Magnesium in PDB 6j6h: Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom

Enzymatic activity of Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom:
2.3.2.27;

Other elements in 6j6h:

The structure of Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 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 Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom (pdb code 6j6h). 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 Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom, PDB code: 6j6h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6j6h

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 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 Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:51.7
occ:1.00
OG1 C:THR147 1.8 48.8 1.0
OG C:SER190 2.0 39.4 1.0
O2B C:GTP1500 2.2 69.6 1.0
O1G C:GTP1500 2.8 69.6 1.0
CB C:SER190 3.0 39.4 1.0
OD2 C:ASP214 3.0 39.2 1.0
O3G C:GTP1500 3.0 69.6 1.0
CB C:THR147 3.1 48.8 1.0
PG C:GTP1500 3.3 69.6 1.0
PB C:GTP1500 3.4 69.6 1.0
O3B C:GTP1500 3.5 69.6 1.0
N C:THR147 3.6 48.8 1.0
OD1 C:ASP179 3.8 51.1 1.0
CA C:THR147 3.9 48.8 1.0
CG C:ASP214 4.0 39.2 1.0
CG2 C:THR147 4.1 48.8 1.0
CA C:SER190 4.2 39.4 1.0
O1B C:GTP1500 4.3 69.6 1.0
OD1 C:ASP214 4.3 39.2 1.0
N C:SER190 4.3 39.4 1.0
O C:ALA215 4.4 35.2 1.0
CB C:LYS146 4.5 69.6 1.0
O3A C:GTP1500 4.6 69.6 1.0
C C:LYS146 4.6 69.6 1.0
CE C:LYS146 4.6 69.6 1.0
O2G C:GTP1500 4.8 69.6 1.0
O2A C:GTP1500 4.8 69.6 1.0
CG C:ASP179 4.8 51.1 1.0
CA C:PRO216 4.9 28.8 1.0
OD2 C:ASP179 4.9 51.1 1.0

Magnesium binding site 2 out of 6 in 6j6h

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 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 Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg200

b:43.0
occ:1.00
OP1 E:G78 2.0 69.6 1.0
OP2 E:U80 2.1 69.6 1.0
P E:G78 3.3 69.6 1.0
P E:U80 3.4 69.6 1.0
OP2 E:G78 4.0 69.6 1.0
O5' E:U80 4.0 69.6 1.0
OP1 E:U80 4.0 69.6 1.0
O3' E:G77 4.1 69.6 1.0
OP1 E:G60 4.1 69.6 1.0
O5' E:G78 4.5 69.6 1.0
O3' E:A79 4.6 69.6 1.0
O5' E:G60 4.7 69.6 1.0
C5' E:U80 4.8 69.6 1.0
C3' E:A79 4.9 69.6 1.0
C5' E:G78 4.9 69.6 1.0
P E:G60 5.0 69.6 1.0

Magnesium binding site 3 out of 6 in 6j6h

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 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 Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:39.7
occ:1.00
OP1 E:U80 2.2 69.6 1.0
P E:U80 3.2 69.6 1.0
O5' E:U80 3.4 69.6 1.0
OP2 E:G60 3.5 69.6 1.0
O3' E:A79 3.6 69.6 1.0
OP2 E:A59 4.4 69.6 1.0
C5' E:U80 4.5 69.6 1.0
N7 E:G52 4.5 69.6 1.0
C2 E:A51 4.5 69.6 1.0
O6 E:G52 4.5 69.6 1.0
OP2 E:U80 4.6 69.6 1.0
P E:G60 4.8 69.6 1.0
O4' E:U80 4.8 69.6 1.0
N3 E:A51 4.9 69.6 1.0
O2' E:A79 5.0 69.6 1.0

Magnesium binding site 4 out of 6 in 6j6h

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 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 Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:69.6
occ:1.00
OP2 E:G81 1.8 69.6 1.0
P E:G81 3.3 69.6 1.0
OP2 E:A62 3.9 69.6 1.0
O3' E:U80 4.1 69.6 1.0
OP2 E:G77 4.2 69.6 1.0
OP1 E:G81 4.2 69.6 1.0
O5' E:G81 4.2 69.6 1.0
N7 E:G78 4.6 69.6 1.0
OP2 E:G78 4.6 69.6 1.0
N7 E:G77 4.7 69.6 1.0
OP2 E:C61 4.7 69.6 1.0
O5' E:G77 4.8 69.6 1.0
C5' E:G81 4.8 69.6 1.0
C8 E:G77 4.9 69.6 1.0
OP1 E:A62 4.9 69.6 1.0
P E:A62 4.9 69.6 1.0

Magnesium binding site 5 out of 6 in 6j6h

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 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 Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg203

b:69.6
occ:1.00
OP1 E:G81 2.3 69.6 1.0
P E:G81 3.5 69.6 1.0
O5' E:G81 3.9 69.6 1.0
OP2 E:G81 4.1 69.6 1.0
O6 E:G63 4.3 69.6 1.0
N7 E:G81 4.4 69.6 1.0
C8 E:G81 4.5 69.6 1.0
N7 E:A82 4.5 69.6 1.0
OP2 E:A82 4.6 69.6 1.0
O3' E:U80 4.8 69.6 1.0
C2' E:U80 4.8 69.6 1.0
N7 E:A62 4.9 69.6 1.0

Magnesium binding site 6 out of 6 in 6j6h

Go back to Magnesium Binding Sites List in 6j6h
Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 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 Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg204

b:69.6
occ:1.00
OP1 E:G77 2.0 69.6 1.0
OP1 E:C61 2.1 69.6 1.0
P E:C61 3.4 69.6 1.0
P E:G77 3.5 69.6 1.0
O3' E:G60 3.6 69.6 1.0
OE1 A:GLN748 4.1 69.6 1.0
C5' E:C61 4.1 69.6 1.0
O5' E:C61 4.2 69.6 1.0
OP2 E:G77 4.3 69.6 1.0
O5' E:G77 4.3 69.6 1.0
O3' E:A76 4.4 69.6 1.0
C5' E:G77 4.4 69.6 1.0
OP2 E:C61 4.5 69.6 1.0

Reference:

R.Wan, R.Bai, C.Yan, J.Lei, Y.Shi. Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Cell V. 177 339 2019.
ISSN: ISSN 1097-4172
PubMed: 30879786
DOI: 10.1016/J.CELL.2019.02.006
Page generated: Mon Dec 14 23:00:00 2020

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