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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:

Zinc (Zn) 6 atoms

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 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 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 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 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 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

Go back to 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: Wed Aug 13 00:45:58 2025

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