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Magnesium in PDB 3jb9: Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution:
5.2.1.8;

Other elements in 3jb9:

The structure of Cryo-Em Structure of the Yeast Spliceosome at 3.6 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 Yeast Spliceosome at 3.6 Angstrom Resolution (pdb code 3jb9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution, PDB code: 3jb9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3jb9

Go back to Magnesium Binding Sites List in 3jb9
Magnesium binding site 1 out of 4 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 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 Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg101

b:50.4
occ:1.00
OP1 N:G66 2.3 75.7 1.0
OP2 N:U68 2.6 87.1 1.0
P N:G66 3.7 75.8 1.0
P N:U68 3.8 89.2 1.0
OP1 N:G48 3.9 89.9 1.0
O3' N:G65 4.1 78.7 1.0
C5' N:G66 4.3 80.2 1.0
OP1 N:U68 4.3 87.3 1.0
O5' N:G66 4.4 77.5 1.0
O5' N:U68 4.5 92.9 1.0
OP2 N:G66 4.8 72.9 1.0

Magnesium binding site 2 out of 4 in 3jb9

Go back to Magnesium Binding Sites List in 3jb9
Magnesium binding site 2 out of 4 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 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 Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg102

b:59.2
occ:1.00
OP1 N:U68 2.9 87.3 1.0
OP2 N:G48 3.7 90.1 1.0
N7 N:G40 3.7 0.3 1.0
O3' N:A67 3.8 88.2 1.0
P N:U68 3.8 89.2 1.0
OP2 N:A47 3.8 0.6 1.0
O5' N:U68 4.0 92.9 1.0
O6 N:G40 4.3 0.6 1.0
C5 N:G40 4.6 0.0 1.0
C8 N:G40 4.6 0.1 1.0
O4' N:U68 4.8 90.0 1.0
C6 N:G40 4.8 1.0 1.0

Magnesium binding site 3 out of 4 in 3jb9

Go back to Magnesium Binding Sites List in 3jb9
Magnesium binding site 3 out of 4 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 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 Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg103

b:58.4
occ:1.00
OP2 N:G69 2.2 83.2 1.0
P N:G69 3.5 82.1 1.0
OP2 N:G66 3.5 72.9 1.0
O3' N:U68 3.7 84.8 1.0
C5' N:G65 3.9 84.9 1.0
N7 N:G66 4.1 80.3 1.0
OP2 N:G65 4.1 76.3 1.0
OP1 N:G69 4.4 82.6 1.0
O5' N:G69 4.5 83.2 1.0
O5' N:G65 4.6 84.0 1.0
C8 N:G65 4.7 77.5 1.0
C5' N:G69 4.7 84.2 1.0
C8 N:G66 4.8 79.2 1.0
N7 N:G65 4.8 73.9 1.0
C3' N:G65 4.8 81.2 1.0
OP2 N:A50 4.9 64.8 1.0
P N:G66 4.9 75.8 1.0
OP2 N:C49 4.9 68.5 1.0
C4' N:G65 5.0 82.6 1.0

Magnesium binding site 4 out of 4 in 3jb9

Go back to Magnesium Binding Sites List in 3jb9
Magnesium binding site 4 out of 4 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 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 Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg104

b:58.9
occ:1.00
OP1 N:G69 2.6 82.6 1.0
O4 N:U51 3.4 0.8 1.0
P N:G69 3.9 82.1 1.0
C4 N:U51 4.2 0.9 1.0
C5 N:U51 4.3 0.1 1.0
OP2 N:G69 4.6 83.2 1.0
O6 N:G52 4.6 0.6 1.0
O5' N:G69 4.7 83.2 1.0
N6 N:A70 4.8 97.1 1.0

Reference:

C.Yan, J.Hang, R.Wan, M.Huang, C.Wong, Y.Shi. Structure of A Yeast Spliceosome at 3.6-Angstrom Resolution Science V. 349 1182 2015.
ISSN: ISSN 0036-8075
PubMed: 26292707
DOI: 10.1126/SCIENCE.AAC7629
Page generated: Mon Dec 14 08:19:58 2020

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