Magnesium in PDB 8olv: Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
Protein crystallography data
The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850, PDB code: 8olv
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)
|
48.42 /
2.81
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.012,
94.722,
225.042,
90,
90,
90
|
R / Rfree (%)
|
19.6 /
23.7
|
Other elements in 8olv:
The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850 also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
21;
Binding sites:
The binding sites of Magnesium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
(pdb code 8olv). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the
Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850, PDB code: 8olv:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 21 in 8olv
Go back to
Magnesium Binding Sites List in 8olv
Magnesium binding site 1 out
of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:107.9
occ:1.00
|
OP2
|
A:C145
|
1.9
|
121.1
|
1.0
|
P
|
A:C145
|
3.1
|
153.3
|
1.0
|
O5'
|
A:C145
|
3.1
|
176.8
|
1.0
|
OP2
|
A:A134
|
3.6
|
129.2
|
1.0
|
OP1
|
A:C145
|
4.1
|
173.6
|
1.0
|
N2
|
A:G142
|
4.1
|
182.0
|
1.0
|
OP2
|
A:U146
|
4.2
|
105.8
|
1.0
|
O3'
|
A:A144
|
4.2
|
151.9
|
1.0
|
C5'
|
A:C145
|
4.5
|
179.6
|
1.0
|
O6
|
A:G136
|
4.6
|
143.2
|
1.0
|
O3'
|
A:C145
|
4.7
|
150.8
|
1.0
|
C3'
|
A:C145
|
4.8
|
174.2
|
1.0
|
C3'
|
A:A144
|
4.9
|
132.0
|
1.0
|
P
|
A:A134
|
4.9
|
137.5
|
1.0
|
P
|
A:U146
|
5.0
|
160.7
|
1.0
|
O2'
|
A:A144
|
5.0
|
133.2
|
1.0
|
|
Magnesium binding site 2 out
of 21 in 8olv
Go back to
Magnesium Binding Sites List in 8olv
Magnesium binding site 2 out
of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:93.2
occ:1.00
|
OP2
|
A:C377
|
1.9
|
100.6
|
1.0
|
OP1
|
A:U375
|
1.9
|
84.4
|
1.0
|
O01
|
A:VTR443
|
2.1
|
111.3
|
1.0
|
O32
|
A:VTR443
|
2.1
|
111.3
|
1.0
|
O
|
A:HOH501
|
2.3
|
85.0
|
1.0
|
C31
|
A:VTR443
|
2.9
|
102.3
|
1.0
|
C02
|
A:VTR443
|
2.9
|
110.5
|
1.0
|
P
|
A:U375
|
3.1
|
99.5
|
1.0
|
P
|
A:C377
|
3.3
|
96.4
|
1.0
|
OP1
|
A:G359
|
3.5
|
131.3
|
1.0
|
OP2
|
A:U375
|
3.7
|
104.5
|
1.0
|
O3'
|
A:G374
|
3.7
|
104.4
|
1.0
|
MG
|
A:MG403
|
3.9
|
108.6
|
1.0
|
OP1
|
A:C377
|
4.0
|
95.0
|
1.0
|
O5'
|
A:C377
|
4.0
|
95.9
|
1.0
|
C5'
|
A:C377
|
4.2
|
83.0
|
1.0
|
C29
|
A:VTR443
|
4.2
|
110.3
|
1.0
|
C03
|
A:VTR443
|
4.2
|
139.6
|
1.0
|
O3'
|
A:A376
|
4.4
|
99.9
|
1.0
|
OP2
|
A:G359
|
4.4
|
119.7
|
1.0
|
O
|
A:HOH503
|
4.5
|
106.4
|
1.0
|
P
|
A:G359
|
4.5
|
95.5
|
1.0
|
O5'
|
A:U375
|
4.5
|
94.7
|
1.0
|
C3'
|
A:A376
|
4.6
|
92.9
|
1.0
|
C4'
|
A:C377
|
4.9
|
98.0
|
1.0
|
O30
|
A:VTR443
|
4.9
|
108.0
|
1.0
|
C5'
|
A:A376
|
4.9
|
98.5
|
1.0
|
C3'
|
A:G374
|
4.9
|
105.3
|
1.0
|
|
Magnesium binding site 3 out
of 21 in 8olv
Go back to
Magnesium Binding Sites List in 8olv
Magnesium binding site 3 out
of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:108.6
occ:1.00
|
O
|
A:HOH503
|
1.9
|
106.4
|
1.0
|
OP1
|
A:C377
|
1.9
|
95.0
|
1.0
|
OP2
|
A:G359
|
1.9
|
119.7
|
1.0
|
OP1
|
A:C358
|
1.9
|
137.4
|
1.0
|
O30
|
A:VTR443
|
2.1
|
108.0
|
1.0
|
O32
|
A:VTR443
|
2.1
|
111.3
|
1.0
|
C29
|
A:VTR443
|
2.8
|
110.3
|
1.0
|
C31
|
A:VTR443
|
2.8
|
102.3
|
1.0
|
P
|
A:C377
|
3.0
|
96.4
|
1.0
|
P
|
A:C358
|
3.1
|
108.9
|
1.0
|
O5'
|
A:C358
|
3.1
|
121.6
|
1.0
|
P
|
A:G359
|
3.3
|
95.5
|
1.0
|
OP2
|
A:C377
|
3.4
|
100.6
|
1.0
|
C5'
|
A:C358
|
3.6
|
113.8
|
1.0
|
K
|
A:K434
|
3.6
|
105.7
|
1.0
|
OP1
|
A:G359
|
3.7
|
131.3
|
1.0
|
MG
|
A:MG402
|
3.9
|
93.2
|
1.0
|
O5'
|
A:C377
|
3.9
|
95.9
|
1.0
|
O
|
A:HOH501
|
3.9
|
85.0
|
1.0
|
O
|
A:HOH506
|
4.0
|
74.0
|
1.0
|
OP2
|
A:C358
|
4.0
|
113.1
|
1.0
|
C02
|
A:VTR443
|
4.1
|
110.5
|
1.0
|
C27
|
A:VTR443
|
4.1
|
137.9
|
1.0
|
O3'
|
A:A376
|
4.2
|
99.9
|
1.0
|
O5'
|
A:G359
|
4.3
|
97.7
|
1.0
|
O3'
|
A:C357
|
4.3
|
102.8
|
1.0
|
O3'
|
A:C358
|
4.3
|
120.1
|
1.0
|
C4'
|
A:C358
|
4.7
|
125.2
|
1.0
|
O01
|
A:VTR443
|
4.7
|
111.3
|
1.0
|
C3'
|
A:C358
|
4.9
|
133.9
|
1.0
|
BR28
|
A:VTR443
|
5.0
|
182.8
|
1.0
|
|
Magnesium binding site 4 out
of 21 in 8olv
Go back to
Magnesium Binding Sites List in 8olv
Magnesium binding site 4 out
of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:106.0
occ:1.00
|
OP2
|
A:U4
|
2.0
|
112.1
|
1.0
|
OP1
|
A:G3
|
2.1
|
127.4
|
1.0
|
P
|
A:U4
|
3.5
|
95.3
|
1.0
|
P
|
A:G3
|
3.6
|
117.3
|
1.0
|
O5'
|
A:G3
|
4.1
|
111.8
|
1.0
|
O3'
|
A:G3
|
4.3
|
89.2
|
1.0
|
O5'
|
A:U4
|
4.4
|
79.5
|
1.0
|
OP1
|
A:U4
|
4.4
|
107.5
|
1.0
|
OP2
|
A:G3
|
4.4
|
106.6
|
1.0
|
C5'
|
A:G3
|
4.5
|
105.3
|
1.0
|
O6
|
A:G5
|
4.5
|
94.3
|
1.0
|
O3'
|
A:U2
|
4.7
|
134.1
|
1.0
|
C3'
|
A:G3
|
4.7
|
90.5
|
1.0
|
N7
|
A:G5
|
4.7
|
93.1
|
1.0
|
|
Magnesium binding site 5 out
of 21 in 8olv
Go back to
Magnesium Binding Sites List in 8olv
Magnesium binding site 5 out
of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:108.9
occ:1.00
|
O6
|
A:G325
|
2.1
|
144.7
|
1.0
|
O
|
A:HOH502
|
3.1
|
92.2
|
1.0
|
C6
|
A:G325
|
3.2
|
158.5
|
1.0
|
N7
|
A:G324
|
3.5
|
164.2
|
1.0
|
N7
|
A:G325
|
3.9
|
182.2
|
1.0
|
C5
|
A:G325
|
3.9
|
166.6
|
1.0
|
OP2
|
A:G324
|
4.0
|
122.5
|
1.0
|
O6
|
A:G324
|
4.1
|
147.6
|
1.0
|
C5
|
A:G324
|
4.4
|
146.0
|
1.0
|
N1
|
A:G325
|
4.4
|
153.8
|
1.0
|
C8
|
A:G324
|
4.5
|
180.1
|
1.0
|
OP2
|
A:C323
|
4.5
|
135.6
|
1.0
|
C6
|
A:G324
|
4.6
|
142.0
|
1.0
|
|
Magnesium binding site 6 out
of 21 in 8olv
Go back to
Magnesium Binding Sites List in 8olv
Magnesium binding site 6 out
of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:118.6
occ:1.00
|
O
|
A:HOH508
|
2.2
|
91.8
|
1.0
|
O
|
A:HOH509
|
2.3
|
76.2
|
1.0
|
O4
|
A:U47
|
2.8
|
70.6
|
1.0
|
OP2
|
A:U59
|
3.1
|
69.4
|
1.0
|
O6
|
A:G46
|
3.4
|
77.2
|
1.0
|
O6
|
A:G48
|
3.8
|
83.1
|
1.0
|
O2'
|
A:G58
|
3.8
|
66.3
|
1.0
|
C4
|
A:U47
|
3.9
|
80.8
|
1.0
|
N1
|
A:G48
|
3.9
|
76.4
|
1.0
|
C6
|
A:G48
|
4.0
|
70.2
|
1.0
|
C6
|
A:G46
|
4.1
|
82.6
|
1.0
|
N7
|
A:G46
|
4.1
|
99.2
|
1.0
|
P
|
A:U59
|
4.3
|
74.1
|
1.0
|
N6
|
A:A61
|
4.3
|
73.2
|
1.0
|
C5
|
A:U47
|
4.4
|
89.2
|
1.0
|
C5
|
A:G46
|
4.4
|
85.0
|
1.0
|
OP1
|
A:U59
|
4.4
|
70.6
|
1.0
|
C2
|
A:G48
|
4.8
|
71.9
|
1.0
|
|
Magnesium binding site 7 out
of 21 in 8olv
Go back to
Magnesium Binding Sites List in 8olv
Magnesium binding site 7 out
of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg407
b:77.6
occ:1.00
|
OP1
|
A:G107
|
2.1
|
97.3
|
1.0
|
P
|
A:G107
|
3.6
|
86.4
|
1.0
|
OP2
|
A:A105
|
4.2
|
95.8
|
1.0
|
OP1
|
A:G108
|
4.2
|
99.1
|
1.0
|
N7
|
A:A105
|
4.2
|
101.8
|
1.0
|
O3'
|
A:A106
|
4.2
|
102.5
|
1.0
|
C8
|
A:A105
|
4.4
|
99.8
|
1.0
|
OP2
|
A:G107
|
4.5
|
86.5
|
1.0
|
O5'
|
A:G107
|
4.5
|
75.9
|
1.0
|
C5'
|
A:G107
|
4.5
|
77.3
|
1.0
|
|
Magnesium binding site 8 out
of 21 in 8olv
Go back to
Magnesium Binding Sites List in 8olv
Magnesium binding site 8 out
of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg408
b:97.9
occ:1.00
|
OP1
|
A:G378
|
3.9
|
97.1
|
1.0
|
O4
|
A:U379
|
4.1
|
103.8
|
1.0
|
O6
|
A:G362
|
4.2
|
122.1
|
1.0
|
N6
|
A:A380
|
4.6
|
127.7
|
1.0
|
O4
|
A:U363
|
4.6
|
146.0
|
1.0
|
N7
|
A:G362
|
4.7
|
120.9
|
1.0
|
N4
|
A:C361
|
4.7
|
120.7
|
1.0
|
C4
|
A:C361
|
4.9
|
120.3
|
1.0
|
|
Magnesium binding site 9 out
of 21 in 8olv
Go back to
Magnesium Binding Sites List in 8olv
Magnesium binding site 9 out
of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg409
b:108.2
occ:1.00
|
OP1
|
A:G239
|
2.1
|
109.2
|
1.0
|
OP1
|
A:C119
|
2.7
|
86.1
|
1.0
|
OP1
|
A:A174
|
3.1
|
71.3
|
1.0
|
P
|
A:G239
|
3.3
|
85.3
|
1.0
|
O3'
|
A:U238
|
3.4
|
95.2
|
1.0
|
C5'
|
A:G239
|
4.1
|
102.5
|
1.0
|
P
|
A:C119
|
4.2
|
95.2
|
1.0
|
O5'
|
A:G239
|
4.2
|
91.6
|
1.0
|
OP2
|
A:G239
|
4.5
|
88.4
|
1.0
|
C5'
|
A:C119
|
4.5
|
79.8
|
1.0
|
P
|
A:A174
|
4.5
|
100.2
|
1.0
|
C5'
|
A:A174
|
4.8
|
108.9
|
1.0
|
C3'
|
A:U238
|
4.8
|
90.5
|
1.0
|
O5'
|
A:C119
|
4.8
|
81.6
|
1.0
|
O5'
|
A:U238
|
5.0
|
91.0
|
1.0
|
|
Magnesium binding site 10 out
of 21 in 8olv
Go back to
Magnesium Binding Sites List in 8olv
Magnesium binding site 10 out
of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and ARN25850
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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg410
b:109.0
occ:1.00
|
OP1
|
A:A105
|
2.0
|
133.3
|
1.0
|
P
|
A:A105
|
3.4
|
98.4
|
1.0
|
O6
|
A:G111
|
3.8
|
95.3
|
1.0
|
N1
|
A:A77
|
4.2
|
113.0
|
1.0
|
O5'
|
A:A105
|
4.2
|
79.8
|
1.0
|
OP2
|
A:A105
|
4.2
|
95.8
|
1.0
|
C3'
|
A:G104
|
4.3
|
91.0
|
1.0
|
O3'
|
A:G104
|
4.4
|
91.8
|
1.0
|
N4
|
A:C76
|
4.6
|
90.7
|
1.0
|
C2
|
A:A77
|
4.6
|
115.0
|
1.0
|
C2'
|
A:G104
|
4.7
|
85.3
|
1.0
|
C5'
|
A:A105
|
4.9
|
90.4
|
1.0
|
C6
|
A:G111
|
5.0
|
92.2
|
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 14:52:45 2024
|