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Magnesium in PDB 6id0: Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution:
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 6id0:

The structure of Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution (pdb code 6id0). 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution, PDB code: 6id0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6id0

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Magnesium binding site 1 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:36.4
occ:1.00
 O1G C:GTP1500 2.0 44.0 1.0
O1B C:GTP1500 2.7 44.0 1.0
CB C:THR143 2.8 42.6 1.0
CG2 C:THR143 3.0 42.6 1.0
PG C:GTP1500 3.1 44.0 1.0
O3G C:GTP1500 3.3 44.0 1.0
OG1 C:THR143 3.7 42.6 1.0
PB C:GTP1500 3.7 44.0 1.0
O3B C:GTP1500 3.9 44.0 1.0
CA C:THR143 3.9 42.6 1.0
N C:THR143 4.0 42.6 1.0
O3A C:GTP1500 4.1 44.0 1.0
CA C:GLY180 4.3 46.7 1.0
O2G C:GTP1500 4.3 44.0 1.0
N C:GLY180 4.4 46.7 1.0
O1A C:GTP1500 4.6 44.0 1.0
CG2 C:THR168 4.7 52.1 1.0
CB C:THR168 4.7 52.1 1.0
PA C:GTP1500 4.7 44.0 1.0
O2A C:GTP1500 4.8 44.0 1.0
O C:THR205 4.8 46.9 1.0
OD1 C:ASP204 4.9 48.0 1.0
OD2 C:ASP204 5.0 48.0 1.0

Magnesium binding site 2 out of 7 in 6id0

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Magnesium binding site 2 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg200

b:16.0
occ:1.00
 OP2 F:U74 2.1 29.0 1.0
OP1 F:G72 2.4 29.0 1.0
P F:U74 3.4 29.0 1.0
OP1 F:G54 3.7 29.0 1.0
O5' F:U74 3.7 29.0 1.0
P F:G72 3.9 29.0 1.0
OP1 F:U74 4.2 29.0 1.0
CB U:LYS628 4.4 55.8 1.0
CG U:LYS628 4.4 55.8 1.0
O5' F:G54 4.4 29.0 1.0
CE U:LYS628 4.4 55.8 1.0
P F:G54 4.6 29.0 1.0
O3' F:G71 4.6 29.0 1.0
O3' F:A73 4.6 22.3 1.0
O5' F:G72 4.7 29.0 1.0
OP2 F:G72 4.7 29.0 1.0
C3' F:A73 5.0 22.3 1.0

Magnesium binding site 3 out of 7 in 6id0

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Magnesium binding site 3 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:20.9
occ:1.00
 OP1 F:U74 2.1 29.0 1.0
OP2 F:G54 2.7 29.0 1.0
OP2 F:A53 2.9 29.3 1.0
P F:U74 3.5 29.0 1.0
O3' F:A73 4.0 22.3 1.0
O6 F:G46 4.1 14.8 1.0
P F:G54 4.1 29.0 1.0
P F:A53 4.2 29.3 1.0
OP2 F:U74 4.4 29.0 1.0
O5' F:U74 4.5 29.0 1.0
N7 F:G46 4.5 14.8 1.0
O4' F:U74 4.6 29.0 1.0
O5' F:A53 4.6 29.3 1.0
C5' F:G54 4.7 29.0 1.0
C5' F:A53 4.7 29.3 1.0
OP1 F:G54 4.8 29.0 1.0
OP1 F:A53 4.8 29.3 1.0
C5' F:U74 4.8 29.0 1.0
O5' F:G54 4.8 29.0 1.0
C6 F:G46 4.9 14.8 1.0

Magnesium binding site 4 out of 7 in 6id0

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Magnesium binding site 4 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:18.0
occ:1.00
 OP1 F:G75 2.5 29.0 1.0
P F:G75 3.9 29.0 1.0
N7 F:G75 4.0 29.0 1.0
O4 F:U57 4.1 22.9 1.0
C8 F:G75 4.2 29.0 1.0
N7 F:A76 4.3 29.0 1.0
O5' F:G75 4.4 29.0 1.0
OP2 F:A76 4.5 29.0 1.0
OP2 F:G75 4.6 29.0 1.0
N4 F:C77 4.6 29.0 1.0
C5 F:G75 4.9 29.0 1.0
N6 F:A76 5.0 29.0 1.0

Magnesium binding site 5 out of 7 in 6id0

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Magnesium binding site 5 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg203

b:7.8
occ:1.00
 OP2 F:G75 2.8 29.0 1.0
OP2 F:G71 3.6 29.0 1.0
P F:G75 3.9 29.0 1.0
OP2 F:C55 4.1 42.3 1.0
O3' F:U74 4.1 29.0 1.0
OP2 F:A56 4.2 29.0 1.0
OP1 F:A56 4.4 29.0 1.0
OP2 F:G72 4.4 29.0 1.0
OP1 F:G75 4.6 29.0 1.0
P F:G71 4.6 29.0 1.0
C5' F:G71 4.7 29.0 1.0
C8 F:G71 4.7 29.0 1.0
OP1 F:C55 4.7 42.3 1.0
N7 F:G71 4.8 29.0 1.0
P F:A56 4.8 29.0 1.0
OP1 F:G71 4.8 29.0 1.0
P F:C55 4.9 42.3 1.0

Magnesium binding site 6 out of 7 in 6id0

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Magnesium binding site 6 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg204

b:11.9
occ:1.00
 OP1 F:G71 2.1 29.0 1.0
OP1 F:C55 2.1 42.3 1.0
OE1 A:GLN675 3.4 5.9 1.0
P F:C55 3.4 42.3 1.0
P F:G71 3.5 29.0 1.0
O3' F:G54 3.7 29.0 1.0
O5' F:G71 4.0 29.0 1.0
C5' F:C55 4.3 42.3 1.0
O3' F:A70 4.3 29.0 1.0
O5' F:C55 4.4 42.3 1.0
OP2 F:C55 4.5 42.3 1.0
CD A:GLN675 4.5 5.9 1.0
C5' F:G71 4.5 29.0 1.0
OP2 F:G71 4.6 29.0 1.0
NE2 A:GLN675 4.9 5.9 1.0

Magnesium binding site 7 out of 7 in 6id0

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Magnesium binding site 7 out of 7 in the Cryo-Em Structure of A Human Intron Lariat Spliceosome Prior to PRP43 Loaded (ILS1 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 Prior to PRP43 Loaded (ILS1 Complex) at 2.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg205

b:15.7
occ:1.00
 OP1 F:A48 2.2 16.1 1.0
P F:A48 3.6 16.1 1.0
OP2 F:A50 3.6 16.4 1.0
O5' F:A47 3.7 25.8 1.0
OP2 F:A47 4.0 25.8 1.0
OP1 F:A47 4.0 25.8 1.0
P F:A47 4.0 25.8 1.0
O5' F:A48 4.2 16.1 1.0
C5' F:A48 4.3 16.1 1.0
O4 F:U52 4.5 17.7 1.0
O3' F:A47 4.6 25.8 1.0
OP2 F:A48 4.6 16.1 1.0
C3' F:A47 4.7 25.8 1.0
C5' F:A47 4.9 25.8 1.0
P F:A50 5.0 16.4 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 03:19:07 2024

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