Potassium 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:
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+ and ARN25850
(pdb code 8olv). 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+ and ARN25850, PDB code: 8olv:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Potassium binding site 1 out
of 18 in 8olv
Go back to
Potassium Binding Sites List in 8olv
Potassium binding site 1 out
of 18 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 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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K422
b:142.2
occ:1.00
|
O6
|
A:G266
|
2.7
|
125.5
|
1.0
|
N7
|
A:G266
|
2.8
|
117.6
|
1.0
|
C6
|
A:G266
|
3.2
|
106.6
|
1.0
|
C5
|
A:G266
|
3.2
|
108.8
|
1.0
|
C8
|
A:G266
|
3.9
|
113.9
|
1.0
|
N7
|
A:G267
|
4.3
|
94.2
|
1.0
|
C4
|
A:G266
|
4.5
|
101.3
|
1.0
|
N1
|
A:G266
|
4.5
|
94.5
|
1.0
|
N9
|
A:G266
|
4.8
|
106.8
|
1.0
|
OP2
|
A:G266
|
4.9
|
100.6
|
1.0
|
C8
|
A:G267
|
5.0
|
103.0
|
1.0
|
O6
|
A:G265
|
5.0
|
115.0
|
1.0
|
|
Potassium binding site 2 out
of 18 in 8olv
Go back to
Potassium Binding Sites List in 8olv
Potassium binding site 2 out
of 18 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 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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K423
b:136.0
occ:1.00
|
O6
|
A:G15
|
2.7
|
120.2
|
1.0
|
O4
|
A:U256
|
3.4
|
115.1
|
1.0
|
O6
|
A:G14
|
3.7
|
131.5
|
1.0
|
C6
|
A:G15
|
3.8
|
110.5
|
1.0
|
O4
|
A:U255
|
4.1
|
131.6
|
1.0
|
N7
|
A:G15
|
4.3
|
102.1
|
1.0
|
C4
|
A:U256
|
4.4
|
114.3
|
1.0
|
C5
|
A:G15
|
4.5
|
104.8
|
1.0
|
C6
|
A:G14
|
4.5
|
105.0
|
1.0
|
N3
|
A:U256
|
4.5
|
118.0
|
1.0
|
O6
|
A:G16
|
4.6
|
117.1
|
1.0
|
N1
|
A:G15
|
5.0
|
103.8
|
1.0
|
|
Potassium binding site 3 out
of 18 in 8olv
Go back to
Potassium Binding Sites List in 8olv
Potassium binding site 3 out
of 18 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 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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K424
b:117.3
occ:1.00
|
OP2
|
A:G269
|
2.6
|
118.2
|
1.0
|
N7
|
A:G270
|
3.6
|
103.7
|
1.0
|
O6
|
A:G270
|
3.7
|
97.3
|
1.0
|
P
|
A:G269
|
3.9
|
105.2
|
1.0
|
O5'
|
A:G269
|
4.0
|
90.7
|
1.0
|
O5'
|
A:A268
|
4.2
|
112.1
|
1.0
|
N7
|
A:G269
|
4.3
|
104.5
|
1.0
|
C8
|
A:G269
|
4.4
|
98.9
|
1.0
|
C5
|
A:G270
|
4.4
|
97.6
|
1.0
|
C6
|
A:G270
|
4.4
|
95.8
|
1.0
|
OP2
|
A:A268
|
4.5
|
95.0
|
1.0
|
C8
|
A:G270
|
4.7
|
112.0
|
1.0
|
OP2
|
A:G270
|
4.8
|
119.8
|
1.0
|
O4
|
A:U271
|
4.8
|
83.5
|
1.0
|
OP1
|
A:G269
|
4.8
|
121.2
|
1.0
|
P
|
A:A268
|
5.0
|
101.8
|
1.0
|
O3'
|
A:A268
|
5.0
|
102.0
|
1.0
|
C3'
|
A:A268
|
5.0
|
110.9
|
1.0
|
|
Potassium binding site 4 out
of 18 in 8olv
Go back to
Potassium Binding Sites List in 8olv
Potassium binding site 4 out
of 18 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 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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K425
b:143.3
occ:1.00
|
O6
|
A:G275
|
2.7
|
126.8
|
1.0
|
O4
|
A:U273
|
3.6
|
96.7
|
1.0
|
O6
|
A:G274
|
3.6
|
91.6
|
1.0
|
C6
|
A:G275
|
3.7
|
95.3
|
1.0
|
C4
|
A:U273
|
4.0
|
86.3
|
1.0
|
C5
|
A:U273
|
4.1
|
92.2
|
1.0
|
K
|
A:K427
|
4.1
|
158.8
|
1.0
|
N1
|
A:G275
|
4.3
|
92.0
|
1.0
|
N7
|
A:G274
|
4.4
|
92.7
|
1.0
|
C6
|
A:G274
|
4.6
|
81.5
|
1.0
|
C5
|
A:G275
|
4.8
|
94.5
|
1.0
|
C5
|
A:G274
|
4.9
|
74.5
|
1.0
|
|
Potassium binding site 5 out
of 18 in 8olv
Go back to
Potassium Binding Sites List in 8olv
Potassium binding site 5 out
of 18 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 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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K426
b:145.7
occ:1.00
|
N7
|
A:G10
|
3.8
|
87.5
|
1.0
|
O6
|
A:G10
|
4.1
|
96.2
|
1.0
|
N7
|
A:G9
|
4.2
|
94.8
|
1.0
|
O6
|
A:G9
|
4.4
|
112.6
|
1.0
|
OP2
|
A:A260
|
4.6
|
95.5
|
1.0
|
N4
|
A:C11
|
4.7
|
90.0
|
1.0
|
C5
|
A:G9
|
4.7
|
94.1
|
1.0
|
C5
|
A:G10
|
4.7
|
87.1
|
1.0
|
C6
|
A:G9
|
4.8
|
104.0
|
1.0
|
C6
|
A:G10
|
4.8
|
89.6
|
1.0
|
C8
|
A:G10
|
4.9
|
100.0
|
1.0
|
C8
|
A:G9
|
5.0
|
101.9
|
1.0
|
|
Potassium binding site 6 out
of 18 in 8olv
Go back to
Potassium Binding Sites List in 8olv
Potassium binding site 6 out
of 18 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 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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K427
b:158.8
occ:1.00
|
O6
|
A:G275
|
2.7
|
126.8
|
1.0
|
C6
|
A:G275
|
3.5
|
95.3
|
1.0
|
N7
|
A:G275
|
3.8
|
102.1
|
1.0
|
C5
|
A:G275
|
3.9
|
94.5
|
1.0
|
K
|
A:K425
|
4.1
|
143.3
|
1.0
|
OP1
|
A:A277
|
4.1
|
101.9
|
1.0
|
OP2
|
A:A277
|
4.3
|
94.7
|
1.0
|
N1
|
A:G275
|
4.6
|
92.0
|
1.0
|
P
|
A:A277
|
4.8
|
112.0
|
1.0
|
C8
|
A:G275
|
5.0
|
87.1
|
1.0
|
|
Potassium binding site 7 out
of 18 in 8olv
Go back to
Potassium Binding Sites List in 8olv
Potassium binding site 7 out
of 18 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 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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K428
b:123.2
occ:1.00
|
O6
|
A:G28
|
2.7
|
99.7
|
1.0
|
N7
|
A:G28
|
2.8
|
96.7
|
1.0
|
C6
|
A:G28
|
3.3
|
97.0
|
1.0
|
C5
|
A:G28
|
3.4
|
86.7
|
1.0
|
OP2
|
A:A27
|
4.0
|
110.3
|
1.0
|
N2
|
A:G41
|
4.0
|
98.8
|
1.0
|
C8
|
A:G28
|
4.1
|
100.7
|
1.0
|
OP1
|
A:U26
|
4.2
|
88.9
|
1.0
|
N7
|
A:G29
|
4.6
|
98.3
|
1.0
|
N1
|
A:G28
|
4.7
|
100.7
|
1.0
|
C2
|
A:G41
|
4.7
|
91.1
|
1.0
|
C4
|
A:G28
|
4.7
|
81.4
|
1.0
|
N4
|
A:C40
|
4.8
|
84.4
|
1.0
|
N1
|
A:G41
|
4.8
|
80.6
|
1.0
|
O6
|
A:G29
|
4.9
|
90.9
|
1.0
|
C3'
|
A:A25
|
5.0
|
87.3
|
1.0
|
O5'
|
A:A25
|
5.0
|
102.6
|
1.0
|
|
Potassium binding site 8 out
of 18 in 8olv
Go back to
Potassium Binding Sites List in 8olv
Potassium binding site 8 out
of 18 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 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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K429
b:115.4
occ:1.00
|
O6
|
A:G264
|
3.4
|
106.9
|
1.0
|
N7
|
A:G264
|
4.0
|
115.5
|
1.0
|
O6
|
A:G265
|
4.0
|
115.0
|
1.0
|
C6
|
A:G264
|
4.3
|
108.9
|
1.0
|
C5
|
A:G264
|
4.5
|
99.8
|
1.0
|
N4
|
A:C263
|
4.6
|
89.5
|
1.0
|
C5
|
A:C263
|
4.9
|
93.0
|
1.0
|
C4
|
A:C263
|
5.0
|
83.2
|
1.0
|
|
Potassium binding site 9 out
of 18 in 8olv
Go back to
Potassium Binding Sites List in 8olv
Potassium binding site 9 out
of 18 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 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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K430
b:113.8
occ:1.00
|
O4
|
A:U96
|
2.7
|
95.5
|
1.0
|
O6
|
A:G87
|
2.7
|
91.9
|
1.0
|
O6
|
A:G97
|
2.7
|
90.3
|
1.0
|
N4
|
A:C86
|
3.3
|
93.1
|
1.0
|
N6
|
A:A95
|
3.4
|
71.9
|
1.0
|
C6
|
A:G97
|
3.6
|
72.8
|
1.0
|
C4
|
A:U96
|
3.6
|
82.2
|
1.0
|
C6
|
A:G87
|
3.7
|
71.8
|
1.0
|
N3
|
A:U96
|
3.8
|
76.6
|
1.0
|
O4
|
A:U88
|
4.0
|
111.6
|
1.0
|
N7
|
A:G87
|
4.0
|
89.0
|
1.0
|
C4
|
A:C86
|
4.1
|
86.8
|
1.0
|
N1
|
A:G97
|
4.2
|
70.2
|
1.0
|
C5
|
A:G87
|
4.2
|
74.3
|
1.0
|
C6
|
A:A95
|
4.4
|
67.8
|
1.0
|
C5
|
A:G97
|
4.6
|
69.1
|
1.0
|
N3
|
A:C86
|
4.6
|
74.1
|
1.0
|
C4
|
A:U88
|
4.7
|
82.5
|
1.0
|
N1
|
A:G87
|
4.9
|
66.6
|
1.0
|
N1
|
A:A95
|
5.0
|
68.3
|
1.0
|
C5
|
A:U96
|
5.0
|
90.0
|
1.0
|
|
Potassium binding site 10 out
of 18 in 8olv
Go back to
Potassium Binding Sites List in 8olv
Potassium binding site 10 out
of 18 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 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+ and ARN25850 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K431
b:123.1
occ:1.00
|
OP2
|
A:G3
|
2.6
|
106.6
|
1.0
|
OP2
|
A:A376
|
2.7
|
118.2
|
1.0
|
O4
|
A:U4
|
2.7
|
120.3
|
1.0
|
O6
|
A:G5
|
2.7
|
94.3
|
1.0
|
C4
|
A:U4
|
3.5
|
99.1
|
1.0
|
C6
|
A:G5
|
3.6
|
80.2
|
1.0
|
O4'
|
A:A376
|
3.9
|
116.3
|
1.0
|
C5
|
A:U4
|
3.9
|
98.1
|
1.0
|
N1
|
A:G5
|
3.9
|
69.8
|
1.0
|
C5'
|
A:A376
|
4.0
|
98.5
|
1.0
|
P
|
A:G3
|
4.0
|
117.3
|
1.0
|
P
|
A:A376
|
4.0
|
99.8
|
1.0
|
C4'
|
A:A376
|
4.4
|
101.5
|
1.0
|
OP1
|
A:G3
|
4.4
|
127.4
|
1.0
|
O5'
|
A:A376
|
4.5
|
94.5
|
1.0
|
O3'
|
A:U375
|
4.6
|
110.8
|
1.0
|
N3
|
A:U4
|
4.7
|
98.8
|
1.0
|
O3'
|
A:U2
|
4.9
|
134.1
|
1.0
|
C5
|
A:G5
|
5.0
|
82.7
|
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 00:14:02 2024
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