Magnesium in PDB 8hmy: Cryo-Em Structure of the Human Pre-Catalytic Tsen/Pre-Trna Complex

All present enzymatic activity of Cryo-Em Structure of the Human Pre-Catalytic Tsen/Pre-Trna Complex:
2.7.1.78; 4.6.1.16;

The binding sites of Magnesium atom in the Cryo-Em Structure of the Human Pre-Catalytic Tsen/Pre-Trna Complex (pdb code 8hmy). 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 Human Pre-Catalytic Tsen/Pre-Trna Complex, PDB code: 8hmy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cryo-Em Structure of the Human Pre-Catalytic Tsen/Pre-Trna 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 Human Pre-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg100 b:19.2 occ:1.00 C5' T:C51 3.3 26.8 1.0 OP2 T:U55 3.5 24.8 1.0 C5' T:U54 3.5 23.7 1.0 OP2 T:C51 3.7 26.8 1.0 OP2 T:U54 3.9 23.7 1.0 C3' T:U54 4.1 23.7 1.0 O5' T:C51 4.2 26.8 1.0 C4' T:C51 4.2 26.8 1.0 OP2 T:A52 4.3 24.9 1.0 C4' T:U54 4.3 23.7 1.0 C6 T:U54 4.3 23.7 1.0 O5' T:U54 4.5 23.7 1.0 C3' T:C51 4.5 26.8 1.0 P T:C51 4.5 26.8 1.0 O3' T:U54 4.6 23.7 1.0 C5 T:U54 4.7 23.7 1.0 P T:U55 4.7 24.8 1.0 C5 T:U55 4.8 24.8 1.0 O4' T:U54 4.9 23.7 1.0 P T:U54 4.9 23.7 1.0 O3' T:G50 4.9 30.0 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Human Pre-Catalytic Tsen/Pre-Trna 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 Human Pre-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg101 b:40.6 occ:1.00 O6 T:G67 3.5 71.2 1.0 O6 T:G66 4.4 63.8 1.0 OP1 T:U75 4.4 50.8 1.0 C6 T:G67 4.6 71.2 1.0 N4 T:C77 4.6 67.1 1.0 N7 T:G67 4.8 71.2 1.0 O6 T:G68 4.8 73.2 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Human Pre-Catalytic Tsen/Pre-Trna 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 Human Pre-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg102 b:40.7 occ:1.00 OP1 T:A74 2.8 43.1 1.0 C2 T:A74 4.1 43.1 1.0 P T:A74 4.2 43.1 1.0 O4 T:U75 4.3 50.8 1.0 OP2 T:A21 4.3 34.3 1.0 N1 T:A74 4.7 43.1 1.0 OP2 T:A74 4.8 43.1 1.0 N3 T:A74 4.9 43.1 1.0 OP1 T:U20 5.0 80.8 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Human Pre-Catalytic Tsen/Pre-Trna 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 Human Pre-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg103 b:16.3 occ:1.00 OP2 T:G12 2.4 18.7 1.0 OP2 T:G9 3.9 30.9 1.0 P T:G12 3.9 18.7 1.0 OP2 T:U8 4.1 37.1 1.0 O5' T:G12 4.5 18.7 1.0 N7 T:G12 4.5 18.7 1.0 O5' T:C11 4.6 30.9 1.0 C5 T:C13 4.6 30.9 1.0 C3' T:C11 4.6 30.9 1.0 OP1 T:U8 4.7 37.1 1.0 C8 T:G12 4.7 18.7 1.0 O3' T:C11 4.8 30.9 1.0 OP1 T:G12 4.8 18.7 1.0 OP2 T:C11 4.8 30.9 1.0 OP1 T:G9 4.8 30.9 1.0 P T:G9 4.9 30.9 1.0 P T:U8 4.9 37.1 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Human Pre-Catalytic Tsen/Pre-Trna 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 Human Pre-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg104 b:31.6 occ:1.00 OP1 T:G9 2.5 30.9 1.0 P T:G9 3.7 30.9 1.0 OP2 T:G10 3.8 30.9 1.0 O3' T:U8 3.9 37.1 1.0 C5' T:G9 4.1 30.9 1.0 OP1 T:U62 4.2 55.7 1.0 O5' T:G9 4.4 30.9 1.0 OP1 T:U8 4.7 37.1 1.0 C4' T:G9 4.9 30.9 1.0 OP2 T:C11 5.0 30.9 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Human Pre-Catalytic Tsen/Pre-Trna Complex


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 Human Pre-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg105 b:35.8 occ:1.00 O4' T:U8 3.5 37.1 1.0 O2' T:A74 3.8 43.1 1.0 OP2 T:G64 4.1 41.3 1.0 O2' T:U63 4.1 38.5 1.0 N1 T:U8 4.1 37.1 1.0 C1' T:U8 4.2 37.1 1.0 C6 T:U8 4.2 37.1 1.0 O2 T:U63 4.3 38.5 1.0 O3' T:U63 4.6 38.5 1.0 P T:G64 4.6 41.3 1.0 N6 T:A15 4.6 34.5 1.0 OP1 T:G64 4.7 41.3 1.0 C2 T:U8 4.7 37.1 1.0 O5' T:U8 4.7 37.1 1.0 C4' T:U8 4.7 37.1 1.0 C5 T:U8 4.8 37.1 1.0 C5' T:U8 4.9 37.1 1.0 C2' T:A74 4.9 43.1 1.0

X.Zhang, F.Yang, X.Zhan, T.Bian, Z.Xing, Y.Lu, Y.Shi. Structural Basis of Pre-Trna Intron Removal By Human Trna Splicing Endonuclease. Mol.Cell 2023.
ISSN: ISSN 1097-2765
PubMed: 37028420
DOI: 10.1016/J.MOLCEL.2023.03.015