Magnesium in PDB 8fli: Cryo-Em Structure of A Group II Intron Immediately Before Branching

The binding sites of Magnesium atom in the Cryo-Em Structure of A Group II Intron Immediately Before Branching (pdb code 8fli). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of A Group II Intron Immediately Before Branching, PDB code: 8fli:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of A Group II Intron Immediately Before Branching


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 A Group II Intron Immediately Before Branching within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:92.0 occ:1.00 OP1 A:A6 1.9 95.2 1.0 OP2 A:C7 2.0 90.8 1.0 OP1 A:A401 2.2 112.4 1.0 P A:A6 3.2 95.2 1.0 P A:C7 3.3 90.8 1.0 P A:A401 3.5 112.4 1.0 O5' A:A6 3.7 95.2 1.0 C5' A:A6 3.9 95.2 1.0 O5' A:A401 3.9 112.4 1.0 OP1 A:C7 3.9 90.8 1.0 OP2 A:A6 4.1 95.2 1.0 O5' A:C7 4.3 90.8 1.0 O3' A:A6 4.4 95.2 1.0 O3' A:G5 4.4 109.9 1.0 OP2 A:A401 4.4 112.4 1.0 C3' A:A6 4.5 95.2 1.0 O3' A:A400 4.6 118.7 1.0 C4' A:A6 4.8 95.2 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of A Group II Intron Immediately Before Branching


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 A Group II Intron Immediately Before Branching within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:119.2 occ:1.00 OP1 A:A792 2.0 113.1 1.0 C5' A:A792 2.3 113.1 1.0 P A:A792 2.3 113.1 1.0 OP2 A:A792 2.5 113.1 1.0 O5' A:A792 2.6 113.1 1.0 OP2 A:A815 2.9 108.6 1.0 OP2 A:G793 3.1 106.3 1.0 OP1 A:A815 3.5 108.6 1.0 P A:A815 3.6 108.6 1.0 C4' A:A792 3.7 113.1 1.0 O3' A:G791 3.9 120.7 1.0 O3' A:A814 4.3 115.6 1.0 C3' A:A792 4.3 113.1 1.0 P A:G793 4.4 106.3 1.0 O4' A:A792 4.5 113.1 1.0 O3' A:A792 4.7 113.1 1.0 O5' A:G793 4.7 106.3 1.0 C3' A:G791 4.9 120.7 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of A Group II Intron Immediately Before Branching


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 A Group II Intron Immediately Before Branching within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:125.5 occ:1.00 O3' A:G0 1.9 104.5 1.0 OP2 A:U1 1.9 134.4 1.0 P A:U1 2.2 134.4 1.0 OP1 A:C813 2.6 103.1 1.0 O5' A:U1 3.0 134.4 1.0 C3' A:G0 3.2 104.5 1.0 OP1 A:U1 3.6 134.4 1.0 O2' A:G0 3.6 104.5 1.0 C4' A:G0 3.9 104.5 1.0 C2' A:G0 4.0 104.5 1.0 P A:C813 4.0 103.1 1.0 C5' A:U1 4.1 134.4 1.0 O2' A:A860 4.2 135.2 1.0 O3' A:A812 4.4 97.1 1.0 C5' A:G0 4.5 104.5 1.0 OP2 A:C813 4.9 103.1 1.0 OP2 A:A815 5.0 108.6 1.0

D.B.Haack, B.Rudolfs, C.Zhang, D.Lyumkis, N.Toor. Structural Basis of Branching During Rna Splicing Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-01150-0