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Magnesium in PDB 5gmk: Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution

Other elements in 5gmk:

The structure of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution 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 Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution (pdb code 5gmk). 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 I Spliceosome (C Complex) at 3.4 Angstrom Resolution, PDB code: 5gmk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5gmk

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 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 I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:30.0
occ:1.00
OG1 C:THR147 1.9 0.6 1.0
OG C:SER190 1.9 0.9 1.0
O2B C:GTP1500 2.0 20.0 1.0
O1G C:GTP1500 2.3 20.0 1.0
O2G C:GTP1500 2.8 20.0 1.0
CB C:SER190 2.8 0.1 1.0
PG C:GTP1500 3.0 20.0 1.0
CB C:THR147 3.1 0.4 1.0
PB C:GTP1500 3.3 20.0 1.0
O3B C:GTP1500 3.8 20.0 1.0
N C:THR147 3.9 0.3 1.0
O1B C:GTP1500 4.0 20.0 1.0
CA C:THR147 4.1 0.2 1.0
CG2 C:THR147 4.1 0.6 1.0
CA C:SER190 4.1 0.0 1.0
OD2 C:ASP214 4.2 0.2 1.0
O3G C:GTP1500 4.3 20.0 1.0
N C:SER190 4.4 0.6 1.0
O3A C:GTP1500 4.5 20.0 1.0
OD1 C:ASP214 4.5 0.8 1.0
O C:ALA215 4.6 0.8 1.0
CB C:LYS146 4.7 0.5 1.0
CG C:ASP214 4.8 0.8 1.0
CE C:LYS146 4.9 0.6 1.0

Magnesium binding site 2 out of 6 in 5gmk

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 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 I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg200

b:50.4
occ:1.00
OP1 E:G78 2.1 75.7 1.0
OP1 N:G100 2.1 0.9 1.0
O3' B:G99 2.2 77.2 1.0
OP2 E:U80 2.4 87.1 1.0
P N:G100 3.3 0.2 1.0
P E:G78 3.6 75.8 1.0
C3' B:G99 3.6 78.2 1.0
P E:U80 3.8 89.2 1.0
OP2 N:G100 3.9 0.0 1.0
O5' N:G100 3.9 0.5 1.0
OP1 E:G60 4.2 89.9 1.0
O3' E:G77 4.2 78.7 1.0
C5' N:G100 4.3 0.6 1.0
C4' B:G99 4.4 78.7 1.0
O2' B:G99 4.4 79.3 1.0
OP1 E:U80 4.4 87.3 1.0
OP2 E:G78 4.4 72.9 1.0
C2' B:G99 4.5 79.3 1.0
O2' M:A501 4.5 0.1 1.0
O5' E:G78 4.5 77.5 1.0
O5' E:U80 4.6 92.9 1.0
C5' E:G78 4.8 80.2 1.0
O3' E:A79 4.8 88.2 1.0
C5' E:A79 4.8 85.6 1.0
C5' B:G99 4.8 77.9 1.0
P E:G60 4.9 88.0 1.0
C3' E:A79 4.9 85.3 1.0
C5' E:U80 4.9 93.8 1.0
C4' E:A79 4.9 86.5 1.0
O5' E:G60 5.0 81.8 1.0
OP2 E:G60 5.0 90.1 1.0

Magnesium binding site 3 out of 6 in 5gmk

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 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 I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:50.4
occ:1.00
OP1 E:U80 2.1 87.3 1.0
OP2 E:A59 2.5 0.6 1.0
P E:U80 3.3 89.2 1.0
P E:A59 3.4 0.9 1.0
OP1 E:A59 3.4 0.7 1.0
O3' E:A79 3.5 88.2 1.0
O5' E:U80 3.8 92.9 1.0
O3' E:C58 4.5 0.0 1.0
O5' E:A59 4.5 0.8 1.0
OP2 E:G60 4.6 90.1 1.0
N7 E:G52 4.6 0.3 1.0
OP2 E:U80 4.6 87.1 1.0
C3' E:A79 4.9 85.3 1.0
O6 E:G52 4.9 0.6 1.0

Magnesium binding site 4 out of 6 in 5gmk

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 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 I Spliceosome (C Complex) at 3.4 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:G77 4.1 76.3 1.0
O3' E:U80 4.2 84.8 1.0
O5' E:G81 4.3 83.2 1.0
OP2 E:A62 4.3 64.8 1.0
OP1 E:G81 4.4 82.6 1.0
N7 E:G77 4.6 73.9 1.0
N7 E:G78 4.6 80.3 1.0
OP2 E:G78 4.7 72.9 1.0
C8 E:G77 4.8 77.5 1.0

Magnesium binding site 5 out of 6 in 5gmk

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 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 I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg203

b:58.9
occ:1.00
OP1 E:G81 2.2 82.6 1.0
P E:G81 3.5 82.1 1.0
O5' E:G81 3.9 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
C2' E:U80 4.6 87.9 1.0
O3' E:U80 4.7 84.8 1.0
OP2 E:A82 4.7 85.3 1.0
N7 E:A82 4.9 92.4 1.0
C3' E:U80 4.9 86.5 1.0
O6 E:G63 4.9 20.0 1.0

Magnesium binding site 6 out of 6 in 5gmk

Go back to Magnesium Binding Sites List in 5gmk
Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 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 I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg204

b:30.0
occ:1.00
OP1 E:G77 2.0 76.0 1.0
OP1 E:C61 2.4 70.8 1.0
P E:G77 3.5 80.7 1.0
P E:C61 3.6 70.3 1.0
O3' E:G60 3.9 72.8 1.0
O5' E:G77 4.1 84.0 1.0
O5' E:C61 4.3 67.4 1.0
O3' E:A76 4.3 81.9 1.0
OE1 A:GLN748 4.4 20.0 1.0
OP2 E:G77 4.4 76.3 1.0
C5' E:G77 4.6 84.9 1.0
O2' B:G99 4.8 79.3 1.0
OP2 E:C61 4.9 68.5 1.0

Reference:

R.Wan, C.Yan, R.Bai, G.Huang, Y.Shi. Structure of A Yeast Catalytic Step I Spliceosome at 3.4 Angstrom Resolution Science V. 353 895 2016.
ISSN: ESSN 1095-9203
PubMed: 27445308
DOI: 10.1126/SCIENCE.AAG2235
Page generated: Mon Dec 14 20:23:55 2020

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