Magnesium in PDB 3e76: Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Enzymatic activity of Crystal Structure of Wild-Type Groel with Bound Thallium Ions
All present enzymatic activity of Crystal Structure of Wild-Type Groel with Bound Thallium Ions:
3.6.4.9;
Protein crystallography data
The structure of Crystal Structure of Wild-Type Groel with Bound Thallium Ions, PDB code: 3e76
was solved by
P.D.Kiser,
G.H.Lorimer,
K.Palczewski,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.39 /
3.94
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.676,
260.954,
287.872,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26.1 /
29.3
|
Other elements in 3e76:
The structure of Crystal Structure of Wild-Type Groel with Bound Thallium Ions also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
(pdb code 3e76). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the
Crystal Structure of Wild-Type Groel with Bound Thallium Ions, PDB code: 3e76:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 14 in 3e76
Go back to
Magnesium Binding Sites List in 3e76
Magnesium binding site 1 out
of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg553
b:0.2
occ:1.00
|
OD1
|
A:ASP87
|
2.1
|
0.2
|
1.0
|
O2A
|
A:AGS549
|
2.2
|
0.2
|
1.0
|
O2G
|
A:AGS549
|
2.2
|
0.2
|
1.0
|
O1B
|
A:AGS549
|
2.3
|
0.2
|
1.0
|
CG
|
A:ASP87
|
3.3
|
0.2
|
1.0
|
PB
|
A:AGS549
|
3.4
|
0.2
|
1.0
|
PG
|
A:AGS549
|
3.5
|
0.2
|
1.0
|
PA
|
A:AGS549
|
3.5
|
0.2
|
1.0
|
O3B
|
A:AGS549
|
3.8
|
0.2
|
1.0
|
O3A
|
A:AGS549
|
3.9
|
0.2
|
1.0
|
CB
|
A:ASP87
|
4.0
|
0.2
|
1.0
|
N
|
A:GLY88
|
4.0
|
0.2
|
1.0
|
C5'
|
A:AGS549
|
4.2
|
0.2
|
1.0
|
CA
|
A:ASP87
|
4.2
|
0.2
|
1.0
|
OD2
|
A:ASP87
|
4.3
|
0.2
|
1.0
|
O5'
|
A:AGS549
|
4.4
|
0.2
|
1.0
|
O3G
|
A:AGS549
|
4.6
|
0.2
|
1.0
|
C
|
A:ASP87
|
4.6
|
0.2
|
1.0
|
O1A
|
A:AGS549
|
4.7
|
0.2
|
1.0
|
S1G
|
A:AGS549
|
4.7
|
0.2
|
1.0
|
O2B
|
A:AGS549
|
4.7
|
0.2
|
1.0
|
CA
|
A:GLY88
|
5.0
|
0.2
|
1.0
|
|
Magnesium binding site 2 out
of 14 in 3e76
Go back to
Magnesium Binding Sites List in 3e76
Magnesium binding site 2 out
of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg553
b:0.2
occ:1.00
|
O2A
|
B:AGS549
|
2.1
|
0.2
|
1.0
|
O1B
|
B:AGS549
|
2.2
|
0.2
|
1.0
|
O2G
|
B:AGS549
|
2.2
|
0.2
|
1.0
|
OD1
|
B:ASP87
|
2.2
|
0.2
|
1.0
|
PB
|
B:AGS549
|
3.3
|
0.2
|
1.0
|
CG
|
B:ASP87
|
3.4
|
0.2
|
1.0
|
PA
|
B:AGS549
|
3.4
|
0.2
|
1.0
|
PG
|
B:AGS549
|
3.5
|
0.2
|
1.0
|
O3B
|
B:AGS549
|
3.7
|
0.2
|
1.0
|
O3A
|
B:AGS549
|
3.8
|
0.2
|
1.0
|
OD2
|
B:ASP87
|
4.0
|
0.2
|
1.0
|
C5'
|
B:AGS549
|
4.1
|
0.2
|
1.0
|
O5'
|
B:AGS549
|
4.3
|
0.2
|
1.0
|
N
|
B:GLY88
|
4.5
|
0.2
|
1.0
|
O3G
|
B:AGS549
|
4.5
|
0.2
|
1.0
|
CB
|
B:ASP87
|
4.6
|
0.2
|
1.0
|
O1A
|
B:AGS549
|
4.6
|
0.2
|
1.0
|
S1G
|
B:AGS549
|
4.6
|
0.2
|
1.0
|
O2B
|
B:AGS549
|
4.7
|
0.2
|
1.0
|
CA
|
B:ASP87
|
4.8
|
0.2
|
1.0
|
|
Magnesium binding site 3 out
of 14 in 3e76
Go back to
Magnesium Binding Sites List in 3e76
Magnesium binding site 3 out
of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg553
b:0.2
occ:1.00
|
OD1
|
C:ASP87
|
2.0
|
0.2
|
1.0
|
O2A
|
C:AGS549
|
2.0
|
0.2
|
1.0
|
O2G
|
C:AGS549
|
2.1
|
0.2
|
1.0
|
O1B
|
C:AGS549
|
2.3
|
0.2
|
1.0
|
CG
|
C:ASP87
|
3.3
|
0.2
|
1.0
|
PA
|
C:AGS549
|
3.4
|
0.2
|
1.0
|
PB
|
C:AGS549
|
3.4
|
0.2
|
1.0
|
PG
|
C:AGS549
|
3.4
|
0.2
|
1.0
|
O3A
|
C:AGS549
|
3.8
|
0.2
|
1.0
|
O3B
|
C:AGS549
|
3.8
|
0.2
|
1.0
|
CB
|
C:ASP87
|
4.1
|
0.2
|
1.0
|
C5'
|
C:AGS549
|
4.1
|
0.2
|
1.0
|
N
|
C:GLY88
|
4.1
|
0.2
|
1.0
|
OD2
|
C:ASP87
|
4.1
|
0.2
|
1.0
|
O5'
|
C:AGS549
|
4.3
|
0.2
|
1.0
|
CA
|
C:ASP87
|
4.4
|
0.2
|
1.0
|
O1A
|
C:AGS549
|
4.5
|
0.2
|
1.0
|
O3G
|
C:AGS549
|
4.5
|
0.2
|
1.0
|
S1G
|
C:AGS549
|
4.7
|
0.2
|
1.0
|
O2B
|
C:AGS549
|
4.7
|
0.2
|
1.0
|
C
|
C:ASP87
|
4.8
|
0.2
|
1.0
|
|
Magnesium binding site 4 out
of 14 in 3e76
Go back to
Magnesium Binding Sites List in 3e76
Magnesium binding site 4 out
of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg553
b:0.2
occ:1.00
|
O2A
|
D:AGS549
|
2.0
|
0.2
|
1.0
|
OD1
|
D:ASP87
|
2.1
|
0.2
|
1.0
|
O2G
|
D:AGS549
|
2.1
|
0.2
|
1.0
|
O1B
|
D:AGS549
|
2.2
|
0.2
|
1.0
|
CG
|
D:ASP87
|
3.2
|
0.2
|
1.0
|
PB
|
D:AGS549
|
3.3
|
0.2
|
1.0
|
PA
|
D:AGS549
|
3.3
|
0.2
|
1.0
|
PG
|
D:AGS549
|
3.3
|
0.2
|
1.0
|
O3B
|
D:AGS549
|
3.6
|
0.2
|
1.0
|
O3A
|
D:AGS549
|
3.7
|
0.2
|
1.0
|
OD2
|
D:ASP87
|
3.8
|
0.2
|
1.0
|
C5'
|
D:AGS549
|
4.1
|
0.2
|
1.0
|
O5'
|
D:AGS549
|
4.2
|
0.2
|
1.0
|
N
|
D:GLY88
|
4.3
|
0.2
|
1.0
|
O3G
|
D:AGS549
|
4.4
|
0.2
|
1.0
|
O1A
|
D:AGS549
|
4.4
|
0.2
|
1.0
|
CB
|
D:ASP87
|
4.5
|
0.2
|
1.0
|
S1G
|
D:AGS549
|
4.6
|
0.2
|
1.0
|
O2B
|
D:AGS549
|
4.6
|
0.2
|
1.0
|
CA
|
D:ASP87
|
4.7
|
0.2
|
1.0
|
|
Magnesium binding site 5 out
of 14 in 3e76
Go back to
Magnesium Binding Sites List in 3e76
Magnesium binding site 5 out
of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg553
b:0.2
occ:1.00
|
OD1
|
E:ASP87
|
2.1
|
0.2
|
1.0
|
O2A
|
E:AGS549
|
2.1
|
0.2
|
1.0
|
O2G
|
E:AGS549
|
2.2
|
0.2
|
1.0
|
O1B
|
E:AGS549
|
2.2
|
0.2
|
1.0
|
CG
|
E:ASP87
|
3.2
|
0.2
|
1.0
|
PB
|
E:AGS549
|
3.4
|
0.2
|
1.0
|
PA
|
E:AGS549
|
3.4
|
0.2
|
1.0
|
PG
|
E:AGS549
|
3.5
|
0.2
|
1.0
|
O3B
|
E:AGS549
|
3.8
|
0.2
|
1.0
|
O3A
|
E:AGS549
|
3.8
|
0.2
|
1.0
|
OD2
|
E:ASP87
|
3.8
|
0.2
|
1.0
|
C5'
|
E:AGS549
|
4.1
|
0.2
|
1.0
|
O5'
|
E:AGS549
|
4.3
|
0.2
|
1.0
|
N
|
E:GLY88
|
4.4
|
0.2
|
1.0
|
CB
|
E:ASP87
|
4.5
|
0.2
|
1.0
|
O1A
|
E:AGS549
|
4.5
|
0.2
|
1.0
|
O3G
|
E:AGS549
|
4.5
|
0.2
|
1.0
|
S1G
|
E:AGS549
|
4.7
|
0.2
|
1.0
|
O2B
|
E:AGS549
|
4.7
|
0.2
|
1.0
|
CA
|
E:ASP87
|
4.7
|
0.2
|
1.0
|
|
Magnesium binding site 6 out
of 14 in 3e76
Go back to
Magnesium Binding Sites List in 3e76
Magnesium binding site 6 out
of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg553
b:0.2
occ:1.00
|
OD1
|
F:ASP87
|
2.0
|
0.2
|
1.0
|
O2G
|
F:AGS549
|
2.1
|
0.2
|
1.0
|
O2A
|
F:AGS549
|
2.1
|
0.2
|
1.0
|
O1B
|
F:AGS549
|
2.2
|
0.2
|
1.0
|
CG
|
F:ASP87
|
3.2
|
0.2
|
1.0
|
PB
|
F:AGS549
|
3.3
|
0.2
|
1.0
|
PG
|
F:AGS549
|
3.3
|
0.2
|
1.0
|
PA
|
F:AGS549
|
3.4
|
0.2
|
1.0
|
O3B
|
F:AGS549
|
3.6
|
0.2
|
1.0
|
O3A
|
F:AGS549
|
3.7
|
0.2
|
1.0
|
OD2
|
F:ASP87
|
3.8
|
0.2
|
1.0
|
C5'
|
F:AGS549
|
4.1
|
0.2
|
1.0
|
N
|
F:GLY88
|
4.3
|
0.2
|
1.0
|
O5'
|
F:AGS549
|
4.3
|
0.2
|
1.0
|
CB
|
F:ASP87
|
4.4
|
0.2
|
1.0
|
O3G
|
F:AGS549
|
4.4
|
0.2
|
1.0
|
O1A
|
F:AGS549
|
4.5
|
0.2
|
1.0
|
S1G
|
F:AGS549
|
4.5
|
0.2
|
1.0
|
O2B
|
F:AGS549
|
4.6
|
0.2
|
1.0
|
CA
|
F:ASP87
|
4.6
|
0.2
|
1.0
|
|
Magnesium binding site 7 out
of 14 in 3e76
Go back to
Magnesium Binding Sites List in 3e76
Magnesium binding site 7 out
of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg553
b:0.2
occ:1.00
|
OD1
|
G:ASP87
|
2.1
|
0.2
|
1.0
|
O2G
|
G:AGS549
|
2.1
|
0.2
|
1.0
|
O2A
|
G:AGS549
|
2.2
|
0.2
|
1.0
|
O1B
|
G:AGS549
|
2.3
|
0.2
|
1.0
|
CG
|
G:ASP87
|
3.3
|
0.2
|
1.0
|
PB
|
G:AGS549
|
3.4
|
0.2
|
1.0
|
PG
|
G:AGS549
|
3.5
|
0.2
|
1.0
|
PA
|
G:AGS549
|
3.5
|
0.2
|
1.0
|
O3B
|
G:AGS549
|
3.8
|
0.2
|
1.0
|
O3A
|
G:AGS549
|
3.9
|
0.2
|
1.0
|
OD2
|
G:ASP87
|
4.1
|
0.2
|
1.0
|
C5'
|
G:AGS549
|
4.2
|
0.2
|
1.0
|
CB
|
G:ASP87
|
4.3
|
0.2
|
1.0
|
N
|
G:GLY88
|
4.3
|
0.2
|
1.0
|
O5'
|
G:AGS549
|
4.4
|
0.2
|
1.0
|
O3G
|
G:AGS549
|
4.5
|
0.2
|
1.0
|
O1A
|
G:AGS549
|
4.6
|
0.2
|
1.0
|
CA
|
G:ASP87
|
4.6
|
0.2
|
1.0
|
S1G
|
G:AGS549
|
4.7
|
0.2
|
1.0
|
O2B
|
G:AGS549
|
4.8
|
0.2
|
1.0
|
|
Magnesium binding site 8 out
of 14 in 3e76
Go back to
Magnesium Binding Sites List in 3e76
Magnesium binding site 8 out
of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg553
b:0.2
occ:1.00
|
O2A
|
H:AGS549
|
2.1
|
0.2
|
1.0
|
O2G
|
H:AGS549
|
2.1
|
0.2
|
1.0
|
O1B
|
H:AGS549
|
2.2
|
0.2
|
1.0
|
OD1
|
H:ASP87
|
2.3
|
0.2
|
1.0
|
PB
|
H:AGS549
|
3.3
|
0.2
|
1.0
|
PG
|
H:AGS549
|
3.4
|
0.2
|
1.0
|
PA
|
H:AGS549
|
3.4
|
0.2
|
1.0
|
CG
|
H:ASP87
|
3.5
|
0.2
|
1.0
|
O3B
|
H:AGS549
|
3.7
|
0.2
|
1.0
|
O3A
|
H:AGS549
|
3.8
|
0.2
|
1.0
|
OD2
|
H:ASP87
|
4.1
|
0.2
|
1.0
|
C5'
|
H:AGS549
|
4.2
|
0.2
|
1.0
|
O5'
|
H:AGS549
|
4.3
|
0.2
|
1.0
|
O3G
|
H:AGS549
|
4.5
|
0.2
|
1.0
|
N
|
H:GLY88
|
4.5
|
0.2
|
1.0
|
O1A
|
H:AGS549
|
4.5
|
0.2
|
1.0
|
S1G
|
H:AGS549
|
4.6
|
0.2
|
1.0
|
CB
|
H:ASP87
|
4.7
|
0.2
|
1.0
|
O2B
|
H:AGS549
|
4.7
|
0.2
|
1.0
|
CA
|
H:ASP87
|
4.8
|
0.2
|
1.0
|
|
Magnesium binding site 9 out
of 14 in 3e76
Go back to
Magnesium Binding Sites List in 3e76
Magnesium binding site 9 out
of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg553
b:0.2
occ:1.00
|
O2A
|
I:AGS549
|
2.0
|
0.2
|
1.0
|
OD1
|
I:ASP87
|
2.1
|
0.2
|
1.0
|
O1B
|
I:AGS549
|
2.2
|
0.2
|
1.0
|
O2G
|
I:AGS549
|
2.2
|
0.2
|
1.0
|
CG
|
I:ASP87
|
3.2
|
0.2
|
1.0
|
PB
|
I:AGS549
|
3.4
|
0.2
|
1.0
|
PA
|
I:AGS549
|
3.4
|
0.2
|
1.0
|
PG
|
I:AGS549
|
3.5
|
0.2
|
1.0
|
O3A
|
I:AGS549
|
3.8
|
0.2
|
1.0
|
O3B
|
I:AGS549
|
3.8
|
0.2
|
1.0
|
C5'
|
I:AGS549
|
4.0
|
0.2
|
1.0
|
N
|
I:GLY88
|
4.0
|
0.2
|
1.0
|
OD2
|
I:ASP87
|
4.0
|
0.2
|
1.0
|
CB
|
I:ASP87
|
4.1
|
0.2
|
1.0
|
O5'
|
I:AGS549
|
4.2
|
0.2
|
1.0
|
CA
|
I:ASP87
|
4.4
|
0.2
|
1.0
|
O1A
|
I:AGS549
|
4.5
|
0.2
|
1.0
|
O3G
|
I:AGS549
|
4.6
|
0.2
|
1.0
|
O2B
|
I:AGS549
|
4.7
|
0.2
|
1.0
|
C
|
I:ASP87
|
4.7
|
0.2
|
1.0
|
S1G
|
I:AGS549
|
4.7
|
0.2
|
1.0
|
CA
|
I:GLY88
|
4.9
|
0.2
|
1.0
|
|
Magnesium binding site 10 out
of 14 in 3e76
Go back to
Magnesium Binding Sites List in 3e76
Magnesium binding site 10 out
of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg553
b:0.2
occ:1.00
|
O2G
|
J:AGS549
|
2.1
|
0.2
|
1.0
|
OD1
|
J:ASP87
|
2.1
|
0.2
|
1.0
|
O1B
|
J:AGS549
|
2.2
|
0.2
|
1.0
|
O2A
|
J:AGS549
|
2.3
|
0.2
|
1.0
|
CG
|
J:ASP87
|
3.3
|
0.2
|
1.0
|
PG
|
J:AGS549
|
3.4
|
0.2
|
1.0
|
PB
|
J:AGS549
|
3.4
|
0.2
|
1.0
|
PA
|
J:AGS549
|
3.6
|
0.2
|
1.0
|
O3B
|
J:AGS549
|
3.7
|
0.2
|
1.0
|
O3A
|
J:AGS549
|
3.9
|
0.2
|
1.0
|
OD2
|
J:ASP87
|
3.9
|
0.2
|
1.0
|
C5'
|
J:AGS549
|
4.3
|
0.2
|
1.0
|
N
|
J:GLY88
|
4.4
|
0.2
|
1.0
|
CB
|
J:ASP87
|
4.5
|
0.2
|
1.0
|
O3G
|
J:AGS549
|
4.5
|
0.2
|
1.0
|
S1G
|
J:AGS549
|
4.5
|
0.2
|
1.0
|
O5'
|
J:AGS549
|
4.5
|
0.2
|
1.0
|
O2B
|
J:AGS549
|
4.7
|
0.2
|
1.0
|
CA
|
J:ASP87
|
4.7
|
0.2
|
1.0
|
O1A
|
J:AGS549
|
4.7
|
0.2
|
1.0
|
|
Reference:
P.D.Kiser,
G.H.Lorimer,
K.Palczewski.
Use of Thallium to Identify Monovalent Cation Binding Sites in Groel. Acta Crystallogr.,Sect.F V. 65 967 2009.
ISSN: ESSN 1744-3091
PubMed: 19851000
DOI: 10.1107/S1744309109032928
Page generated: Wed Aug 14 12:56:04 2024
|