Magnesium in PDB 8olz: Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Protein crystallography data
The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking, PDB code: 8olz
was solved by
I.Silvestri,
M.Marcia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.84 /
3.31
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
87.672,
93.968,
223.433,
90,
90,
90
|
R / Rfree (%)
|
19.2 /
27.3
|
Other elements in 8olz:
The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Binding sites:
The binding sites of Magnesium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
(pdb code 8olz). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 30 binding sites of Magnesium where determined in the
Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking, PDB code: 8olz:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 30 in 8olz
Go back to
Magnesium Binding Sites List in 8olz
Magnesium binding site 1 out
of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Mono view
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 the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:105.5
occ:1.00
|
O24
|
A:VTE453
|
2.0
|
122.8
|
1.0
|
O22
|
A:VTE453
|
2.0
|
181.6
|
1.0
|
OP2
|
A:C377
|
2.0
|
96.0
|
1.0
|
O3'
|
B:U0
|
2.0
|
122.8
|
1.0
|
OP1
|
A:U375
|
2.0
|
93.0
|
1.0
|
C21
|
A:VTE453
|
2.7
|
201.7
|
1.0
|
C23
|
A:VTE453
|
2.7
|
183.7
|
1.0
|
P
|
A:C377
|
3.1
|
109.0
|
1.0
|
C3'
|
B:U0
|
3.2
|
146.9
|
1.0
|
P
|
A:U375
|
3.4
|
102.9
|
1.0
|
OP1
|
A:C377
|
3.5
|
114.8
|
1.0
|
MG
|
A:MG403
|
3.7
|
119.7
|
1.0
|
C4'
|
B:U0
|
3.8
|
143.8
|
1.0
|
O3'
|
A:A376
|
3.9
|
115.2
|
1.0
|
OP2
|
A:G359
|
3.9
|
111.8
|
1.0
|
OP2
|
A:U375
|
4.0
|
109.0
|
1.0
|
C25
|
A:VTE453
|
4.0
|
215.7
|
1.0
|
C20
|
A:VTE453
|
4.1
|
216.8
|
1.0
|
C3'
|
A:A376
|
4.1
|
113.7
|
1.0
|
O3'
|
A:G374
|
4.2
|
107.9
|
1.0
|
C5'
|
B:U0
|
4.2
|
142.1
|
1.0
|
C4'
|
A:A376
|
4.3
|
124.3
|
1.0
|
C5'
|
A:A376
|
4.4
|
119.0
|
1.0
|
O5'
|
A:C377
|
4.4
|
115.6
|
1.0
|
C2'
|
B:U0
|
4.4
|
161.4
|
1.0
|
O2'
|
B:U0
|
4.5
|
194.0
|
1.0
|
O5'
|
A:U375
|
4.6
|
96.6
|
1.0
|
OP1
|
A:G359
|
4.6
|
141.8
|
1.0
|
C5'
|
A:C377
|
4.7
|
127.2
|
1.0
|
P
|
A:G359
|
4.7
|
117.2
|
1.0
|
O26
|
A:VTE453
|
4.7
|
179.5
|
1.0
|
C5'
|
A:U375
|
4.8
|
108.5
|
1.0
|
|
Magnesium binding site 2 out
of 30 in 8olz
Go back to
Magnesium Binding Sites List in 8olz
Magnesium binding site 2 out
of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Mono view
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 the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:91.4
occ:1.00
|
OP2
|
A:U26
|
2.0
|
107.5
|
1.0
|
P
|
A:U26
|
3.5
|
115.5
|
1.0
|
O3'
|
A:A25
|
4.1
|
106.3
|
1.0
|
OP2
|
A:G64
|
4.1
|
112.1
|
1.0
|
O5'
|
A:U26
|
4.2
|
118.1
|
1.0
|
O2'
|
A:A25
|
4.2
|
115.8
|
1.0
|
O4
|
A:U65
|
4.4
|
136.5
|
1.0
|
OP1
|
A:U26
|
4.6
|
107.1
|
1.0
|
C5
|
A:U65
|
4.7
|
121.7
|
1.0
|
O6
|
A:G41
|
4.8
|
160.3
|
1.0
|
C4
|
A:U65
|
4.9
|
117.3
|
1.0
|
|
Magnesium binding site 3 out
of 30 in 8olz
Go back to
Magnesium Binding Sites List in 8olz
Magnesium binding site 3 out
of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Mono view
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 the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:119.7
occ:1.00
|
O24
|
A:VTE453
|
1.9
|
122.8
|
1.0
|
O26
|
A:VTE453
|
1.9
|
179.5
|
1.0
|
OP2
|
A:G359
|
2.0
|
111.8
|
1.0
|
OP1
|
A:C377
|
2.0
|
114.8
|
1.0
|
OP1
|
A:C358
|
2.0
|
132.0
|
1.0
|
C25
|
A:VTE453
|
2.6
|
215.7
|
1.0
|
C23
|
A:VTE453
|
2.6
|
183.7
|
1.0
|
P
|
A:C358
|
3.2
|
123.0
|
1.0
|
P
|
A:C377
|
3.2
|
109.0
|
1.0
|
O5'
|
A:C358
|
3.2
|
124.5
|
1.0
|
P
|
A:G359
|
3.4
|
117.2
|
1.0
|
C5'
|
A:C358
|
3.4
|
115.2
|
1.0
|
OP2
|
A:C377
|
3.6
|
96.0
|
1.0
|
MG
|
A:MG401
|
3.7
|
105.5
|
1.0
|
K
|
A:K441
|
3.8
|
130.1
|
1.0
|
O5'
|
A:G359
|
3.9
|
105.3
|
1.0
|
C21
|
A:VTE453
|
3.9
|
201.7
|
1.0
|
O3'
|
A:C357
|
4.0
|
115.5
|
1.0
|
C27
|
A:VTE453
|
4.0
|
241.5
|
1.0
|
O
|
A:HOH504
|
4.0
|
61.5
|
1.0
|
O3'
|
A:C358
|
4.2
|
128.2
|
1.0
|
O3'
|
A:A376
|
4.3
|
115.2
|
1.0
|
OP1
|
A:G359
|
4.4
|
141.8
|
1.0
|
O5'
|
A:C377
|
4.4
|
115.6
|
1.0
|
C4'
|
A:C358
|
4.4
|
129.7
|
1.0
|
OP2
|
A:C358
|
4.4
|
129.7
|
1.0
|
O22
|
A:VTE453
|
4.5
|
181.6
|
1.0
|
O3'
|
B:U0
|
4.6
|
122.8
|
1.0
|
C3'
|
A:C358
|
4.6
|
130.9
|
1.0
|
C19
|
A:VTE453
|
4.9
|
236.8
|
1.0
|
C20
|
A:VTE453
|
4.9
|
216.8
|
1.0
|
|
Magnesium binding site 4 out
of 30 in 8olz
Go back to
Magnesium Binding Sites List in 8olz
Magnesium binding site 4 out
of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Mono view
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 the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:104.5
occ:1.00
|
OP2
|
A:C145
|
2.0
|
132.5
|
1.0
|
P
|
A:C145
|
3.4
|
170.8
|
1.0
|
OP2
|
A:A134
|
3.5
|
128.1
|
1.0
|
O6
|
A:G136
|
3.8
|
134.7
|
1.0
|
OP1
|
A:C145
|
4.0
|
177.6
|
1.0
|
N2
|
A:G142
|
4.0
|
197.2
|
1.0
|
O3'
|
A:A144
|
4.3
|
162.8
|
1.0
|
O5'
|
A:C145
|
4.5
|
197.6
|
1.0
|
OP2
|
A:U146
|
4.8
|
149.8
|
1.0
|
P
|
A:A134
|
4.8
|
143.4
|
1.0
|
O6
|
A:G135
|
4.8
|
127.4
|
1.0
|
C6
|
A:G136
|
4.9
|
157.3
|
1.0
|
|
Magnesium binding site 5 out
of 30 in 8olz
Go back to
Magnesium Binding Sites List in 8olz
Magnesium binding site 5 out
of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Mono view
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 the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:94.6
occ:1.00
|
OP2
|
A:U4
|
2.6
|
122.0
|
1.0
|
O
|
A:HOH506
|
3.0
|
77.2
|
1.0
|
OP1
|
A:G3
|
3.1
|
134.0
|
1.0
|
O5'
|
A:G3
|
3.4
|
153.1
|
1.0
|
P
|
A:G3
|
3.6
|
171.7
|
1.0
|
OP2
|
A:G3
|
3.8
|
177.7
|
1.0
|
P
|
A:U4
|
4.0
|
122.6
|
1.0
|
O6
|
A:G5
|
4.0
|
125.3
|
1.0
|
C2
|
A:A376
|
4.2
|
140.2
|
1.0
|
C5'
|
A:G3
|
4.4
|
133.1
|
1.0
|
C3'
|
A:G3
|
4.6
|
100.9
|
1.0
|
N1
|
A:A376
|
4.6
|
133.1
|
1.0
|
O3'
|
A:G3
|
4.7
|
100.3
|
1.0
|
O5'
|
A:U4
|
4.7
|
102.8
|
1.0
|
C5
|
A:U4
|
4.7
|
120.6
|
1.0
|
N7
|
A:G5
|
4.7
|
119.0
|
1.0
|
K
|
A:K439
|
4.7
|
121.9
|
1.0
|
N3
|
A:A376
|
4.9
|
140.3
|
1.0
|
C6
|
A:G5
|
5.0
|
125.6
|
1.0
|
|
Magnesium binding site 6 out
of 30 in 8olz
Go back to
Magnesium Binding Sites List in 8olz
Magnesium binding site 6 out
of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Mono view
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 the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:88.6
occ:1.00
|
OP2
|
A:G374
|
2.0
|
106.1
|
1.0
|
OP1
|
A:C360
|
2.7
|
129.0
|
1.0
|
P
|
A:G374
|
3.5
|
130.0
|
1.0
|
O5'
|
A:G373
|
3.8
|
115.0
|
1.0
|
C3'
|
A:G373
|
4.0
|
121.9
|
1.0
|
P
|
A:C360
|
4.1
|
130.1
|
1.0
|
C5'
|
A:G374
|
4.2
|
123.2
|
1.0
|
O3'
|
A:G373
|
4.2
|
120.8
|
1.0
|
OP2
|
A:G373
|
4.3
|
113.6
|
1.0
|
O5'
|
A:G374
|
4.4
|
123.8
|
1.0
|
OP1
|
A:G374
|
4.5
|
108.1
|
1.0
|
P
|
A:G373
|
4.5
|
121.2
|
1.0
|
OP2
|
A:C360
|
4.5
|
119.0
|
1.0
|
C8
|
A:G374
|
4.6
|
100.9
|
1.0
|
OP1
|
A:G373
|
4.7
|
137.8
|
1.0
|
N7
|
A:G374
|
4.8
|
98.5
|
1.0
|
C5'
|
A:G373
|
4.8
|
116.3
|
1.0
|
OP2
|
A:C361
|
4.9
|
131.2
|
1.0
|
C8
|
A:G373
|
4.9
|
131.2
|
1.0
|
|
Magnesium binding site 7 out
of 30 in 8olz
Go back to
Magnesium Binding Sites List in 8olz
Magnesium binding site 7 out
of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Mono view
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 the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg407
b:111.8
occ:1.00
|
O6
|
A:G325
|
2.7
|
175.1
|
1.0
|
O
|
A:HOH505
|
3.3
|
97.2
|
1.0
|
OP2
|
A:G324
|
3.6
|
147.9
|
1.0
|
C6
|
A:G325
|
3.8
|
178.6
|
1.0
|
OP2
|
A:C323
|
3.9
|
165.1
|
1.0
|
N7
|
A:G324
|
3.9
|
186.3
|
1.0
|
OP1
|
A:C323
|
4.2
|
124.9
|
1.0
|
N7
|
A:G325
|
4.3
|
226.6
|
1.0
|
P
|
A:C323
|
4.3
|
143.3
|
1.0
|
O6
|
A:G324
|
4.4
|
147.4
|
1.0
|
O5'
|
A:C323
|
4.4
|
147.4
|
1.0
|
C5
|
A:G325
|
4.4
|
202.6
|
1.0
|
C5
|
A:G324
|
4.7
|
179.2
|
1.0
|
C8
|
A:G324
|
4.8
|
198.6
|
1.0
|
C6
|
A:G324
|
4.9
|
160.7
|
1.0
|
|
Magnesium binding site 8 out
of 30 in 8olz
Go back to
Magnesium Binding Sites List in 8olz
Magnesium binding site 8 out
of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Mono view
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 the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg408
b:81.4
occ:1.00
|
O6
|
A:G46
|
3.3
|
113.5
|
1.0
|
OP2
|
A:U59
|
3.4
|
109.7
|
1.0
|
O4
|
A:U45
|
3.6
|
127.0
|
1.0
|
C4
|
A:U45
|
4.3
|
131.7
|
1.0
|
OP1
|
A:U59
|
4.3
|
108.5
|
1.0
|
C5
|
A:U45
|
4.3
|
139.4
|
1.0
|
P
|
A:U59
|
4.3
|
112.8
|
1.0
|
C6
|
A:G46
|
4.4
|
110.4
|
1.0
|
N7
|
A:G46
|
4.6
|
109.7
|
1.0
|
O2'
|
A:G58
|
4.8
|
119.3
|
1.0
|
C5
|
A:G46
|
4.9
|
104.0
|
1.0
|
O4
|
A:U47
|
5.0
|
76.7
|
1.0
|
|
Magnesium binding site 9 out
of 30 in 8olz
Go back to
Magnesium Binding Sites List in 8olz
Magnesium binding site 9 out
of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Mono view
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 the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg409
b:61.0
occ:1.00
|
OP1
|
A:G107
|
2.0
|
93.5
|
1.0
|
P
|
A:G107
|
3.4
|
109.0
|
1.0
|
O3'
|
A:A106
|
3.9
|
115.2
|
1.0
|
OP2
|
A:A105
|
4.0
|
129.1
|
1.0
|
C5'
|
A:G107
|
4.0
|
93.6
|
1.0
|
N7
|
A:A105
|
4.1
|
104.1
|
1.0
|
OP2
|
A:A106
|
4.1
|
98.0
|
1.0
|
C8
|
A:A105
|
4.2
|
101.4
|
1.0
|
O5'
|
A:G107
|
4.3
|
90.5
|
1.0
|
OP1
|
A:G108
|
4.4
|
90.1
|
1.0
|
OP2
|
A:G107
|
4.6
|
85.0
|
1.0
|
C5
|
A:C261
|
4.7
|
123.5
|
1.0
|
|
Magnesium binding site 10 out
of 30 in 8olz
Go back to
Magnesium Binding Sites List in 8olz
Magnesium binding site 10 out
of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking
Mono view
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 the Presence of K+, MG2+, 5'-Exon, and Intronistat B After 2H30 Soaking within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg410
b:75.3
occ:1.00
|
OP2
|
A:C372
|
2.0
|
147.9
|
1.0
|
OP1
|
A:A371
|
3.4
|
111.2
|
1.0
|
O6
|
A:G373
|
3.5
|
114.6
|
1.0
|
P
|
A:C372
|
3.5
|
125.1
|
1.0
|
OP2
|
A:A371
|
4.1
|
147.3
|
1.0
|
P
|
A:A371
|
4.2
|
127.9
|
1.0
|
O5'
|
A:C372
|
4.3
|
95.7
|
1.0
|
OP1
|
A:C372
|
4.4
|
103.2
|
1.0
|
N7
|
A:G373
|
4.4
|
126.6
|
1.0
|
C6
|
A:G373
|
4.5
|
118.6
|
1.0
|
O6
|
A:G374
|
4.5
|
86.3
|
1.0
|
O3'
|
A:A371
|
4.6
|
96.3
|
1.0
|
O5'
|
A:A371
|
4.6
|
128.0
|
1.0
|
C3'
|
A:A371
|
4.8
|
107.7
|
1.0
|
C5'
|
A:A371
|
4.8
|
135.4
|
1.0
|
C5
|
A:C372
|
4.9
|
151.2
|
1.0
|
C5
|
A:G373
|
4.9
|
128.0
|
1.0
|
|
Reference:
I.Silvestri,
J.Manigrasso,
A.Andreani,
N.Brindani,
C.Mas,
J.B.Reiser,
P.Vidossich,
G.Martino,
A.Mccarthy,
M.De Vivo,
M.Marcia.
Targeting the Conserved Active Site of Splicing Machines with Specific and Selective Small Molecule Modulators Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-48697-0
Page generated: Fri Oct 4 14:57:47 2024
|