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Magnesium in PDB 6j6q: Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom

Enzymatic activity of Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom:
2.3.2.27;

Other elements in 6j6q:

The structure of Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom 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 the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom (pdb code 6j6q). 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*-B2 Complex at An Average Resolution of 3.7 Angstrom, PDB code: 6j6q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6j6q

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:54.0
occ:1.00
 OG C:SER190 2.0 21.3 1.0
O1G C:GTP1500 2.2 35.4 1.0
O2B C:GTP1500 2.2 35.4 1.0
OG1 C:THR147 2.3 18.7 1.0
O3G C:GTP1500 2.8 35.4 1.0
CB C:SER190 2.8 21.3 1.0
PG C:GTP1500 2.9 35.4 1.0
PB C:GTP1500 3.2 35.4 1.0
O3B C:GTP1500 3.4 35.4 1.0
CB C:THR147 3.6 18.7 1.0
O1B C:GTP1500 3.7 35.4 1.0
CA C:SER190 3.9 21.3 1.0
N C:SER190 3.9 21.3 1.0
N C:THR147 4.0 18.7 1.0
OD2 C:ASP179 4.1 23.9 1.0
O2G C:GTP1500 4.3 35.4 1.0
OD1 C:ASP179 4.3 23.9 1.0
O C:ALA215 4.4 16.8 1.0
CA C:THR147 4.4 18.7 1.0
CG2 C:THR147 4.5 18.7 1.0
O3A C:GTP1500 4.6 35.4 1.0
CA C:PRO216 4.7 19.1 1.0
CB C:LYS146 4.7 15.4 1.0
CG C:ASP179 4.7 23.9 1.0
O2A C:GTP1500 4.7 35.4 1.0
CE C:LYS146 4.7 15.4 1.0
OD2 C:ASP214 4.7 18.6 1.0
N C:GLY217 4.9 20.4 1.0

Magnesium binding site 2 out of 6 in 6j6q

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg200

b:28.6
occ:1.00
 OP2 B:G1 1.5 0.1 1.0
OP1 E:G78 1.7 49.9 1.0
OP2 E:U80 2.5 55.9 1.0
P B:G1 2.5 0.9 1.0
O3' B:G0 2.7 77.2 1.0
P E:G78 3.1 49.9 1.0
OP1 B:G1 3.5 0.4 1.0
O5' B:G1 3.7 0.3 1.0
P E:U80 3.8 55.9 1.0
O3' E:G77 3.9 49.5 1.0
O5' E:G78 4.0 49.9 1.0
OP2 E:G78 4.1 49.9 1.0
O5' E:U80 4.1 55.9 1.0
C5' B:G1 4.1 0.5 1.0
C3' B:G0 4.2 78.2 1.0
OP1 E:G60 4.3 57.3 1.0
C5' E:G78 4.3 49.9 1.0
O2' B:G0 4.5 79.3 1.0
O3' E:A79 4.7 55.2 1.0
C3' E:A79 4.8 55.2 1.0
OP1 E:U80 4.8 55.9 1.0
C4' B:G0 4.9 78.7 1.0
C2' B:G0 4.9 79.3 1.0
C5' E:A79 5.0 55.2 1.0
C4' E:A79 5.0 55.2 1.0

Magnesium binding site 3 out of 6 in 6j6q

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:21.9
occ:1.00
 OP1 E:U80 1.7 55.9 1.0
OP1 E:A59 2.1 61.9 1.0
OP2 E:G60 2.1 57.3 1.0
P E:A59 2.9 61.9 1.0
OP2 E:A59 3.0 61.9 1.0
P E:U80 3.1 55.9 1.0
P E:G60 3.2 57.3 1.0
O5' E:A59 3.6 61.9 1.0
OP1 E:G60 3.6 57.3 1.0
OP2 E:U80 3.8 55.9 1.0
O5' E:U80 4.0 55.9 1.0
O3' E:A79 4.0 55.2 1.0
O5' E:G60 4.0 57.3 1.0
O3' E:C58 4.3 77.0 1.0
C5' E:G60 4.3 57.3 1.0
C5' E:U80 4.3 55.9 1.0
O2' B:A70 4.4 0.1 1.0
O3' E:A59 4.5 61.9 1.0
O6 E:G52 4.8 57.2 1.0
N7 E:G52 4.9 57.2 1.0
C3' E:A59 4.9 61.9 1.0
C5' E:A59 4.9 61.9 1.0

Magnesium binding site 4 out of 6 in 6j6q

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:21.4
occ:1.00
 OP2 E:G81 2.0 65.7 1.0
P E:G81 3.5 65.7 1.0
O5' E:G81 4.0 65.7 1.0
OP2 E:G77 4.1 49.5 1.0
OP2 E:A62 4.2 53.8 1.0
OP2 E:G78 4.3 49.9 1.0
O3' E:U80 4.3 55.9 1.0
OP1 E:G81 4.4 65.7 1.0
N7 E:G78 4.5 49.9 1.0
C5' E:G77 4.5 49.5 1.0
N7 E:G77 4.6 49.5 1.0
OP2 E:C61 4.7 52.4 1.0
OP1 E:A62 4.7 53.8 1.0
C8 E:G77 4.8 49.5 1.0
C8 E:G78 5.0 49.9 1.0

Magnesium binding site 5 out of 6 in 6j6q

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg203

b:24.2
occ:1.00
 OP1 E:G81 2.4 65.7 1.0
P E:G81 3.8 65.7 1.0
O6 E:G63 4.1 47.7 1.0
N7 E:G81 4.2 65.7 1.0
OP2 E:A82 4.2 47.7 1.0
C8 E:G81 4.3 65.7 1.0
N7 E:A82 4.3 47.7 1.0
OP2 E:G81 4.4 65.7 1.0
O5' E:G81 4.5 65.7 1.0
C2' E:U80 4.7 55.9 1.0
O3' E:U80 4.9 55.9 1.0
N7 E:A62 4.9 53.8 1.0
C3' E:U80 5.0 55.9 1.0
N6 E:A82 5.0 47.7 1.0

Magnesium binding site 6 out of 6 in 6j6q

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Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg204

b:23.1
occ:1.00
 OP1 E:G77 1.6 49.5 1.0
OP1 E:C61 1.8 52.4 1.0
P E:G77 2.9 49.5 1.0
P E:C61 3.2 52.4 1.0
NE2 A:GLN748 3.2 35.9 1.0
O5' E:G77 3.3 49.5 1.0
O3' E:G60 3.7 57.3 1.0
O5' E:C61 3.8 52.4 1.0
OP2 E:G77 3.8 49.5 1.0
O3' E:A76 4.1 47.7 1.0
CD A:GLN748 4.3 35.9 1.0
OP2 E:C61 4.4 52.4 1.0
C5' E:G77 4.4 49.5 1.0
C5' E:C61 4.9 52.4 1.0
CG A:GLN748 5.0 35.9 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 04:38:31 2024

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