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

All present enzymatic activity of Cryo-Em Structure of the Human Post-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 Post-Catalytic Tsen/Pre-Trna Complex (pdb code 8hmz). 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 Post-Catalytic Tsen/Pre-Trna Complex, PDB code: 8hmz:
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 Post-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 Post-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg101 b:23.3 occ:1.00 OP2 5:G12 2.7 20.5 1.0 OP2 5:U8 3.7 20.5 1.0 OP2 5:G9 3.8 20.5 1.0 P 5:G12 4.2 20.5 1.0 OP1 5:U8 4.4 20.5 1.0 P 5:U8 4.5 20.5 1.0 C5 5:C13 4.7 20.5 1.0 O5' 5:G12 4.7 20.5 1.0 N7 5:G12 4.8 20.5 1.0 C8 5:G12 5.0 20.5 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Human Post-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 Post-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg102 b:24.4 occ:1.00 OP1 5:G9 2.1 20.5 1.0 OP2 5:G10 2.8 20.5 1.0 P 5:G9 3.6 20.5 1.0 C5' 5:G9 4.1 20.5 1.0 OP2 5:C11 4.2 20.5 1.0 P 5:G10 4.2 20.5 1.0 OP1 3:U62 4.2 41.0 1.0 O5' 5:G9 4.3 20.5 1.0 O3' 5:U8 4.3 20.5 1.0 C3' 5:G9 4.4 20.5 1.0 C4' 5:G9 4.6 20.5 1.0 OP2 5:G9 4.6 20.5 1.0 O5' 5:G10 4.8 20.5 1.0 O3' 5:G9 4.9 20.5 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Human Post-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 Post-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg103 b:20.9 occ:1.00 O4' 5:U8 3.1 20.5 1.0 C6 5:U8 3.7 20.5 1.0 N1 5:U8 3.8 20.5 1.0 C1' 5:U8 3.8 20.5 1.0 O5' 5:U8 3.9 20.5 1.0 OP2 3:G64 4.0 20.5 1.0 C4' 5:U8 4.2 20.5 1.0 C5' 5:U8 4.3 20.5 1.0 C5 5:U8 4.3 20.5 1.0 O3' 3:U63 4.4 18.7 1.0 C3' 5:G7 4.4 20.5 1.0 O2' 3:U63 4.5 18.7 1.0 C2 5:U8 4.6 20.5 1.0 P 3:G64 4.6 20.5 1.0 O2 3:U63 4.6 18.7 1.0 C2' 5:G7 4.8 20.5 1.0 O5' 5:G7 4.8 20.5 1.0 OP1 5:G7 4.9 20.5 1.0 O2' 3:A74 4.9 20.0 1.0 OP1 3:G64 4.9 20.5 1.0 N6 5:A15 5.0 18.8 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Human Post-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 Post-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg101 b:15.6 occ:1.00 C6 3:U54 3.5 12.4 1.0 O5' 5:C51 3.6 12.7 1.0 OP2 3:U55 3.6 12.6 1.0 C5 3:U54 3.7 12.4 1.0 OP2 5:C51 3.8 12.7 1.0 C5 3:U55 3.8 12.6 1.0 C5' 3:U54 3.9 12.4 1.0 C3' 3:U54 4.0 12.4 1.0 OP2 3:U54 4.2 12.4 1.0 P 5:C51 4.2 12.7 1.0 C4' 3:U54 4.4 12.4 1.0 N1 3:U54 4.4 12.4 1.0 O3' 5:G50 4.5 16.6 1.0 C5' 5:C51 4.6 12.7 1.0 C6 3:U55 4.6 12.6 1.0 O4' 3:U54 4.7 12.4 1.0 C4 3:U54 4.7 12.4 1.0 C4 3:U55 4.8 12.6 1.0 O3' 3:U54 4.8 12.4 1.0 P 3:U55 4.8 12.6 1.0 O4 3:U55 4.8 12.6 1.0 C2' 3:U54 4.9 12.4 1.0 C1' 3:U54 4.9 12.4 1.0 O5' 3:U54 5.0 12.4 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Human Post-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 Post-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg102 b:23.7 occ:1.00 O4 3:U65 2.9 17.7 1.0 O6 3:G66 3.6 27.4 1.0 C4 3:U65 3.7 17.7 1.0 C5 3:U65 4.1 17.7 1.0 C6 3:G66 4.6 27.4 1.0 N6 3:A79 4.7 32.6 1.0 N4 3:C78 4.7 31.4 1.0 N7 3:G66 4.8 27.4 1.0 N3 3:U65 4.8 17.7 1.0 O6 3:G67 5.0 30.4 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Human Post-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 Post-Catalytic Tsen/Pre-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg103 b:23.0 occ:1.00 C2 3:A74 2.7 20.0 1.0 N1 3:A74 2.9 20.0 1.0 N3 3:A74 3.8 20.0 1.0 OP1 3:A74 3.9 20.0 1.0 O4 3:U63 4.0 18.7 1.0 C6 3:A74 4.2 20.0 1.0 O4 3:U75 4.2 22.8 1.0 O4' 5:A21 4.5 16.5 1.0 OP2 5:A21 4.7 16.5 1.0 OP2 5:U20 4.8 53.5 1.0 C4 3:A74 4.8 20.0 1.0 O5' 5:A21 4.9 16.5 1.0 N6 3:A74 4.9 20.0 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