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:
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
|