Calcium in PDB 8olw: Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
Protein crystallography data
The structure of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B, PDB code: 8olw
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)
|
48.68 /
4.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.147,
94.133,
222.878,
90,
90,
90
|
R / Rfree (%)
|
22 /
25.8
|
Other elements in 8olw:
The structure of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
(pdb code 8olw). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the
Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B, PDB code: 8olw:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Calcium binding site 1 out
of 9 in 8olw
Go back to
Calcium Binding Sites List in 8olw
Calcium binding site 1 out
of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:238.1
occ:1.00
|
CA
|
A:CA402
|
2.0
|
238.8
|
1.0
|
OP1
|
A:G1
|
2.2
|
241.8
|
1.0
|
OP2
|
A:C377
|
2.3
|
162.1
|
1.0
|
O5'
|
A:G1
|
2.3
|
275.4
|
1.0
|
P
|
A:G1
|
2.4
|
262.6
|
1.0
|
OP2
|
A:G359
|
2.6
|
209.5
|
1.0
|
O3'
|
A:U0
|
2.6
|
215.0
|
1.0
|
O
|
A:HOH507
|
2.7
|
139.5
|
1.0
|
OP1
|
A:C377
|
3.0
|
177.2
|
1.0
|
P
|
A:C377
|
3.1
|
168.3
|
1.0
|
OP1
|
A:G359
|
3.4
|
228.6
|
1.0
|
P
|
A:G359
|
3.4
|
207.8
|
1.0
|
C5'
|
A:G1
|
3.5
|
279.6
|
1.0
|
O2'
|
A:U0
|
3.9
|
203.4
|
1.0
|
OP2
|
A:G1
|
3.9
|
298.0
|
1.0
|
C3'
|
A:U0
|
4.0
|
207.3
|
1.0
|
OP1
|
A:C358
|
4.1
|
192.4
|
1.0
|
O3'
|
A:A376
|
4.2
|
172.8
|
1.0
|
O5'
|
A:C377
|
4.4
|
172.6
|
1.0
|
C2'
|
A:U0
|
4.4
|
209.8
|
1.0
|
O5'
|
A:G359
|
4.5
|
195.1
|
1.0
|
O5'
|
A:C358
|
4.6
|
209.6
|
1.0
|
OP1
|
A:U375
|
4.6
|
170.3
|
1.0
|
O3'
|
A:C358
|
4.7
|
199.2
|
1.0
|
C4'
|
A:G1
|
4.7
|
277.6
|
1.0
|
K
|
A:K418
|
4.8
|
179.8
|
1.0
|
C3'
|
A:A376
|
4.9
|
178.1
|
1.0
|
P
|
A:C358
|
4.9
|
193.9
|
1.0
|
C4'
|
A:U0
|
5.0
|
208.2
|
1.0
|
|
Calcium binding site 2 out
of 9 in 8olw
Go back to
Calcium Binding Sites List in 8olw
Calcium binding site 2 out
of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:238.8
occ:1.00
|
CA
|
A:CA401
|
2.0
|
238.1
|
1.0
|
OP1
|
A:C358
|
2.1
|
192.4
|
1.0
|
OP2
|
A:G359
|
2.2
|
209.5
|
1.0
|
OP1
|
A:C377
|
2.3
|
177.2
|
1.0
|
O
|
A:HOH507
|
2.5
|
139.5
|
1.0
|
O5'
|
A:G1
|
2.8
|
275.4
|
1.0
|
O5'
|
A:C358
|
3.1
|
209.6
|
1.0
|
P
|
A:C358
|
3.1
|
193.9
|
1.0
|
P
|
A:C377
|
3.3
|
168.3
|
1.0
|
OP2
|
A:C377
|
3.3
|
162.1
|
1.0
|
P
|
A:G359
|
3.6
|
207.8
|
1.0
|
OP1
|
A:G1
|
3.7
|
241.8
|
1.0
|
C5'
|
A:G1
|
3.7
|
279.6
|
1.0
|
P
|
A:G1
|
3.8
|
262.6
|
1.0
|
C5'
|
A:C358
|
3.8
|
215.9
|
1.0
|
OP2
|
A:C358
|
4.0
|
189.8
|
1.0
|
K
|
A:K418
|
4.1
|
179.8
|
1.0
|
OP1
|
A:G359
|
4.3
|
228.6
|
1.0
|
O3'
|
A:U0
|
4.3
|
215.0
|
1.0
|
O3'
|
A:A376
|
4.3
|
172.8
|
1.0
|
O3'
|
A:C357
|
4.3
|
193.0
|
1.0
|
O5'
|
A:C377
|
4.5
|
172.6
|
1.0
|
O3'
|
A:C358
|
4.5
|
199.2
|
1.0
|
C4'
|
A:G1
|
4.5
|
277.6
|
1.0
|
O5'
|
A:G359
|
4.6
|
195.1
|
1.0
|
C4'
|
A:C358
|
4.8
|
215.6
|
1.0
|
C3'
|
A:C358
|
4.9
|
202.9
|
1.0
|
|
Calcium binding site 3 out
of 9 in 8olw
Go back to
Calcium Binding Sites List in 8olw
Calcium binding site 3 out
of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:186.7
occ:1.00
|
OP2
|
A:G374
|
2.5
|
169.4
|
1.0
|
OP1
|
A:C360
|
2.7
|
170.0
|
1.0
|
OP2
|
A:C360
|
3.5
|
167.1
|
1.0
|
P
|
A:C360
|
3.6
|
170.7
|
1.0
|
P
|
A:G374
|
4.0
|
179.2
|
1.0
|
N7
|
A:G374
|
4.2
|
195.9
|
1.0
|
C5'
|
A:G374
|
4.2
|
183.3
|
1.0
|
C8
|
A:G374
|
4.3
|
188.6
|
1.0
|
O5'
|
A:C360
|
4.5
|
185.2
|
1.0
|
O5'
|
A:G373
|
4.5
|
210.7
|
1.0
|
OP2
|
A:G373
|
4.6
|
215.5
|
1.0
|
C3'
|
A:G373
|
4.6
|
209.2
|
1.0
|
O5'
|
A:G374
|
4.6
|
180.3
|
1.0
|
O3'
|
A:G373
|
4.8
|
197.5
|
1.0
|
OP2
|
A:C361
|
5.0
|
217.6
|
1.0
|
O3'
|
A:G359
|
5.0
|
175.5
|
1.0
|
|
Calcium binding site 4 out
of 9 in 8olw
Go back to
Calcium Binding Sites List in 8olw
Calcium binding site 4 out
of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca404
b:184.6
occ:1.00
|
O
|
A:HOH501
|
1.9
|
162.8
|
1.0
|
O4
|
A:U45
|
3.2
|
185.1
|
1.0
|
O6
|
A:G46
|
3.5
|
155.9
|
1.0
|
OP2
|
A:U59
|
3.6
|
138.0
|
1.0
|
C4
|
A:U45
|
4.0
|
193.9
|
1.0
|
C5
|
A:U45
|
4.3
|
204.2
|
1.0
|
C6
|
A:G46
|
4.5
|
154.0
|
1.0
|
O4
|
A:U47
|
4.5
|
129.2
|
1.0
|
N7
|
A:G46
|
4.7
|
176.7
|
1.0
|
P
|
A:U59
|
4.7
|
142.8
|
1.0
|
OP1
|
A:U59
|
4.8
|
140.6
|
1.0
|
C5
|
A:G46
|
5.0
|
166.3
|
1.0
|
|
Calcium binding site 5 out
of 9 in 8olw
Go back to
Calcium Binding Sites List in 8olw
Calcium binding site 5 out
of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca405
b:201.7
occ:1.00
|
OP1
|
A:G239
|
2.0
|
186.0
|
1.0
|
P
|
A:G239
|
3.3
|
196.4
|
1.0
|
OP1
|
A:C119
|
3.4
|
200.4
|
1.0
|
OP2
|
A:A120
|
3.7
|
224.1
|
1.0
|
OP2
|
A:G239
|
3.9
|
208.4
|
1.0
|
OP1
|
A:A174
|
3.9
|
180.5
|
1.0
|
C5'
|
A:C119
|
4.0
|
200.0
|
1.0
|
O3'
|
A:U238
|
4.2
|
189.9
|
1.0
|
P
|
A:A120
|
4.4
|
224.6
|
1.0
|
P
|
A:C119
|
4.5
|
186.1
|
1.0
|
O5'
|
A:G239
|
4.5
|
193.4
|
1.0
|
O5'
|
A:C119
|
4.5
|
188.3
|
1.0
|
OP1
|
A:A120
|
4.5
|
248.2
|
1.0
|
O3'
|
A:C119
|
4.5
|
209.8
|
1.0
|
OP1
|
A:U238
|
4.7
|
268.0
|
1.0
|
C5'
|
A:G239
|
4.8
|
193.8
|
1.0
|
|
Calcium binding site 6 out
of 9 in 8olw
Go back to
Calcium Binding Sites List in 8olw
Calcium binding site 6 out
of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca406
b:265.5
occ:1.00
|
O
|
A:HOH505
|
1.9
|
172.3
|
1.0
|
O
|
A:HOH506
|
2.2
|
208.5
|
1.0
|
O
|
A:HOH504
|
2.6
|
221.0
|
1.0
|
OP2
|
A:A154
|
2.6
|
240.3
|
1.0
|
O6
|
A:G156
|
3.3
|
226.5
|
1.0
|
O4
|
A:U221
|
3.5
|
267.1
|
1.0
|
P
|
A:A154
|
3.7
|
254.8
|
1.0
|
OP1
|
A:A154
|
3.9
|
253.8
|
1.0
|
N7
|
A:G155
|
4.0
|
238.0
|
1.0
|
O6
|
A:G155
|
4.0
|
233.1
|
1.0
|
N4
|
A:C157
|
4.2
|
224.4
|
1.0
|
C6
|
A:G156
|
4.4
|
230.8
|
1.0
|
C4
|
A:U221
|
4.4
|
269.4
|
1.0
|
N3
|
A:U221
|
4.5
|
263.2
|
1.0
|
N7
|
A:G156
|
4.5
|
251.3
|
1.0
|
C6
|
A:G155
|
4.6
|
230.2
|
1.0
|
C5
|
A:G155
|
4.6
|
235.6
|
1.0
|
O3'
|
A:G153
|
4.6
|
268.9
|
1.0
|
O6
|
A:G220
|
4.8
|
269.9
|
1.0
|
C5
|
A:G156
|
4.9
|
237.1
|
1.0
|
O2'
|
A:G153
|
5.0
|
281.4
|
1.0
|
C8
|
A:G155
|
5.0
|
245.3
|
1.0
|
O5'
|
A:A154
|
5.0
|
264.5
|
1.0
|
OP2
|
A:G155
|
5.0
|
269.3
|
1.0
|
|
Calcium binding site 7 out
of 9 in 8olw
Go back to
Calcium Binding Sites List in 8olw
Calcium binding site 7 out
of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca407
b:189.8
occ:1.00
|
O4
|
A:U65
|
3.0
|
250.1
|
1.0
|
N7
|
A:G64
|
3.8
|
195.1
|
1.0
|
C4
|
A:U65
|
4.0
|
242.5
|
1.0
|
OP2
|
A:A63
|
4.2
|
177.1
|
1.0
|
O6
|
A:G64
|
4.3
|
217.2
|
1.0
|
C5
|
A:U65
|
4.5
|
249.2
|
1.0
|
C5
|
A:G64
|
4.7
|
191.7
|
1.0
|
N7
|
A:A63
|
4.7
|
187.5
|
1.0
|
OP2
|
A:G64
|
4.7
|
209.0
|
1.0
|
C8
|
A:G64
|
4.7
|
197.1
|
1.0
|
C6
|
A:G64
|
4.9
|
191.9
|
1.0
|
|
Calcium binding site 8 out
of 9 in 8olw
Go back to
Calcium Binding Sites List in 8olw
Calcium binding site 8 out
of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca408
b:195.5
occ:1.00
|
O
|
A:HOH509
|
2.3
|
174.7
|
1.0
|
OP2
|
A:A283
|
2.4
|
199.6
|
1.0
|
O6
|
A:G284
|
3.5
|
165.5
|
1.0
|
P
|
A:A283
|
3.8
|
198.0
|
1.0
|
N7
|
A:G284
|
3.9
|
180.1
|
1.0
|
N7
|
A:A283
|
4.1
|
210.1
|
1.0
|
C6
|
A:G284
|
4.3
|
166.1
|
1.0
|
O5'
|
A:A283
|
4.4
|
198.7
|
1.0
|
OP1
|
A:A283
|
4.4
|
192.4
|
1.0
|
C8
|
A:A283
|
4.4
|
210.4
|
1.0
|
C5
|
A:G284
|
4.5
|
171.8
|
1.0
|
OP2
|
A:A282
|
4.9
|
191.7
|
1.0
|
O5'
|
A:A282
|
4.9
|
196.6
|
1.0
|
C3'
|
A:A282
|
5.0
|
187.1
|
1.0
|
O3'
|
A:A282
|
5.0
|
189.8
|
1.0
|
|
Calcium binding site 9 out
of 9 in 8olw
Go back to
Calcium Binding Sites List in 8olw
Calcium binding site 9 out
of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca409
b:209.9
occ:1.00
|
OP1
|
A:A49
|
3.3
|
152.2
|
1.0
|
C5'
|
A:A49
|
4.3
|
162.3
|
1.0
|
P
|
A:A49
|
4.7
|
151.5
|
1.0
|
O5'
|
A:A49
|
5.0
|
158.1
|
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 Jul 19 11:00:58 2024
|