Magnesium in PDB 9gmw: SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State)

The structure of SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State) also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Manganese	(Mn)	3 atoms

The binding sites of Magnesium atom in the SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State) (pdb code 9gmw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State), PDB code: 9gmw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State) within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg101 b:25.1 occ:1.00 OP1 T:C58 1.9 67.0 1.0 OP2 T:U60 1.9 51.5 1.0 P T:U60 3.1 54.2 1.0 P T:C58 3.3 62.6 1.0 O5' T:U60 3.5 48.6 1.0 OP1 T:U60 3.9 45.2 1.0 O3' T:G57 3.9 66.4 1.0 OP2 T:C58 4.2 52.2 1.0 C5 T:U60 4.2 42.1 1.0 OP2 T:G61 4.2 34.9 1.0 O5' T:C58 4.3 59.7 1.0 O3' T:G59 4.4 63.4 1.0 C6 T:U60 4.4 44.1 1.0 C5' T:C58 4.5 59.4 1.0 C3' T:G59 4.7 52.5 1.0 C3' T:C58 4.9 57.8 1.0 C5' T:U60 4.9 45.5 1.0 OP1 T:G59 5.0 59.4 1.0

Magnesium binding site 2 out of 4 in the SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State) within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg102 b:31.8 occ:1.00 N7 T:G15 2.1 69.7 1.0 C8 T:G15 3.0 73.4 1.0 C5 T:G15 3.2 70.9 1.0 O6 T:G15 3.5 70.3 1.0 C6 T:G15 3.7 70.8 1.0 O4 T:U8 3.9 69.2 1.0 C4 T:U8 4.2 73.2 1.0 N9 T:G15 4.2 73.8 1.0 C4 T:G15 4.3 70.4 1.0 O4 T:U16 4.3 83.1 1.0 N3 T:U8 4.4 73.0 1.0 OP2 T:A14 4.5 86.3 1.0 OP2 T:G15 4.5 69.0 1.0 N7 T:A14 4.9 75.1 1.0 C5 T:U8 4.9 68.7 1.0 C8 T:A14 4.9 78.2 1.0 OP1 T:A7 5.0 74.8 1.0

Magnesium binding site 3 out of 4 in the SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State) within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg103 b:30.1 occ:1.00 N7 T:G13 2.3 83.6 1.0 C8 T:G13 3.1 84.8 1.0 C5 T:G13 3.4 82.2 1.0 OP2 T:C12 3.7 94.1 1.0 O6 T:G13 3.8 78.0 1.0 C6 T:G13 4.0 79.5 1.0 OP2 T:G13 4.1 87.4 1.0 C5 T:U8 4.1 68.7 1.0 OP2 T:G9 4.2 78.9 1.0 N9 T:G13 4.4 82.8 1.0 OP2 T:U8 4.4 69.8 1.0 C6 T:U8 4.5 67.7 1.0 C4 T:G13 4.5 82.2 1.0 C5 T:C12 4.7 88.3 1.0 O5' T:C12 4.8 101.2 1.0 C6 T:C12 4.8 91.2 1.0 P T:C12 4.9 102.8 1.0 C4 T:U8 4.9 73.2 1.0

Magnesium binding site 4 out of 4 in the SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SLFN11 Wt Dimer Bound to Trna-Leu-Taa (Pre-Cleavage State) within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg104 b:27.5 occ:1.00 OP2 T:A69 2.3 59.3 1.0 P T:A69 3.6 56.8 1.0 OP2 T:G57 3.9 63.1 1.0 N7 T:G57 4.1 59.8 1.0 OP1 T:A69 4.2 56.4 1.0 OP2 T:C56 4.3 71.9 1.0 OP1 T:A68 4.4 52.0 1.0 C3' T:A68 4.4 50.4 1.0 O3' T:A68 4.5 55.0 1.0 O5' T:A69 4.7 52.8 1.0 C8 T:G57 4.7 56.1 1.0

M.Kugler, F.J.Metzner, K.P.Hopfner, K.Lammens. Phosphorylation-Mediated Conformational Change Regulates Human SLFN11 Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-54833-7