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Magnesium in PDB 7dvq: Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)

Enzymatic activity of Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)

All present enzymatic activity of Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex):
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 7dvq:

The structure of Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex) also contains other interesting chemical elements:

Zinc (Zn) 7 atoms
Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex) (pdb code 7dvq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex), PDB code: 7dvq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7dvq

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Magnesium binding site 1 out of 5 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:40.0
occ:1.00
 O2B C:GTP1500 2.1 23.7 1.0
O1G C:GTP1500 2.1 23.7 1.0
OG1 C:THR143 2.1 27.7 1.0
O C:HOH1602 2.1 46.7 1.0
O C:HOH1601 2.1 33.4 1.0
O C:HOH1603 2.1 30.2 1.0
CB C:THR143 3.1 27.7 1.0
PG C:GTP1500 3.3 23.7 1.0
PB C:GTP1500 3.3 23.7 1.0
O3B C:GTP1500 3.7 23.7 1.0
O2G C:GTP1500 3.8 23.7 1.0
N C:THR143 3.9 27.7 1.0
CG2 C:THR143 4.1 27.7 1.0
CA C:THR143 4.1 27.7 1.0
OD1 C:ASP169 4.1 38.4 1.0
O1B C:GTP1500 4.2 23.7 1.0
OD2 C:ASP204 4.2 38.1 1.0
O2A C:GTP1500 4.2 23.7 1.0
OD1 C:ASP204 4.3 38.1 1.0
O3A C:GTP1500 4.3 23.7 1.0
O3G C:GTP1500 4.4 23.7 1.0
CA C:GLY180 4.5 31.3 1.0
OD2 C:ASP169 4.5 38.4 1.0
CG C:ASP204 4.6 38.1 1.0
CG C:ASP169 4.7 38.4 1.0
O C:THR205 4.7 31.5 1.0
CE C:LYS142 4.8 20.8 1.0
PA C:GTP1500 4.8 23.7 1.0
N C:GLY180 4.8 31.3 1.0
CB C:LYS142 4.8 20.8 1.0
C C:LYS142 5.0 20.8 1.0

Magnesium binding site 2 out of 5 in 7dvq

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Magnesium binding site 2 out of 5 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:31.4
occ:1.00
 OP1 F:G44 2.7 36.9 1.0
OP2 F:U46 2.8 34.9 1.0
O2' G:A0 3.1 34.5 1.0
O3' G:A0 3.4 34.5 1.0
OP1 F:G27 3.6 36.9 1.0
OP2 G:A1 3.7 28.7 1.0
O5' F:G27 3.8 36.9 1.0
P F:U46 3.8 34.9 1.0
P F:G44 3.9 36.9 1.0
O5' F:U46 4.1 34.9 1.0
C3' G:A0 4.2 34.5 1.0
C2' G:A0 4.2 34.5 1.0
P F:G27 4.2 36.9 1.0
P G:A1 4.2 28.7 1.0
OP1 F:U46 4.3 34.9 1.0
OP2 F:G44 4.4 36.9 1.0
C4' G:A0 4.5 34.5 1.0
MG F:MG202 4.5 24.5 1.0
C5' F:U46 4.5 34.9 1.0
O3' F:G43 4.6 37.0 1.0
C5' F:G27 4.7 36.9 1.0
OP2 F:G27 4.7 36.9 1.0
O5' G:A1 4.9 28.7 1.0

Magnesium binding site 3 out of 5 in 7dvq

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Magnesium binding site 3 out of 5 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:24.5
occ:1.00
 OP1 F:U46 2.1 34.9 1.0
OP1 F:A26 2.2 39.6 1.0
OP2 F:G27 3.0 36.9 1.0
OP1 F:G27 3.3 36.9 1.0
P F:U46 3.4 34.9 1.0
P F:A26 3.6 39.6 1.0
P F:G27 3.6 36.9 1.0
OP2 F:U46 3.8 34.9 1.0
OP2 G:A1 3.9 28.7 1.0
O5' F:A26 4.2 39.6 1.0
NZ v:LYS4 4.2 24.0 1.0
C5' F:A26 4.3 39.6 1.0
O5' F:U46 4.3 34.9 1.0
K F:K205 4.4 25.9 1.0
O3' F:A45 4.5 37.4 1.0
MG F:MG201 4.5 31.4 1.0
OP2 F:A26 4.5 39.6 1.0
O3' F:U25 4.6 38.0 1.0
O5' F:G27 4.7 36.9 1.0
O3' F:A26 4.8 39.6 1.0

Magnesium binding site 4 out of 5 in 7dvq

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Magnesium binding site 4 out of 5 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg203

b:35.1
occ:1.00
 OP2 F:G47 2.3 37.7 1.0
P F:G47 3.7 37.7 1.0
OP2 F:G43 3.8 37.0 1.0
O5' F:G47 4.1 37.7 1.0
OP2 F:A29 4.3 35.1 1.0
O3' F:U46 4.3 34.9 1.0
OP2 F:G44 4.4 36.9 1.0
N7 F:G43 4.6 37.0 1.0
C8 F:G43 4.6 37.0 1.0
OP2 F:C28 4.7 36.8 1.0
OP1 F:C28 4.7 36.8 1.0
C5' F:G43 4.8 37.0 1.0
OP1 F:G47 4.9 37.7 1.0
P F:G43 4.9 37.0 1.0

Magnesium binding site 5 out of 5 in 7dvq

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Magnesium binding site 5 out of 5 in the Cryo-Em Structure of the Activated Human Minor Spliceosome (Minor Bact Complex)


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 Activated Human Minor Spliceosome (Minor Bact Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg204

b:35.1
occ:1.00
 OP1 F:G43 2.0 37.0 1.0
OP1 F:C28 2.5 36.8 1.0
P F:G43 3.4 37.0 1.0
P F:C28 3.7 36.8 1.0
O5' F:G43 3.8 37.0 1.0
O3' F:G27 3.9 36.9 1.0
NE2 A:GLN675 3.9 35.1 1.0
C5' F:G43 4.2 37.0 1.0
O3' F:A42 4.3 36.9 1.0
OP2 F:G43 4.4 37.0 1.0
C5' F:C28 4.6 36.8 1.0
O5' F:C28 4.7 36.8 1.0
OP2 F:C28 4.8 36.8 1.0
CD A:GLN675 4.9 35.1 1.0

Reference:

R.Bai, R.Wan, L.Wang, K.Xu, Q.Zhang, J.Lei, Y.Shi. Structure of the Activated Human Minor Spliceosome. Science V. 371 2021.
ISSN: ESSN 1095-9203
PubMed: 33509932
DOI: 10.1126/SCIENCE.ABG0879
Page generated: Wed Oct 2 16:28:45 2024

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