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Magnesium in PDB 5wsg: Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution:
3.6.4.13;

Other elements in 5wsg:

The structure of Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution 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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution (pdb code 5wsg). 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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution, PDB code: 5wsg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5wsg

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution


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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:30.0
occ:1.00
 OG1 C:THR147 2.3 0.6 1.0
O1G C:GTP1500 2.4 20.0 1.0
O2G C:GTP1500 2.4 20.0 1.0
O2B C:GTP1500 2.5 20.0 1.0
OG C:SER190 2.8 0.9 1.0
O1B C:GTP1500 2.8 20.0 1.0
PG C:GTP1500 2.9 20.0 1.0
PB C:GTP1500 3.1 20.0 1.0
CB C:THR147 3.1 0.4 1.0
O3B C:GTP1500 3.6 20.0 1.0
CB C:SER190 3.7 0.1 1.0
OD2 C:ASP214 3.7 0.2 1.0
N C:THR147 3.7 0.3 1.0
CA C:THR147 4.0 0.2 1.0
O3G C:GTP1500 4.2 20.0 1.0
CG2 C:THR147 4.3 0.6 1.0
O2A C:GTP1500 4.5 20.0 1.0
O3A C:GTP1500 4.5 20.0 1.0
CG C:ASP214 4.6 0.8 1.0
OD1 C:ASP214 4.6 0.8 1.0
CB C:LYS146 4.6 0.5 1.0
O1A C:GTP1500 4.8 20.0 1.0
PA C:GTP1500 4.8 20.0 1.0
N C:SER190 4.8 0.6 1.0
O C:LEU189 4.8 0.9 1.0
CA C:SER190 4.9 0.0 1.0
C C:LYS146 4.9 0.6 1.0
CE C:LYS146 4.9 0.6 1.0
O C:ALA215 5.0 0.8 1.0
C C:LEU189 5.0 1.0 1.0

Magnesium binding site 2 out of 6 in 5wsg

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution


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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg200

b:50.4
occ:1.00
 OP2 E:U80 1.8 87.1 1.0
O3' B:G99 2.6 77.2 1.0
OP1 E:G78 2.7 75.7 1.0
OP2 b:U1 3.0 78.6 1.0
P E:U80 3.1 89.2 1.0
P b:U1 3.6 76.9 1.0
OP1 E:U80 3.7 87.3 1.0
OP1 b:U1 3.7 75.2 1.0
O5' b:U1 3.8 78.8 1.0
C3' B:G99 3.8 78.2 1.0
O5' E:U80 3.9 92.9 1.0
O2' B:G99 4.0 79.3 1.0
P E:G78 4.1 75.8 1.0
OP1 E:G60 4.1 89.9 1.0
C4' B:G99 4.2 78.7 1.0
O3' E:A79 4.3 88.2 1.0
C5' b:U1 4.3 77.9 1.0
C5' E:U80 4.4 93.8 1.0
C4' E:A79 4.5 86.5 1.0
C2' B:G99 4.5 79.3 1.0
C3' E:A79 4.5 85.3 1.0
OP2 E:G60 4.6 90.1 1.0
C5' E:A79 4.7 85.6 1.0
P E:G60 4.7 88.0 1.0
OP2 E:G78 4.8 72.9 1.0
C5' B:G99 4.9 77.9 1.0
O3' E:G77 5.0 78.7 1.0
O5' E:G60 5.0 81.8 1.0

Magnesium binding site 3 out of 6 in 5wsg

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution


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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:50.4
occ:1.00
 OP1 E:U80 2.2 87.3 1.0
OP2 E:A59 2.6 0.6 1.0
P E:U80 3.3 89.2 1.0
OP1 E:A59 3.3 0.7 1.0
P E:A59 3.4 0.9 1.0
O3' E:A79 3.6 88.2 1.0
O5' E:U80 3.8 92.9 1.0
N7 E:G52 4.3 0.3 1.0
O3' E:C58 4.5 0.0 1.0
OP2 E:G60 4.6 90.1 1.0
O5' E:A59 4.6 0.8 1.0
N3 E:A51 4.6 0.9 1.0
OP2 E:U80 4.6 87.1 1.0
C2 E:A51 4.7 0.8 1.0
O6 E:G52 4.7 0.6 1.0
C3' E:A79 5.0 85.3 1.0

Magnesium binding site 4 out of 6 in 5wsg

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution


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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:58.4
occ:1.00
 OP2 E:G81 2.0 83.2 1.0
P E:G81 3.5 82.1 1.0
OP2 E:A62 4.1 64.8 1.0
O3' E:U80 4.2 84.8 1.0
OP2 E:G77 4.2 76.3 1.0
O5' E:G81 4.4 83.2 1.0
N7 E:G77 4.4 73.9 1.0
OP1 E:G81 4.4 82.6 1.0
N7 E:G78 4.6 80.3 1.0
C8 E:G77 4.7 77.5 1.0
OP2 E:G78 4.9 72.9 1.0

Magnesium binding site 5 out of 6 in 5wsg

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution


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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg203

b:58.9
occ:1.00
 OP1 E:G81 2.5 82.6 1.0
P E:G81 3.6 82.1 1.0
O5' E:G81 4.0 83.2 1.0
OP2 E:G81 4.2 83.2 1.0
N7 E:G81 4.4 88.7 1.0
C8 E:G81 4.5 86.4 1.0
O6 E:G63 4.6 20.0 1.0
OP2 E:A82 4.8 85.3 1.0
O3' E:U80 4.9 84.8 1.0
N7 E:A62 4.9 75.6 1.0
C2' E:U80 5.0 87.9 1.0

Magnesium binding site 6 out of 6 in 5wsg

Go back to Magnesium Binding Sites List in 5wsg
Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution


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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg204

b:30.0
occ:1.00
 OP1 E:G77 1.9 76.0 1.0
OP1 E:C61 2.3 70.8 1.0
P E:G77 3.4 80.7 1.0
P E:C61 3.6 70.3 1.0
O3' E:G60 3.8 72.8 1.0
O5' E:G77 4.0 84.0 1.0
OE1 A:GLN748 4.0 20.0 1.0
O5' E:C61 4.1 67.4 1.0
OP2 E:G77 4.3 76.3 1.0
O3' E:A76 4.3 81.9 1.0
C5' E:G77 4.4 84.9 1.0
OP2 E:C61 4.8 68.5 1.0
CD A:GLN748 4.9 20.0 1.0
C5' E:C61 4.9 65.9 1.0

Reference:

C.Yan, R.Wan, R.Bai, G.Huang, Y.Shi. Structure of A Yeast Step II Catalytically Activated Spliceosome Science V. 355 149 2017.
ISSN: ESSN 1095-9203
PubMed: 27980089
DOI: 10.1126/SCIENCE.AAK9979
Page generated: Mon Sep 30 08:27:40 2024

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