Magnesium in PDB 5y88: Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom
Enzymatic activity of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom
All present enzymatic activity of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom:
2.3.2.27;
3.6.4.13;
Other elements in 5y88:
The structure of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom
(pdb code 5y88). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom, PDB code: 5y88:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 5y88
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Magnesium Binding Sites List in 5y88
Magnesium binding site 1 out
of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1501
b:30.0
occ:1.00
|
O2B
|
C:GTP1500
|
1.7
|
44.9
|
1.0
|
OG1
|
C:THR147
|
2.0
|
52.6
|
1.0
|
O1G
|
C:GTP1500
|
2.1
|
51.3
|
1.0
|
OG
|
C:SER190
|
2.1
|
67.1
|
1.0
|
O2G
|
C:GTP1500
|
2.7
|
53.0
|
1.0
|
PG
|
C:GTP1500
|
2.8
|
51.4
|
1.0
|
CB
|
C:SER190
|
2.9
|
70.5
|
1.0
|
PB
|
C:GTP1500
|
3.1
|
48.1
|
1.0
|
CB
|
C:THR147
|
3.2
|
60.3
|
1.0
|
O3B
|
C:GTP1500
|
3.5
|
49.1
|
1.0
|
O1B
|
C:GTP1500
|
3.8
|
47.3
|
1.0
|
N
|
C:THR147
|
3.9
|
52.1
|
1.0
|
CA
|
C:THR147
|
4.1
|
55.3
|
1.0
|
O3G
|
C:GTP1500
|
4.1
|
48.2
|
1.0
|
O3A
|
C:GTP1500
|
4.2
|
47.3
|
1.0
|
CG2
|
C:THR147
|
4.2
|
70.1
|
1.0
|
CA
|
C:SER190
|
4.3
|
61.3
|
1.0
|
OD2
|
C:ASP214
|
4.4
|
0.4
|
1.0
|
N
|
C:SER190
|
4.5
|
60.2
|
1.0
|
OD1
|
C:ASP214
|
4.6
|
0.5
|
1.0
|
O
|
C:ALA215
|
4.6
|
57.6
|
1.0
|
CB
|
C:LYS146
|
4.7
|
52.3
|
1.0
|
CE
|
C:LYS146
|
4.8
|
64.8
|
1.0
|
CG
|
C:ASP214
|
4.9
|
0.1
|
1.0
|
O1A
|
C:GTP1500
|
5.0
|
57.5
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 5y88
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Magnesium Binding Sites List in 5y88
Magnesium binding site 2 out
of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg200
b:16.5
occ:1.00
|
OP1
|
D:G78
|
2.2
|
51.6
|
1.0
|
OP2
|
D:U80
|
2.4
|
48.5
|
1.0
|
P
|
D:G78
|
3.6
|
45.0
|
1.0
|
P
|
D:U80
|
3.8
|
56.7
|
1.0
|
OP1
|
D:G60
|
4.1
|
59.7
|
1.0
|
O3'
|
D:G77
|
4.2
|
43.4
|
1.0
|
O5'
|
D:U80
|
4.4
|
52.2
|
1.0
|
OP2
|
D:G78
|
4.5
|
44.7
|
1.0
|
OP1
|
D:U80
|
4.6
|
56.0
|
1.0
|
O5'
|
D:G78
|
4.6
|
40.8
|
1.0
|
C5'
|
D:U80
|
4.8
|
51.6
|
1.0
|
O5'
|
D:G60
|
4.9
|
50.8
|
1.0
|
C5'
|
D:G78
|
4.9
|
43.0
|
1.0
|
C5'
|
D:A79
|
4.9
|
48.2
|
1.0
|
O3'
|
D:A79
|
4.9
|
50.5
|
1.0
|
P
|
D:G60
|
4.9
|
55.7
|
1.0
|
C3'
|
D:A79
|
4.9
|
46.8
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 5y88
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Magnesium Binding Sites List in 5y88
Magnesium binding site 3 out
of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg201
b:52.3
occ:1.00
|
OP1
|
D:U80
|
2.1
|
56.0
|
1.0
|
P
|
D:U80
|
3.3
|
56.7
|
1.0
|
OP2
|
D:A59
|
3.5
|
0.3
|
1.0
|
O3'
|
D:A79
|
3.7
|
50.5
|
1.0
|
O5'
|
D:U80
|
3.7
|
52.2
|
1.0
|
O6
|
D:G52
|
4.0
|
83.3
|
1.0
|
OP2
|
D:G60
|
4.1
|
58.5
|
1.0
|
N7
|
D:G52
|
4.4
|
78.9
|
1.0
|
OP2
|
D:U80
|
4.7
|
48.5
|
1.0
|
C6
|
D:G52
|
4.8
|
74.0
|
1.0
|
P
|
D:A59
|
4.9
|
0.5
|
1.0
|
C5'
|
D:U80
|
5.0
|
51.6
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 5y88
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Magnesium Binding Sites List in 5y88
Magnesium binding site 4 out
of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg202
b:21.3
occ:1.00
|
OP2
|
D:G81
|
2.0
|
46.3
|
1.0
|
P
|
D:G81
|
3.5
|
43.5
|
1.0
|
OP2
|
D:G77
|
4.0
|
38.8
|
1.0
|
O5'
|
D:G81
|
4.2
|
39.8
|
1.0
|
O3'
|
D:U80
|
4.2
|
46.8
|
1.0
|
OP2
|
D:G78
|
4.3
|
44.7
|
1.0
|
N7
|
D:G78
|
4.4
|
44.2
|
1.0
|
N7
|
D:G77
|
4.5
|
35.9
|
1.0
|
OP1
|
D:G81
|
4.5
|
47.8
|
1.0
|
OP2
|
D:A62
|
4.5
|
33.4
|
1.0
|
C8
|
D:G77
|
4.6
|
36.7
|
1.0
|
C5'
|
D:G77
|
5.0
|
49.9
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 5y88
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Magnesium Binding Sites List in 5y88
Magnesium binding site 5 out
of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg203
b:13.6
occ:1.00
|
OP1
|
D:G81
|
2.3
|
47.8
|
1.0
|
P
|
D:G81
|
3.5
|
43.5
|
1.0
|
O5'
|
D:G81
|
3.8
|
39.8
|
1.0
|
N7
|
D:G81
|
4.1
|
46.8
|
1.0
|
OP2
|
D:G81
|
4.2
|
46.3
|
1.0
|
C8
|
D:G81
|
4.2
|
47.2
|
1.0
|
OP2
|
D:A82
|
4.4
|
51.3
|
1.0
|
N7
|
D:A82
|
4.5
|
48.2
|
1.0
|
O3'
|
D:U80
|
4.8
|
46.8
|
1.0
|
C2'
|
D:U80
|
4.9
|
49.5
|
1.0
|
O6
|
D:G63
|
4.9
|
55.2
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 5y88
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Magnesium Binding Sites List in 5y88
Magnesium binding site 6 out
of 6 in the Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Cryo-Em Structure of the Intron-Lariat Spliceosome Ready For Disassembly From S.Cerevisiae at 3.5 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg204
b:32.7
occ:1.00
|
OP1
|
D:G77
|
2.0
|
44.3
|
1.0
|
OP1
|
D:C61
|
2.3
|
32.6
|
1.0
|
P
|
D:G77
|
3.5
|
43.5
|
1.0
|
P
|
D:C61
|
3.5
|
33.1
|
1.0
|
O3'
|
D:G60
|
3.8
|
38.6
|
1.0
|
O5'
|
D:C61
|
4.1
|
32.4
|
1.0
|
O5'
|
D:G77
|
4.1
|
46.8
|
1.0
|
O3'
|
D:A76
|
4.3
|
44.0
|
1.0
|
OP2
|
D:G77
|
4.4
|
38.8
|
1.0
|
OE1
|
A:GLN748
|
4.6
|
57.7
|
1.0
|
C5'
|
D:G77
|
4.6
|
49.9
|
1.0
|
OP2
|
D:C61
|
4.8
|
32.4
|
1.0
|
C5'
|
D:C61
|
4.9
|
35.0
|
1.0
|
|
Reference:
R.Wan,
C.Yan,
R.Bai,
J.Lei,
Y.Shi.
Structure of An Intron Lariat Spliceosome From Saccharomyces Cerevisiae Cell(Cambridge,Mass.) V. 171 120 2017.
ISSN: ISSN 0092-8674
PubMed: 28919079
DOI: 10.1016/J.CELL.2017.08.029
Page generated: Mon Sep 30 11:02:35 2024
|