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Magnesium in PDB 6j6g: Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 Angstrom

Enzymatic activity of Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 Angstrom:
2.3.2.27;

Other elements in 6j6g:

The structure of Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom (pdb code 6j6g). 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*-A2 Complex at An Average Resolution of 3.2 Angstrom, PDB code: 6j6g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6j6g

Go back to Magnesium Binding Sites List in 6j6g
Magnesium binding site 1 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:41.2
occ:1.00
 O2B C:GTP1500 2.1 44.6 1.0
OG C:SER190 2.1 27.9 1.0
OG1 C:THR147 2.3 30.7 1.0
O3G C:GTP1500 2.6 44.6 1.0
O1G C:GTP1500 2.8 44.6 1.0
CB C:SER190 2.9 27.9 1.0
PG C:GTP1500 3.1 44.6 1.0
PB C:GTP1500 3.3 44.6 1.0
CB C:THR147 3.6 30.7 1.0
O3B C:GTP1500 3.6 44.6 1.0
N C:THR147 3.9 30.7 1.0
O1B C:GTP1500 4.1 44.6 1.0
CA C:SER190 4.1 27.9 1.0
N C:SER190 4.2 27.9 1.0
O C:ALA215 4.2 24.8 1.0
CE C:LYS146 4.3 30.2 1.0
CA C:THR147 4.3 30.7 1.0
CB C:LYS146 4.4 30.2 1.0
OD2 C:ASP179 4.4 30.4 1.0
OD1 C:ASP179 4.4 30.4 1.0
O2G C:GTP1500 4.5 44.6 1.0
O3A C:GTP1500 4.5 44.6 1.0
CG2 C:THR147 4.6 30.7 1.0
CA C:PRO216 4.7 24.2 1.0
OD2 C:ASP214 4.7 28.3 1.0
O2A C:GTP1500 4.8 44.6 1.0
C C:LYS146 4.8 30.2 1.0
CG C:ASP179 4.9 30.4 1.0
NZ C:LYS146 4.9 30.2 1.0
N C:GLY217 5.0 25.9 1.0

Magnesium binding site 2 out of 6 in 6j6g

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg200

b:29.2
occ:1.00
 OP1 E:G78 2.1 44.6 1.0
OP2 E:U80 2.1 44.6 1.0
P E:U80 3.4 44.6 1.0
P E:G78 3.5 44.6 1.0
OP1 E:U80 3.9 44.6 1.0
OP1 E:G60 4.1 41.2 1.0
OP2 E:G78 4.2 44.6 1.0
O3' E:G77 4.2 44.6 1.0
O5' E:U80 4.2 44.6 1.0
C5' E:U80 4.3 44.6 1.0
O5' E:G78 4.6 44.6 1.0
O3' E:A79 4.6 47.2 1.0
O5' E:G60 4.6 41.2 1.0
C3' E:A79 4.8 47.2 1.0
C5' E:G78 4.9 44.6 1.0
P E:G60 4.9 41.2 1.0

Magnesium binding site 3 out of 6 in 6j6g

Go back to Magnesium Binding Sites List in 6j6g
Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:37.3
occ:1.00
 OP1 E:U80 2.2 44.6 1.0
P E:U80 3.3 44.6 1.0
O5' E:U80 3.6 44.6 1.0
O3' E:A79 3.7 47.2 1.0
OP2 E:G60 3.8 41.2 1.0
C2 E:A51 4.4 71.9 1.0
N7 E:G52 4.5 53.7 1.0
OP2 E:U80 4.6 44.6 1.0
OP2 E:A59 4.7 44.6 1.0
N3 E:A51 4.7 71.9 1.0
O6 E:G52 4.8 53.7 1.0

Magnesium binding site 4 out of 6 in 6j6g

Go back to Magnesium Binding Sites List in 6j6g
Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:20.7
occ:1.00
 OP2 E:G81 2.2 44.6 1.0
P E:G81 3.4 44.6 1.0
OP1 E:G81 4.0 44.6 1.0
O3' E:U80 4.1 44.6 1.0
OP2 E:A62 4.1 44.6 1.0
N7 E:G78 4.4 44.6 1.0
OP2 E:G77 4.4 44.6 1.0
O5' E:G81 4.6 44.6 1.0
N7 E:G77 4.7 44.6 1.0
OP2 E:G78 4.9 44.6 1.0
C8 E:G77 5.0 44.6 1.0

Magnesium binding site 5 out of 6 in 6j6g

Go back to Magnesium Binding Sites List in 6j6g
Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg203

b:22.6
occ:1.00
 OP1 E:G81 2.7 44.6 1.0
O6 E:G63 3.8 44.6 1.0
P E:G81 4.0 44.6 1.0
N7 E:G81 4.0 44.6 1.0
N7 E:A82 4.1 44.6 1.0
C8 E:G81 4.3 44.6 1.0
O5' E:G81 4.3 44.6 1.0
OP2 E:A82 4.4 44.6 1.0
N6 E:A82 4.6 44.6 1.0
OP2 E:G81 4.7 44.6 1.0
N7 E:G63 4.9 44.6 1.0
C6 E:G63 4.9 44.6 1.0

Magnesium binding site 6 out of 6 in 6j6g

Go back to Magnesium Binding Sites List in 6j6g
Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg204

b:26.8
occ:1.00
 OP1 E:G77 2.2 44.6 1.0
OP1 E:C61 2.2 39.2 1.0
P E:C61 3.3 39.2 1.0
O3' E:G60 3.3 41.2 1.0
P E:G77 3.6 44.6 1.0
NE2 A:GLN748 3.7 44.6 1.0
OP2 E:C61 4.3 39.2 1.0
O5' E:G77 4.4 44.6 1.0
O5' E:C61 4.4 39.2 1.0
OP2 E:G77 4.4 44.6 1.0
C5' E:C61 4.5 39.2 1.0
O3' E:A76 4.5 44.6 1.0
C5' E:G77 4.5 44.6 1.0
C3' E:G60 4.7 41.2 1.0
CD A:GLN748 4.9 44.6 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: Tue Oct 1 04:36:32 2024

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