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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

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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

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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

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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

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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

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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

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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

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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

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