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Magnesium in PDB 5mq0: Structure of A Spliceosome Remodeled For Exon Ligation

Enzymatic activity of Structure of A Spliceosome Remodeled For Exon Ligation

All present enzymatic activity of Structure of A Spliceosome Remodeled For Exon Ligation:
3.6.4.13;

Other elements in 5mq0:

The structure of Structure of A Spliceosome Remodeled For Exon Ligation also contains other interesting chemical elements:

Potassium (K) 2 atoms
Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Spliceosome Remodeled For Exon Ligation (pdb code 5mq0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of A Spliceosome Remodeled For Exon Ligation, PDB code: 5mq0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5mq0

Go back to Magnesium Binding Sites List in 5mq0
Magnesium binding site 1 out of 3 in the Structure of A Spliceosome Remodeled For Exon Ligation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Spliceosome Remodeled For Exon Ligation within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg1001

b:42.6
occ:1.00
OP1 6:G78 2.1 53.0 1.0
OP2 6:U80 2.1 48.5 1.0
P 6:U80 3.1 52.8 1.0
O3' 6:A79 3.3 52.8 1.0
P 6:G78 3.3 57.6 1.0
C3' 6:A79 3.3 50.9 1.0
C5' 6:U80 3.5 53.0 1.0
O5' 6:G78 3.7 54.5 1.0
O5' 6:U80 3.7 53.2 1.0
O3' E:G-1 3.8 0.9 1.0
C4' 6:A79 3.9 51.3 1.0
OP2 6:G78 4.0 55.1 1.0
C5' 6:A79 4.1 52.0 1.0
OP1 6:G60 4.1 78.4 1.0
C5' 6:G78 4.3 53.1 1.0
OP1 6:U80 4.5 51.2 1.0
O3' 6:G77 4.5 55.1 1.0
MG 6:MG1002 4.6 54.4 1.0
C4' 6:U80 4.7 54.6 1.0
C2' 6:A79 4.8 49.2 1.0
P 6:G60 4.9 77.4 1.0

Magnesium binding site 2 out of 3 in 5mq0

Go back to Magnesium Binding Sites List in 5mq0
Magnesium binding site 2 out of 3 in the Structure of A Spliceosome Remodeled For Exon Ligation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Spliceosome Remodeled For Exon Ligation within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg1002

b:54.4
occ:1.00
OP1 6:U80 2.1 51.2 1.0
OP2 6:G60 2.2 78.9 1.0
OP2 6:U80 2.8 48.5 1.0
P 6:U80 2.8 52.8 1.0
P 6:G60 3.3 77.4 1.0
OP2 6:A59 3.4 0.6 1.0
O5' 6:G60 3.6 70.6 1.0
O3' 6:A79 3.7 52.8 1.0
OP1 6:G60 4.1 78.4 1.0
O5' 6:U80 4.1 53.2 1.0
O5' 6:A59 4.3 0.1 1.0
P 6:A59 4.3 0.3 1.0
C5' 6:A59 4.5 98.7 1.0
O3' 6:A59 4.6 77.3 1.0
MG 6:MG1001 4.6 42.6 1.0
C5' 6:G60 4.7 62.5 1.0
C2 6:A51 4.8 0.0 1.0
OP1 6:A59 4.8 0.9 1.0
C3' 6:A59 5.0 80.7 1.0
O6 6:G52 5.0 65.2 1.0

Magnesium binding site 3 out of 3 in 5mq0

Go back to Magnesium Binding Sites List in 5mq0
Magnesium binding site 3 out of 3 in the Structure of A Spliceosome Remodeled For Exon Ligation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Spliceosome Remodeled For Exon Ligation within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg1003

b:23.2
occ:1.00
OP1 6:C61 2.2 53.5 1.0
OP1 6:G77 2.3 55.0 1.0
O3' 6:G60 3.1 52.7 1.0
P 6:C61 3.2 53.1 1.0
P 6:G77 3.8 54.7 1.0
C5' 6:C61 4.1 54.0 1.0
O5' 6:C61 4.1 52.7 1.0
OE1 A:GLN748 4.1 87.2 1.0
OP2 6:C61 4.4 55.2 1.0
C3' 6:G60 4.5 53.2 1.0
OP2 6:G77 4.5 56.4 1.0
O3' 6:A76 4.6 52.8 1.0
O5' 6:G77 4.7 54.9 1.0
O2' 6:G60 4.7 53.1 1.0
C5' 6:G77 4.8 56.8 1.0
C4' 6:G60 4.9 57.2 1.0

Reference:

S.M.Fica, C.Oubridge, W.P.Galej, M.E.Wilkinson, X.C.Bai, A.J.Newman, K.Nagai. Structure of A Spliceosome Remodelled For Exon Ligation. Nature V. 542 377 2017.
ISSN: ESSN 1476-4687
PubMed: 28076345
DOI: 10.1038/NATURE21078
Page generated: Mon Dec 14 20:54:13 2020

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