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Magnesium in PDB 6id1: Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution:
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 6id1:

The structure of Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution also contains other interesting chemical elements:

Zinc (Zn) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution (pdb code 6id1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution, PDB code: 6id1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6id1

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Magnesium binding site 1 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:34.4
occ:1.00
 OG1 C:THR143 1.7 39.6 1.0
O1G C:GTP1500 2.0 20.1 1.0
O1B C:GTP1500 2.1 20.1 1.0
CB C:THR143 3.0 39.6 1.0
PG C:GTP1500 3.4 20.1 1.0
PB C:GTP1500 3.4 20.1 1.0
N C:THR143 3.6 39.6 1.0
O3B C:GTP1500 3.8 20.1 1.0
CA C:THR143 3.8 39.6 1.0
CG2 C:THR143 4.0 39.6 1.0
O3A C:GTP1500 4.1 20.1 1.0
O3G C:GTP1500 4.2 20.1 1.0
O1A C:GTP1500 4.2 20.1 1.0
O2A C:GTP1500 4.3 20.1 1.0
PA C:GTP1500 4.4 20.1 1.0
CG2 C:THR168 4.4 47.8 1.0
O2G C:GTP1500 4.5 20.1 1.0
CB C:THR168 4.6 47.8 1.0
C C:LYS142 4.6 39.1 1.0
CA C:GLY180 4.6 43.6 1.0
N C:GLY180 4.7 43.6 1.0
O2B C:GTP1500 4.7 20.1 1.0
CB C:LYS142 4.7 39.1 1.0
OD1 C:ASP204 4.8 41.3 1.0
O C:THR168 4.8 47.8 1.0
CE C:LYS142 4.9 39.1 1.0
O C:THR205 5.0 37.7 1.0

Magnesium binding site 2 out of 7 in 6id1

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Magnesium binding site 2 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg200

b:12.7
occ:1.00
 OP1 F:G72 2.2 20.1 1.0
OP2 F:U74 2.4 20.1 1.0
P F:G72 3.7 20.1 1.0
OP1 F:G54 3.7 20.1 1.0
P F:U74 3.7 20.1 1.0
OP1 F:U74 4.2 20.1 1.0
O3' F:G71 4.3 20.1 1.0
O5' F:G54 4.3 20.1 1.0
O5' F:U74 4.4 20.1 1.0
O5' F:G72 4.5 20.1 1.0
OP2 F:G72 4.5 20.1 1.0
P F:G54 4.6 20.1 1.0
C5' F:U74 4.8 20.1 1.0
CB U:LYS628 4.8 42.0 1.0
C5' F:G72 4.8 20.1 1.0
O3' F:A73 4.9 20.1 1.0
CE U:LYS628 5.0 42.0 1.0

Magnesium binding site 3 out of 7 in 6id1

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Magnesium binding site 3 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:21.4
occ:1.00
 OP1 F:U74 2.3 20.1 1.0
OP2 F:A53 2.8 20.1 1.0
OP2 F:G54 2.9 20.1 1.0
P F:U74 3.5 20.1 1.0
O5' F:U74 3.7 20.1 1.0
P F:A53 4.0 20.1 1.0
O3' F:A73 4.1 20.1 1.0
O5' F:A53 4.3 20.1 1.0
P F:G54 4.3 20.1 1.0
O6 F:G46 4.4 2.3 1.0
C5' F:A53 4.6 20.1 1.0
OP1 F:A53 4.7 20.1 1.0
N7 F:G46 4.7 2.3 1.0
OP2 F:U74 4.8 20.1 1.0
OP1 F:G54 4.8 20.1 1.0
O4' F:U74 4.9 20.1 1.0

Magnesium binding site 4 out of 7 in 6id1

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Magnesium binding site 4 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:6.1
occ:1.00
 OP1 F:G75 2.2 20.1 1.0
P F:G75 3.6 20.1 1.0
OP2 F:G75 4.1 20.1 1.0
N7 F:G75 4.2 20.1 1.0
O4 F:U57 4.2 20.1 1.0
O5' F:G75 4.4 20.1 1.0
C8 F:G75 4.5 20.1 1.0
O3' F:U74 4.6 20.1 1.0
C5 F:U57 5.0 20.1 1.0
C2' F:U74 5.0 20.1 1.0
C4 F:U57 5.0 20.1 1.0

Magnesium binding site 5 out of 7 in 6id1

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Magnesium binding site 5 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg203

b:20.1
occ:1.00
 OP2 F:G75 2.5 20.1 1.0
OP2 F:G71 3.6 20.1 1.0
P F:G75 3.7 20.1 1.0
O3' F:U74 4.0 20.1 1.0
OP2 F:G72 4.0 20.1 1.0
OP2 F:C55 4.3 20.1 1.0
OP1 F:G75 4.4 20.1 1.0
C5' F:G71 4.4 20.1 1.0
OP2 F:A56 4.6 20.1 1.0
OP1 F:C55 4.6 20.1 1.0
P F:G71 4.7 20.1 1.0
C8 F:G71 4.7 20.1 1.0
N7 F:G71 4.8 20.1 1.0
OP1 F:A56 4.8 20.1 1.0
O5' F:G75 4.9 20.1 1.0
P F:C55 4.9 20.1 1.0
N7 F:G72 5.0 20.1 1.0

Magnesium binding site 6 out of 7 in 6id1

Go back to Magnesium Binding Sites List in 6id1
Magnesium binding site 6 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


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 A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg204

b:10.3
occ:1.00
 OP1 F:G71 2.1 20.1 1.0
OP1 F:C55 2.3 20.1 1.0
P F:G71 3.5 20.1 1.0
P F:C55 3.5 20.1 1.0
O3' F:G54 3.6 20.1 1.0
OE1 A:GLN675 3.6 20.1 1.0
O5' F:G71 4.0 20.1 1.0
O3' F:A70 4.4 20.1 1.0
C5' F:C55 4.4 20.1 1.0
O5' F:C55 4.5 20.1 1.0
OP2 F:G71 4.5 20.1 1.0
C5' F:G71 4.6 20.1 1.0
OP2 F:C55 4.6 20.1 1.0
CD A:GLN675 4.7 20.1 1.0
C3' F:G54 4.9 20.1 1.0

Magnesium binding site 7 out of 7 in 6id1

Go back to Magnesium Binding Sites List in 6id1
Magnesium binding site 7 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of A Human Intron Lariat Spliceosome After PRP43 Loaded (ILS2 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg205

b:17.8
occ:1.00
 OP1 F:A48 3.2 14.9 1.0
OP2 F:A47 3.6 20.1 1.0
OP2 F:A50 4.0 72.9 1.0
OP1 F:A47 4.0 20.1 1.0
P F:A47 4.0 20.1 1.0
O4 F:U52 4.1 36.9 1.0
O5' F:A47 4.1 20.1 1.0
O5' F:A48 4.1 14.9 1.0
P F:A48 4.3 14.9 1.0
O4 F:U51 4.8 20.1 1.0
C5 F:U51 4.9 20.1 1.0
C4 F:U52 4.9 36.9 1.0
C5' F:A48 5.0 14.9 1.0
C5 F:U52 5.0 36.9 1.0

Reference:

X.Zhang, X.Zhan, C.Yan, W.Zhang, D.Liu, J.Lei, Y.Shi. Structures of the Human Spliceosomes Before and After Release of the Ligated Exon. Cell Res. V. 29 274 2019.
ISSN: ISSN 1748-7838
PubMed: 30728453
DOI: 10.1038/S41422-019-0143-X
Page generated: Tue Oct 1 03:19:10 2024

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