Atomistry » Magnesium » PDB 5ylv-5yvt » 5ylz
Atomistry »
  Magnesium »
    PDB 5ylv-5yvt »
      5ylz »

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

Go back to Magnesium Binding Sites List in 5ylz
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

Go back to Magnesium Binding Sites List in 5ylz
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

Go back to Magnesium Binding Sites List in 5ylz
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

Go back to Magnesium Binding Sites List in 5ylz
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

Go back to Magnesium Binding Sites List in 5ylz
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

Go back to Magnesium Binding Sites List in 5ylz
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

Last articles

Mg in 5SH2
Mg in 5SH1
Mg in 5SH0
Mg in 5SGZ
Mg in 5SGY
Mg in 5SGX
Mg in 5SGW
Mg in 5SGV
Mg in 5SGU
Mg in 5SGT
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy