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Magnesium in PDB 5ylz: Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom

Enzymatic activity of Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom:
2.3.2.27; 3.6.4.13;

Other elements in 5ylz:

The structure of Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom (pdb code 5ylz). 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom, PDB code: 5ylz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5ylz

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:30.3
occ:1.00
 OG1 C:THR147 2.3 60.5 1.0
O1G C:GTP1500 2.4 50.4 1.0
O2B C:GTP1500 2.5 51.0 1.0
O2G C:GTP1500 2.7 45.7 1.0
OG C:SER190 2.7 62.2 1.0
O1B C:GTP1500 3.0 34.5 1.0
PG C:GTP1500 3.0 47.2 1.0
CB C:THR147 3.1 57.9 1.0
PB C:GTP1500 3.2 40.8 1.0
CB C:SER190 3.6 68.1 1.0
OD2 C:ASP214 3.6 0.8 1.0
O3B C:GTP1500 3.7 43.6 1.0
N C:THR147 3.8 55.4 1.0
CA C:THR147 4.0 54.4 1.0
CG2 C:THR147 4.2 64.0 1.0
O3G C:GTP1500 4.3 46.7 1.0
OD1 C:ASP214 4.4 0.6 1.0
O2A C:GTP1500 4.4 47.4 1.0
CG C:ASP214 4.5 0.9 1.0
O3A C:GTP1500 4.5 46.5 1.0
CB C:LYS146 4.6 57.1 1.0
O C:ALA215 4.8 50.8 1.0
PA C:GTP1500 4.8 48.0 1.0
CA C:SER190 4.8 65.4 1.0
CE C:LYS146 4.9 81.6 1.0
O1A C:GTP1500 4.9 50.0 1.0
N C:SER190 4.9 63.1 1.0
C C:LYS146 4.9 52.8 1.0

Magnesium binding site 2 out of 6 in 5ylz

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg200

b:69.4
occ:1.00
 OP1 E:U351 2.2 0.5 1.0
OP1 D:G78 2.4 29.3 1.0
OP2 D:U80 2.4 64.4 1.0
O3' E:G-1 2.9 0.8 1.0
P E:U351 3.1 0.3 1.0
P D:U80 3.7 70.2 1.0
P D:G78 3.8 31.7 1.0
OP1 D:G60 3.8 60.4 1.0
O3' E:G350 4.0 0.7 1.0
OP2 E:U351 4.0 0.9 1.0
MG D:MG201 4.1 0.1 1.0
C3' E:G-1 4.2 0.1 1.0
OP1 D:U80 4.2 85.2 1.0
O5' D:U80 4.3 66.7 1.0
O5' E:U351 4.3 0.3 1.0
OP2 D:G78 4.4 30.8 1.0
O3' D:G77 4.5 31.4 1.0
P D:G60 4.6 50.7 1.0
O5' D:G60 4.6 46.9 1.0
C4' E:G-1 4.6 0.5 1.0
O2' E:G-1 4.7 0.7 1.0
O5' D:G78 4.8 31.9 1.0
C5' D:U80 4.8 64.6 1.0
OP2 D:G60 4.9 49.7 1.0
O3' D:A79 4.9 62.8 1.0
C5' E:U351 5.0 0.5 1.0

Magnesium binding site 3 out of 6 in 5ylz

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:0.1
occ:1.00
 OP1 D:A59 2.0 91.9 1.0
OP2 D:G60 2.0 49.7 1.0
O2' E:G350 2.2 1.0 1.0
OP1 D:U80 2.3 85.2 1.0
P D:G60 3.0 50.7 1.0
O3' E:G350 3.1 0.7 1.0
OP1 D:G60 3.2 60.4 1.0
C2' E:G350 3.2 0.7 1.0
P D:A59 3.3 90.7 1.0
P D:U80 3.4 70.2 1.0
OP1 E:U351 3.5 0.5 1.0
O5' D:A59 3.7 80.8 1.0
C3' E:G350 3.8 0.0 1.0
OP2 D:U80 3.8 64.4 1.0
C5' D:A59 3.8 71.3 1.0
O5' D:G60 4.0 46.9 1.0
MG D:MG200 4.1 69.4 1.0
O5' D:U80 4.1 66.7 1.0
O3' D:A59 4.2 47.1 1.0
OP2 D:A59 4.2 83.8 1.0
O3' D:C58 4.4 82.0 1.0
C1' E:G350 4.5 0.9 1.0
C3' D:A59 4.7 48.5 1.0
C5' D:G60 4.7 44.1 1.0
O3' D:A79 4.7 62.8 1.0
C4' D:A59 4.8 55.5 1.0
C5' E:U351 4.8 0.5 1.0
C4' E:G350 4.8 0.9 1.0
P E:U351 4.9 0.3 1.0

Magnesium binding site 4 out of 6 in 5ylz

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:12.6
occ:1.00
 OP2 D:G81 1.9 46.7 1.0
P D:G81 3.3 42.9 1.0
O3' D:U80 3.9 47.4 1.0
OP1 D:G81 4.1 44.9 1.0
OP2 D:G77 4.2 26.6 1.0
OP2 D:A62 4.3 32.2 1.0
O5' D:G81 4.4 39.9 1.0
OP2 D:G78 4.4 30.8 1.0
N7 D:G77 4.8 22.3 1.0
N7 D:G78 4.8 28.3 1.0
C8 D:G77 4.8 24.1 1.0
OP2 D:C61 4.9 34.6 1.0
C5' D:G81 5.0 36.4 1.0

Magnesium binding site 5 out of 6 in 5ylz

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:47.3
occ:1.00
 OP1 D:G81 2.4 44.9 1.0
P D:G81 3.7 42.9 1.0
O5' D:G81 3.9 39.9 1.0
OP2 D:A82 4.5 59.0 1.0
N7 D:G81 4.5 37.4 1.0
N7 D:A82 4.5 39.4 1.0
OP2 D:G81 4.6 46.7 1.0
C2' D:U80 4.6 52.3 1.0
C8 D:G81 4.6 36.7 1.0
N7 D:A62 4.7 46.5 1.0
O6 D:G63 4.8 0.4 1.0
O3' D:U80 4.8 47.4 1.0
C3' D:U80 4.9 50.9 1.0

Magnesium binding site 6 out of 6 in 5ylz

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Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 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 Post-Catalytic Spliceosome From Saccharomyces Cerevisiae at 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg204

b:31.4
occ:1.00
 OP1 D:G77 2.1 30.3 1.0
OP1 D:C61 2.3 35.2 1.0
P D:C61 3.5 35.0 1.0
P D:G77 3.5 30.7 1.0
O3' D:G60 3.8 38.3 1.0
O5' D:G77 4.0 31.7 1.0
O5' D:C61 4.1 31.8 1.0
C5' D:G77 4.3 31.5 1.0
OE1 A:GLN748 4.5 58.2 1.0
OP2 D:G77 4.5 26.6 1.0
O3' D:A76 4.5 31.2 1.0
OP2 D:C61 4.8 34.6 1.0
O2' E:G-1 5.0 0.7 1.0
C5' D:C61 5.0 31.8 1.0

Reference:

R.Bai, C.Yan, R.Wan, J.Lei, Y.Shi. Structure of the Post-Catalytic Spliceosome From Saccharomyces Cerevisiae Cell V. 171 1589 2017.
ISSN: ISSN 1097-4172
PubMed: 29153833
DOI: 10.1016/J.CELL.2017.10.038
Page generated: Mon Sep 30 11:25:05 2024

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