Magnesium in PDB 4e8p: Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
Protein crystallography data
The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+, PDB code: 4e8p
was solved by
M.Marcia,
A.M.Pyle,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.16 /
3.28
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.987,
95.024,
223.492,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.9 /
24.4
|
Other elements in 4e8p:
The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
27;
Binding sites:
The binding sites of Magnesium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
(pdb code 4e8p). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 27 binding sites of Magnesium where determined in the
Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+, PDB code: 4e8p:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 27 in 4e8p
Go back to
Magnesium Binding Sites List in 4e8p
Magnesium binding site 1 out
of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:82.0
occ:1.00
|
O3'
|
A:C286
|
2.3
|
0.6
|
1.0
|
O5'
|
A:A287
|
2.6
|
0.7
|
1.0
|
P
|
A:A287
|
2.9
|
0.6
|
1.0
|
OP1
|
A:A287
|
3.3
|
0.2
|
1.0
|
C3'
|
A:C286
|
3.5
|
0.5
|
1.0
|
C5'
|
A:A287
|
3.8
|
0.4
|
1.0
|
C4'
|
A:C286
|
4.0
|
0.2
|
1.0
|
OP2
|
A:G321
|
4.2
|
93.7
|
1.0
|
OP2
|
A:A287
|
4.2
|
0.8
|
1.0
|
OP1
|
A:G288
|
4.3
|
0.2
|
1.0
|
O2'
|
A:C286
|
4.3
|
0.1
|
1.0
|
OP1
|
A:G321
|
4.3
|
97.6
|
1.0
|
C1'
|
A:C286
|
4.3
|
97.5
|
1.0
|
C2'
|
A:C286
|
4.3
|
0.3
|
1.0
|
OP2
|
A:G288
|
4.5
|
1.0
|
1.0
|
O4'
|
A:C286
|
4.5
|
96.3
|
1.0
|
P
|
A:G321
|
4.6
|
0.5
|
1.0
|
P
|
A:G288
|
4.6
|
0.2
|
1.0
|
O3'
|
A:G320
|
4.7
|
86.8
|
1.0
|
O3'
|
A:A287
|
4.7
|
0.0
|
1.0
|
C3'
|
A:A287
|
4.8
|
1.0
|
1.0
|
C4'
|
A:A287
|
4.8
|
0.5
|
1.0
|
|
Magnesium binding site 2 out
of 27 in 4e8p
Go back to
Magnesium Binding Sites List in 4e8p
Magnesium binding site 2 out
of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:66.0
occ:1.00
|
OP1
|
A:U375
|
2.1
|
91.5
|
1.0
|
OP2
|
A:C377
|
2.4
|
78.0
|
1.0
|
O
|
A:HOH924
|
2.5
|
51.4
|
1.0
|
P
|
A:C377
|
3.4
|
83.9
|
1.0
|
P
|
A:U375
|
3.5
|
96.9
|
1.0
|
OP1
|
A:C377
|
3.6
|
84.5
|
1.0
|
O3'
|
A:G374
|
3.9
|
87.4
|
1.0
|
MG
|
A:MG403
|
4.2
|
64.8
|
1.0
|
OP1
|
A:G359
|
4.3
|
0.7
|
1.0
|
OP2
|
A:U375
|
4.4
|
99.4
|
1.0
|
OP2
|
A:G359
|
4.5
|
94.9
|
1.0
|
O5'
|
A:C377
|
4.6
|
86.8
|
1.0
|
O3'
|
A:A376
|
4.6
|
87.7
|
1.0
|
O5'
|
A:U375
|
4.7
|
83.0
|
1.0
|
C3'
|
A:A376
|
4.8
|
95.1
|
1.0
|
C5'
|
A:U375
|
4.9
|
79.9
|
1.0
|
C5'
|
A:A376
|
4.9
|
87.0
|
1.0
|
O
|
A:HOH921
|
4.9
|
80.2
|
1.0
|
C4'
|
A:A376
|
4.9
|
92.5
|
1.0
|
P
|
A:G359
|
5.0
|
0.7
|
1.0
|
|
Magnesium binding site 3 out
of 27 in 4e8p
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Magnesium Binding Sites List in 4e8p
Magnesium binding site 3 out
of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:64.8
occ:1.00
|
OP1
|
A:C377
|
1.4
|
84.5
|
1.0
|
OP1
|
A:C358
|
1.9
|
96.1
|
1.0
|
OP2
|
A:G359
|
2.0
|
94.9
|
1.0
|
O
|
A:HOH921
|
2.4
|
80.2
|
1.0
|
P
|
A:C377
|
2.8
|
83.9
|
1.0
|
O
|
A:HOH924
|
2.8
|
51.4
|
1.0
|
P
|
A:C358
|
2.9
|
94.4
|
1.0
|
O5'
|
A:C358
|
2.9
|
97.0
|
1.0
|
P
|
A:G359
|
3.4
|
0.7
|
1.0
|
O5'
|
A:C377
|
3.4
|
86.8
|
1.0
|
RB
|
A:RB437
|
3.5
|
93.0
|
1.0
|
RB
|
A:RB428
|
3.5
|
54.0
|
0.3
|
OP2
|
A:C377
|
3.7
|
78.0
|
1.0
|
O3'
|
A:A376
|
3.8
|
87.7
|
1.0
|
C5'
|
A:C358
|
3.9
|
0.7
|
1.0
|
OP2
|
A:C358
|
3.9
|
98.4
|
1.0
|
O5'
|
A:G359
|
4.1
|
99.5
|
1.0
|
O3'
|
A:C357
|
4.1
|
95.2
|
1.0
|
OP1
|
A:G359
|
4.2
|
0.7
|
1.0
|
MG
|
A:MG402
|
4.2
|
66.0
|
1.0
|
O3'
|
A:C358
|
4.4
|
0.8
|
1.0
|
C3'
|
A:C358
|
4.7
|
0.0
|
1.0
|
C5'
|
A:C377
|
4.8
|
86.2
|
1.0
|
C4'
|
A:C358
|
4.9
|
0.4
|
1.0
|
|
Magnesium binding site 4 out
of 27 in 4e8p
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Magnesium Binding Sites List in 4e8p
Magnesium binding site 4 out
of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:77.3
occ:1.00
|
OP2
|
A:U4
|
2.2
|
88.2
|
1.0
|
OP1
|
A:G3
|
2.3
|
0.8
|
1.0
|
P
|
A:U4
|
3.7
|
92.3
|
1.0
|
P
|
A:G3
|
3.8
|
0.7
|
1.0
|
O3'
|
A:G3
|
4.5
|
92.9
|
1.0
|
O3'
|
A:U2
|
4.5
|
0.3
|
1.0
|
OP1
|
A:U4
|
4.5
|
94.5
|
1.0
|
O5'
|
A:G3
|
4.5
|
0.4
|
1.0
|
O6
|
A:G5
|
4.6
|
85.6
|
1.0
|
C5'
|
A:G3
|
4.7
|
98.5
|
1.0
|
O5'
|
A:U4
|
4.7
|
80.2
|
1.0
|
OP2
|
A:G3
|
4.7
|
0.4
|
1.0
|
C3'
|
A:G3
|
4.9
|
95.1
|
1.0
|
C2
|
A:A376
|
4.9
|
95.7
|
1.0
|
|
Magnesium binding site 5 out
of 27 in 4e8p
Go back to
Magnesium Binding Sites List in 4e8p
Magnesium binding site 5 out
of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_05.jpg) Mono view
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:85.1
occ:1.00
|
O6
|
A:G386
|
3.1
|
0.7
|
1.0
|
OP2
|
A:A290
|
3.7
|
0.2
|
1.0
|
O3'
|
A:C289
|
4.1
|
0.3
|
1.0
|
C6
|
A:G386
|
4.2
|
0.6
|
1.0
|
O6
|
A:G385
|
4.3
|
0.7
|
1.0
|
P
|
A:A290
|
4.4
|
0.0
|
1.0
|
C5'
|
A:A290
|
4.4
|
0.6
|
1.0
|
N7
|
A:G386
|
4.7
|
0.4
|
1.0
|
C5
|
A:G386
|
4.9
|
0.8
|
1.0
|
|
Magnesium binding site 6 out
of 27 in 4e8p
Go back to
Magnesium Binding Sites List in 4e8p
Magnesium binding site 6 out
of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_06.jpg) Mono view
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:70.9
occ:1.00
|
OP2
|
A:G374
|
2.5
|
96.7
|
1.0
|
OP1
|
A:C360
|
3.1
|
95.0
|
1.0
|
OP2
|
A:G373
|
3.6
|
0.3
|
1.0
|
OP2
|
A:C360
|
3.9
|
89.3
|
1.0
|
P
|
A:G374
|
4.0
|
0.9
|
1.0
|
P
|
A:C360
|
4.0
|
0.3
|
1.0
|
P
|
A:G373
|
4.3
|
0.3
|
1.0
|
OP1
|
A:G373
|
4.4
|
99.7
|
1.0
|
O5'
|
A:G373
|
4.4
|
93.2
|
1.0
|
OP1
|
A:G374
|
4.7
|
0.3
|
1.0
|
C3'
|
A:G373
|
4.8
|
97.8
|
1.0
|
O5'
|
A:C360
|
4.8
|
1.0
|
1.0
|
C5'
|
A:G374
|
4.8
|
86.8
|
1.0
|
O3'
|
A:G373
|
4.9
|
96.0
|
1.0
|
O5'
|
A:G374
|
4.9
|
95.4
|
1.0
|
|
Magnesium binding site 7 out
of 27 in 4e8p
Go back to
Magnesium Binding Sites List in 4e8p
Magnesium binding site 7 out
of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_07.jpg) Mono view
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg407
b:79.3
occ:1.00
|
O6
|
A:G325
|
2.4
|
0.1
|
1.0
|
N7
|
A:G324
|
3.1
|
0.4
|
1.0
|
C6
|
A:G325
|
3.5
|
0.2
|
1.0
|
O6
|
A:G324
|
3.6
|
0.0
|
1.0
|
C5
|
A:G324
|
3.9
|
0.9
|
1.0
|
OP2
|
A:G324
|
4.0
|
0.5
|
1.0
|
C8
|
A:G324
|
4.1
|
0.8
|
1.0
|
C6
|
A:G324
|
4.1
|
0.7
|
1.0
|
C5
|
A:G325
|
4.3
|
0.3
|
1.0
|
N1
|
A:G325
|
4.4
|
0.9
|
1.0
|
N7
|
A:G325
|
4.5
|
0.1
|
1.0
|
OP2
|
A:C323
|
4.5
|
0.0
|
1.0
|
|
Magnesium binding site 8 out
of 27 in 4e8p
Go back to
Magnesium Binding Sites List in 4e8p
Magnesium binding site 8 out
of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_08.jpg) Mono view
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg408
b:61.9
occ:1.00
|
O6
|
A:G46
|
3.6
|
67.8
|
1.0
|
O4
|
A:U47
|
3.9
|
66.5
|
1.0
|
OP1
|
A:U59
|
3.9
|
65.7
|
1.0
|
RB
|
A:RB441
|
4.0
|
0.3
|
1.0
|
N7
|
A:G46
|
4.2
|
69.5
|
1.0
|
OP2
|
A:U59
|
4.4
|
68.7
|
1.0
|
C6
|
A:G46
|
4.5
|
68.5
|
1.0
|
O4
|
A:U45
|
4.5
|
79.5
|
1.0
|
C5
|
A:G46
|
4.7
|
67.9
|
1.0
|
P
|
A:U59
|
4.7
|
65.8
|
1.0
|
O6
|
A:G48
|
4.9
|
57.6
|
1.0
|
C4
|
A:U47
|
4.9
|
67.1
|
1.0
|
C5
|
A:U45
|
4.9
|
78.0
|
1.0
|
O2'
|
A:G58
|
4.9
|
72.9
|
1.0
|
C4
|
A:U45
|
4.9
|
74.8
|
1.0
|
|
Magnesium binding site 9 out
of 27 in 4e8p
Go back to
Magnesium Binding Sites List in 4e8p
Magnesium binding site 9 out
of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_09.jpg) Mono view
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg409
b:75.3
occ:1.00
|
OP1
|
A:G239
|
2.2
|
78.0
|
1.0
|
OP1
|
A:C119
|
2.9
|
81.4
|
1.0
|
O3'
|
A:U238
|
3.1
|
73.6
|
1.0
|
OP1
|
A:A174
|
3.2
|
75.7
|
1.0
|
P
|
A:G239
|
3.2
|
76.2
|
1.0
|
O5'
|
A:G239
|
4.2
|
74.8
|
1.0
|
C5'
|
A:C119
|
4.2
|
61.8
|
1.0
|
C5'
|
A:G239
|
4.2
|
74.5
|
1.0
|
P
|
A:C119
|
4.3
|
80.7
|
1.0
|
C3'
|
A:U238
|
4.4
|
73.9
|
1.0
|
OP2
|
A:G239
|
4.5
|
81.8
|
1.0
|
O5'
|
A:U238
|
4.5
|
70.8
|
1.0
|
O5'
|
A:C119
|
4.6
|
68.8
|
1.0
|
P
|
A:A174
|
4.6
|
92.0
|
1.0
|
O3'
|
A:G118
|
4.7
|
80.3
|
1.0
|
C5'
|
A:A174
|
4.9
|
80.1
|
1.0
|
C4'
|
A:U238
|
4.9
|
73.7
|
1.0
|
|
Magnesium binding site 10 out
of 27 in 4e8p
Go back to
Magnesium Binding Sites List in 4e8p
Magnesium binding site 10 out
of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_10.jpg) Mono view
![](/pictures/MG/pdb/e8/4e8p-MG-sphere_10_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg410
b:61.8
occ:1.00
|
OP1
|
A:G107
|
2.1
|
81.5
|
1.0
|
P
|
A:G107
|
3.6
|
84.2
|
1.0
|
N7
|
A:A105
|
3.8
|
94.9
|
1.0
|
OP2
|
A:A105
|
4.0
|
78.5
|
1.0
|
C8
|
A:A105
|
4.1
|
95.2
|
1.0
|
O3'
|
A:A106
|
4.2
|
91.4
|
1.0
|
OP2
|
A:G107
|
4.3
|
82.9
|
1.0
|
OP1
|
A:G108
|
4.6
|
92.3
|
1.0
|
O5'
|
A:G107
|
4.7
|
73.5
|
1.0
|
OP2
|
A:A106
|
4.8
|
96.2
|
1.0
|
C5'
|
A:A106
|
4.8
|
84.5
|
1.0
|
|
Reference:
M.Marcia,
A.M.Pyle.
Visualizing Group II Intron Catalysis Through the Stages of Splicing. Cell(Cambridge,Mass.) V. 151 497 2012.
ISSN: ISSN 0092-8674
PubMed: 23101623
DOI: 10.1016/J.CELL.2012.09.033
Page generated: Fri Aug 16 14:16:46 2024
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