Potassium 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:
Potassium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Potassium 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 Potassium atom.
In total 18 binding sites of Potassium 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 Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Potassium binding site 1 out
of 18 in 8olz
Go back to
Potassium Binding Sites List in 8olz
Potassium binding site 1 out
of 18 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 Potassium with other atoms in the K 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:K431
b:140.7
occ:1.00
|
O6
|
A:G15
|
2.8
|
125.2
|
1.0
|
O4
|
A:U256
|
3.5
|
115.7
|
1.0
|
O6
|
A:G14
|
3.5
|
146.6
|
1.0
|
O4
|
A:U255
|
3.6
|
128.7
|
1.0
|
C6
|
A:G15
|
3.9
|
135.0
|
1.0
|
C6
|
A:G14
|
4.4
|
143.2
|
1.0
|
C4
|
A:U255
|
4.5
|
153.4
|
1.0
|
O6
|
A:G16
|
4.5
|
131.1
|
1.0
|
N7
|
A:G15
|
4.6
|
159.1
|
1.0
|
N3
|
A:U255
|
4.6
|
159.6
|
1.0
|
C5
|
A:G15
|
4.6
|
148.6
|
1.0
|
C4
|
A:U256
|
4.7
|
125.0
|
1.0
|
N7
|
A:G14
|
4.9
|
111.5
|
1.0
|
C5
|
A:G14
|
5.0
|
123.1
|
1.0
|
|
Potassium binding site 2 out
of 18 in 8olz
Go back to
Potassium Binding Sites List in 8olz
Potassium binding site 2 out
of 18 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 Potassium with other atoms in the K 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:K432
b:107.3
occ:1.00
|
OP2
|
A:G269
|
2.7
|
117.9
|
1.0
|
O5'
|
A:A268
|
3.5
|
136.8
|
1.0
|
N7
|
A:G270
|
3.7
|
115.6
|
1.0
|
P
|
A:G269
|
3.8
|
144.6
|
1.0
|
O5'
|
A:G269
|
3.8
|
116.9
|
1.0
|
N7
|
A:G269
|
3.9
|
134.6
|
1.0
|
C8
|
A:G269
|
4.0
|
151.8
|
1.0
|
OP2
|
A:A268
|
4.1
|
119.9
|
1.0
|
O6
|
A:G270
|
4.3
|
99.7
|
1.0
|
P
|
A:A268
|
4.3
|
130.9
|
1.0
|
C5'
|
A:A268
|
4.4
|
135.9
|
1.0
|
O4
|
A:U271
|
4.5
|
126.4
|
1.0
|
C3'
|
A:A268
|
4.6
|
141.8
|
1.0
|
C8
|
A:G270
|
4.6
|
123.6
|
1.0
|
C5
|
A:G270
|
4.6
|
105.4
|
1.0
|
OP2
|
A:G270
|
4.7
|
128.0
|
1.0
|
O3'
|
A:A268
|
4.8
|
136.2
|
1.0
|
OP1
|
A:G269
|
4.9
|
139.3
|
1.0
|
OP1
|
A:A268
|
4.9
|
114.2
|
1.0
|
C6
|
A:G270
|
4.9
|
103.7
|
1.0
|
N2
|
A:G284
|
4.9
|
88.4
|
1.0
|
|
Potassium binding site 3 out
of 18 in 8olz
Go back to
Potassium Binding Sites List in 8olz
Potassium binding site 3 out
of 18 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 Potassium with other atoms in the K 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:K433
b:136.9
occ:1.00
|
O6
|
A:G275
|
2.8
|
142.5
|
1.0
|
O4
|
A:U273
|
2.8
|
106.2
|
1.0
|
C6
|
A:G275
|
3.5
|
131.7
|
1.0
|
C4
|
A:U273
|
3.7
|
110.5
|
1.0
|
O6
|
A:G274
|
3.7
|
88.4
|
1.0
|
K
|
A:K437
|
3.8
|
139.6
|
1.0
|
N1
|
A:G275
|
3.9
|
117.7
|
1.0
|
C5
|
A:U273
|
4.1
|
126.4
|
1.0
|
C5
|
A:G275
|
4.6
|
129.8
|
1.0
|
N3
|
A:U273
|
4.7
|
98.7
|
1.0
|
C6
|
A:G274
|
4.8
|
96.8
|
1.0
|
N4
|
A:C279
|
4.9
|
105.9
|
1.0
|
N6
|
A:A280
|
4.9
|
100.6
|
1.0
|
|
Potassium binding site 4 out
of 18 in 8olz
Go back to
Potassium Binding Sites List in 8olz
Potassium binding site 4 out
of 18 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 Potassium with other atoms in the K 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:K434
b:144.9
occ:1.00
|
O6
|
A:G28
|
2.8
|
124.8
|
1.0
|
N7
|
A:G28
|
2.8
|
129.8
|
1.0
|
C6
|
A:G28
|
3.4
|
122.0
|
1.0
|
C5
|
A:G28
|
3.4
|
130.5
|
1.0
|
C8
|
A:G28
|
4.1
|
123.3
|
1.0
|
O6
|
A:G29
|
4.1
|
129.7
|
1.0
|
OP2
|
A:A27
|
4.2
|
160.4
|
1.0
|
C5'
|
A:A25
|
4.3
|
101.1
|
1.0
|
N2
|
A:G41
|
4.5
|
136.1
|
1.0
|
OP1
|
A:A25
|
4.5
|
112.5
|
1.0
|
N7
|
A:G29
|
4.7
|
132.6
|
1.0
|
OP1
|
A:U26
|
4.7
|
107.1
|
1.0
|
C4
|
A:G28
|
4.7
|
123.0
|
1.0
|
N1
|
A:G28
|
4.7
|
109.4
|
1.0
|
C6
|
A:G29
|
4.8
|
116.0
|
1.0
|
O5'
|
A:A25
|
4.9
|
97.7
|
1.0
|
N4
|
A:C40
|
4.9
|
145.7
|
1.0
|
|
Potassium binding site 5 out
of 18 in 8olz
Go back to
Potassium Binding Sites List in 8olz
Potassium binding site 5 out
of 18 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 Potassium with other atoms in the K 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:K435
b:130.7
occ:1.00
|
O4
|
A:U4
|
2.8
|
143.0
|
1.0
|
O2'
|
A:U375
|
2.8
|
128.1
|
1.0
|
O3'
|
A:U375
|
2.8
|
121.8
|
1.0
|
O6
|
A:G107
|
2.8
|
110.2
|
1.0
|
OP2
|
A:A376
|
3.5
|
113.2
|
1.0
|
P
|
A:A376
|
3.6
|
106.1
|
1.0
|
C4
|
A:U4
|
3.7
|
125.6
|
1.0
|
C2'
|
A:U375
|
3.8
|
114.0
|
1.0
|
C3'
|
A:U375
|
3.8
|
119.5
|
1.0
|
C6
|
A:G107
|
3.8
|
113.2
|
1.0
|
N3
|
A:U4
|
3.9
|
117.3
|
1.0
|
N7
|
A:G107
|
4.1
|
116.3
|
1.0
|
OP1
|
A:A376
|
4.3
|
105.3
|
1.0
|
O6
|
A:G3
|
4.3
|
147.9
|
1.0
|
C5
|
A:G107
|
4.4
|
119.7
|
1.0
|
K
|
A:K439
|
4.4
|
121.9
|
1.0
|
C8
|
A:A106
|
4.4
|
99.0
|
1.0
|
C4'
|
A:U375
|
4.4
|
114.4
|
1.0
|
N7
|
A:A106
|
4.5
|
105.0
|
1.0
|
N1
|
A:G5
|
4.8
|
131.7
|
1.0
|
C1'
|
A:U375
|
4.9
|
106.7
|
1.0
|
C5
|
A:U4
|
4.9
|
120.6
|
1.0
|
|
Potassium binding site 6 out
of 18 in 8olz
Go back to
Potassium Binding Sites List in 8olz
Potassium binding site 6 out
of 18 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 Potassium with other atoms in the K 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:K436
b:123.1
occ:1.00
|
O6
|
A:G265
|
3.3
|
124.9
|
1.0
|
O6
|
A:G264
|
3.5
|
141.1
|
1.0
|
N7
|
A:G264
|
3.9
|
138.5
|
1.0
|
C6
|
A:G265
|
4.3
|
115.8
|
1.0
|
C6
|
A:G264
|
4.3
|
133.1
|
1.0
|
N7
|
A:G265
|
4.4
|
150.2
|
1.0
|
C5
|
A:G264
|
4.5
|
137.8
|
1.0
|
N4
|
A:C263
|
4.6
|
132.7
|
1.0
|
C5
|
A:G265
|
4.7
|
121.5
|
1.0
|
C5
|
A:C263
|
4.9
|
126.9
|
1.0
|
C4
|
A:C263
|
4.9
|
121.4
|
1.0
|
|
Potassium binding site 7 out
of 18 in 8olz
Go back to
Potassium Binding Sites List in 8olz
Potassium binding site 7 out
of 18 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 Potassium with other atoms in the K 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:K437
b:139.6
occ:1.00
|
O6
|
A:G275
|
2.8
|
142.5
|
1.0
|
N7
|
A:G275
|
2.8
|
126.1
|
1.0
|
C6
|
A:G275
|
3.4
|
131.7
|
1.0
|
C5
|
A:G275
|
3.4
|
129.8
|
1.0
|
N7
|
A:G274
|
3.6
|
109.2
|
1.0
|
K
|
A:K433
|
3.8
|
136.9
|
1.0
|
C8
|
A:G275
|
4.0
|
134.2
|
1.0
|
OP2
|
A:G274
|
4.1
|
117.9
|
1.0
|
C8
|
A:G274
|
4.4
|
105.2
|
1.0
|
O6
|
A:G274
|
4.6
|
88.4
|
1.0
|
C5
|
A:G274
|
4.6
|
101.3
|
1.0
|
C5
|
A:U273
|
4.7
|
126.4
|
1.0
|
C4
|
A:G275
|
4.7
|
124.7
|
1.0
|
N1
|
A:G275
|
4.7
|
117.7
|
1.0
|
C4
|
A:U273
|
4.7
|
110.5
|
1.0
|
O4
|
A:U273
|
4.8
|
106.2
|
1.0
|
OP2
|
A:A277
|
4.9
|
136.5
|
1.0
|
C6
|
A:G274
|
4.9
|
96.8
|
1.0
|
|
Potassium binding site 8 out
of 18 in 8olz
Go back to
Potassium Binding Sites List in 8olz
Potassium binding site 8 out
of 18 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 Potassium with other atoms in the K 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:K438
b:132.8
occ:1.00
|
O6
|
A:G97
|
2.8
|
108.3
|
1.0
|
O6
|
A:G87
|
2.8
|
133.8
|
1.0
|
O4
|
A:U96
|
2.8
|
123.8
|
1.0
|
N4
|
A:C86
|
3.5
|
121.2
|
1.0
|
C6
|
A:G97
|
3.6
|
102.9
|
1.0
|
N6
|
A:A95
|
3.8
|
108.7
|
1.0
|
C4
|
A:U96
|
3.8
|
106.2
|
1.0
|
C6
|
A:G87
|
3.9
|
117.3
|
1.0
|
N3
|
A:U96
|
4.0
|
102.3
|
1.0
|
N1
|
A:G97
|
4.1
|
95.8
|
1.0
|
C4
|
A:C86
|
4.4
|
114.0
|
1.0
|
N7
|
A:G87
|
4.4
|
133.8
|
1.0
|
O4
|
A:U88
|
4.5
|
132.5
|
1.0
|
C5
|
A:G87
|
4.5
|
117.5
|
1.0
|
C5
|
A:G97
|
4.6
|
102.3
|
1.0
|
C6
|
A:A95
|
4.9
|
104.5
|
1.0
|
N3
|
A:C86
|
4.9
|
109.1
|
1.0
|
O3S
|
A:EPE451
|
4.9
|
76.1
|
0.5
|
N1
|
A:G87
|
5.0
|
107.3
|
1.0
|
|
Potassium binding site 9 out
of 18 in 8olz
Go back to
Potassium Binding Sites List in 8olz
Potassium binding site 9 out
of 18 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 Potassium with other atoms in the K 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:K439
b:121.9
occ:1.00
|
O4
|
A:U4
|
2.8
|
143.0
|
1.0
|
OP2
|
A:A376
|
2.8
|
113.2
|
1.0
|
OP2
|
A:G3
|
2.8
|
177.7
|
1.0
|
O6
|
A:G5
|
2.8
|
125.3
|
1.0
|
C4
|
A:U4
|
3.7
|
125.6
|
1.0
|
C6
|
A:G5
|
3.9
|
125.6
|
1.0
|
C5
|
A:U4
|
4.0
|
120.6
|
1.0
|
O4'
|
A:A376
|
4.0
|
134.9
|
1.0
|
P
|
A:A376
|
4.1
|
106.1
|
1.0
|
N1
|
A:G5
|
4.2
|
131.7
|
1.0
|
C5'
|
A:A376
|
4.2
|
119.0
|
1.0
|
P
|
A:G3
|
4.2
|
171.7
|
1.0
|
K
|
A:K435
|
4.4
|
130.7
|
1.0
|
O3'
|
A:U375
|
4.5
|
121.8
|
1.0
|
O18
|
A:VTE453
|
4.5
|
201.7
|
1.0
|
C4'
|
A:A376
|
4.6
|
124.3
|
1.0
|
O5'
|
A:A376
|
4.7
|
107.7
|
1.0
|
N3
|
A:A376
|
4.7
|
140.3
|
1.0
|
MG
|
A:MG405
|
4.7
|
94.6
|
1.0
|
OP1
|
A:G3
|
4.8
|
134.0
|
1.0
|
N3
|
A:U4
|
4.9
|
117.3
|
1.0
|
|
Potassium binding site 10 out
of 18 in 8olz
Go back to
Potassium Binding Sites List in 8olz
Potassium binding site 10 out
of 18 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 Potassium with other atoms in the K 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:K440
b:147.3
occ:1.00
|
O2'
|
A:G32
|
3.3
|
112.4
|
1.0
|
O6
|
A:G34
|
3.5
|
113.9
|
1.0
|
O3'
|
A:G32
|
3.9
|
134.5
|
1.0
|
N7
|
A:A33
|
4.3
|
107.9
|
1.0
|
C2'
|
A:G32
|
4.4
|
131.8
|
1.0
|
C4'
|
A:G32
|
4.5
|
128.8
|
1.0
|
C3'
|
A:G32
|
4.5
|
133.3
|
1.0
|
C6
|
A:G34
|
4.6
|
108.0
|
1.0
|
C8
|
A:A33
|
4.8
|
99.4
|
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: Tue Aug 13 00:14:24 2024
|