43.1 1.0
CA G:ASP87 4.7 31.4 1.0
O G:HOH1710 4.8 25.7 1.0
CA G:GLY88 4.9 28.0 1.0
O2A G:ADP1600 4.9 43.1 1.0
O G:HOH1729 4.9 35.8 1.0
C G:ASP87 4.9 31.4 1.0
CG G:ASP398 5.0 35.8 1.0

Reference:

J.Wagner, A.I.Caravajal, F.Beck, A.Bracher, W.Wan, S.Bohn, R.Koerner, W.Baumeister, R.Fernandez-Busnadiego, F.U.Hartl. Visualizing Chaperonin Function in Situ By Cryo-Electron Tomography Nature 2024.
ISSN: ESSN 1476-4687
Page generated: Fri Oct 4 15:47:33 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy