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Magnesium in PDB 6j6n: Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 Angstrom

Enzymatic activity of Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 Angstrom:
2.3.2.27;

Other elements in 6j6n:

The structure of Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom (pdb code 6j6n). 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*-B1 Complex at An Average Resolution of 3.86 Angstrom, PDB code: 6j6n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6j6n

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:36.0
occ:1.00
 OG C:SER190 2.1 29.9 1.0
O3B C:GTP1500 2.2 55.0 1.0
O2B C:GTP1500 2.2 55.0 1.0
OG1 C:THR147 2.6 32.6 1.0
PB C:GTP1500 2.7 55.0 1.0
O1G C:GTP1500 2.8 55.0 1.0
CB C:SER190 2.9 29.9 1.0
PG C:GTP1500 3.1 55.0 1.0
CB C:THR147 3.8 32.6 1.0
O1B C:GTP1500 3.8 55.0 1.0
N C:SER190 3.8 29.9 1.0
O3A C:GTP1500 3.9 55.0 1.0
CA C:SER190 4.0 29.9 1.0
O2G C:GTP1500 4.0 55.0 1.0
OD1 C:ASP179 4.1 27.2 1.0
N C:THR147 4.1 32.6 1.0
O3G C:GTP1500 4.2 55.0 1.0
O2A C:GTP1500 4.4 55.0 1.0
O C:ALA215 4.6 55.0 1.0
CA C:THR147 4.6 32.6 1.0
PA C:GTP1500 4.8 55.0 1.0
CG2 C:THR147 4.8 32.6 1.0
CB C:LYS146 4.9 29.9 1.0
CA C:PRO216 5.0 29.0 1.0
C C:LEU189 5.0 17.3 1.0
CG C:ASP179 5.0 27.2 1.0
OD2 C:ASP179 5.0 27.2 1.0

Magnesium binding site 2 out of 6 in 6j6n

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg200

b:28.6
occ:1.00
 OP1 E:G78 1.9 49.9 1.0
OP2 E:U80 2.5 55.9 1.0
P E:G78 3.3 49.9 1.0
P E:U80 3.7 55.9 1.0
O5' E:U80 3.9 55.9 1.0
OP2 E:G78 3.9 49.9 1.0
O3' E:G77 4.0 49.5 1.0
OP1 E:G60 4.2 55.0 1.0
O5' E:G60 4.3 55.0 1.0
O5' E:G78 4.4 49.9 1.0
OP1 E:U80 4.7 55.9 1.0
O3' E:A79 4.8 55.2 1.0
C5' E:G78 4.9 49.9 1.0
P E:G60 4.9 55.0 1.0

Magnesium binding site 3 out of 6 in 6j6n

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:21.9
occ:1.00
 OP1 E:U80 2.3 55.9 1.0
OP2 E:G60 2.7 55.0 1.0
OP2 E:A59 3.1 61.9 1.0
P E:U80 3.7 55.9 1.0
P E:G60 3.9 55.0 1.0
OP1 E:G60 4.2 55.0 1.0
P E:A59 4.3 61.9 1.0
OP2 E:U80 4.4 55.9 1.0
O3' E:A79 4.5 55.2 1.0
N7 E:G52 4.5 48.6 1.0
C5' E:A59 4.6 61.9 1.0
O5' E:G60 4.6 55.0 1.0
O6 E:G52 4.6 48.6 1.0
O5' E:A59 4.7 61.9 1.0
O5' E:U80 4.7 55.9 1.0
C5' E:G60 4.8 55.0 1.0
OP1 E:A59 4.8 61.9 1.0
C5' E:U80 4.9 55.9 1.0

Magnesium binding site 4 out of 6 in 6j6n

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 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
OP2 E:G77 3.9 49.5 1.0
OP2 E:A62 3.9 55.0 1.0
O5' E:G81 4.0 65.7 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
N7 E:G77 4.6 49.5 1.0
C8 E:G77 4.8 49.5 1.0
OP2 E:C61 4.8 55.0 1.0
C5' E:G77 4.8 49.5 1.0
OP1 E:A62 4.9 55.0 1.0
P E:A62 4.9 55.0 1.0
C8 E:G78 5.0 49.9 1.0

Magnesium binding site 5 out of 6 in 6j6n

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 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 55.0 1.0
N7 E:G81 4.2 65.7 1.0
C8 E:G81 4.3 65.7 1.0
N7 E:A82 4.3 55.0 1.0
OP2 E:A82 4.3 55.0 1.0
OP2 E:G81 4.4 65.7 1.0
O5' E:G81 4.5 65.7 1.0
C2' E:U80 4.6 55.9 1.0
O2 E:U80 4.8 55.9 1.0
O3' E:U80 4.9 55.9 1.0
C3' E:U80 4.9 55.9 1.0
N6 E:A82 4.9 55.0 1.0
N7 E:A62 5.0 55.0 1.0

Magnesium binding site 6 out of 6 in 6j6n

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Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg204

b:23.1
occ:1.00
 OP1 E:C61 2.1 55.0 1.0
OP1 E:G77 2.7 49.5 1.0
P E:C61 3.2 55.0 1.0
O3' E:G60 3.2 55.0 1.0
O5' E:C61 3.9 55.0 1.0
P E:G77 4.1 49.5 1.0
O5' E:G77 4.3 49.5 1.0
OP2 E:C61 4.5 55.0 1.0
C3' E:G60 4.6 55.0 1.0
O2' E:G60 4.7 55.0 1.0
OE1 A:GLN748 4.8 46.7 1.0
C5' E:G77 4.8 49.5 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: Wed Aug 13 08:58:25 2025

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