Manganese in PDB 9erf: SLFN11 Dimer Bound to Trna-Met-Cat

The structure of SLFN11 Dimer Bound to Trna-Met-Cat also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Magnesium	(Mg)	3 atoms

The binding sites of Manganese atom in the SLFN11 Dimer Bound to Trna-Met-Cat (pdb code 9erf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the SLFN11 Dimer Bound to Trna-Met-Cat, PDB code: 9erf:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the SLFN11 Dimer Bound to Trna-Met-Cat


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of SLFN11 Dimer Bound to Trna-Met-Cat within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:53.0 occ:1.00 OE2 A:GLU214 2.0 26.0 1.0 OE2 A:GLU209 2.4 31.1 1.0 OD2 A:ASP252 2.5 51.5 1.0 OP1 T:U54 2.6 48.9 1.0 O A:PHE215 2.9 36.6 1.0 CD A:GLU214 3.1 23.4 1.0 CD A:GLU209 3.2 31.6 1.0 OE1 A:GLU209 3.3 35.1 1.0 OE1 A:GLU214 3.6 24.8 1.0 CG A:ASP252 3.6 50.2 1.0 OP2 T:C55 4.0 48.4 1.0 CD A:LYS216 4.0 36.2 1.0 C A:PHE215 4.0 30.7 1.0 P T:U54 4.1 42.3 1.0 CB A:ASP252 4.1 47.7 1.0 CG A:GLU214 4.2 21.1 1.0 N A:PHE215 4.2 24.8 1.0 C5' T:U54 4.6 38.0 1.0 NZ A:LYS216 4.6 33.1 1.0 CG A:GLU209 4.6 24.8 1.0 CA A:PHE215 4.6 26.5 1.0 O5' T:U54 4.7 41.1 1.0 OD1 A:ASP252 4.7 46.8 1.0 OH A:TYR234 4.8 36.3 1.0 O3' T:A53 4.8 50.4 1.0 CE A:LYS216 4.9 30.4 1.0

Manganese binding site 2 out of 3 in the SLFN11 Dimer Bound to Trna-Met-Cat


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of SLFN11 Dimer Bound to Trna-Met-Cat within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:30.2 occ:1.00 OP1 U:U66 1.9 53.5 1.0 OE2 B:GLU214 2.1 18.7 1.0 O B:PHE215 2.1 31.3 1.0 OE2 B:GLU209 2.2 28.2 1.0 OD1 B:ASP252 2.9 54.5 1.0 P U:U66 2.9 56.5 1.0 CD B:GLU209 3.2 28.2 1.0 CD B:GLU214 3.2 15.5 1.0 C B:PHE215 3.2 25.4 1.0 OE1 B:GLU209 3.4 33.5 1.0 N B:PHE215 3.6 26.4 1.0 CA B:PHE215 3.8 24.0 1.0 OP2 U:U66 3.8 54.4 1.0 OE1 B:GLU214 3.9 20.5 1.0 MN B:MN1003 4.0 52.0 1.0 CG B:ASP252 4.0 51.4 1.0 CB B:PHE215 4.2 25.0 1.0 CG B:GLU214 4.2 16.1 1.0 CD B:LYS216 4.2 33.5 1.0 O5' U:U66 4.2 56.3 1.0 CE B:LYS216 4.2 31.6 1.0 N B:LYS216 4.3 35.1 1.0 OD2 B:ASP252 4.4 52.8 1.0 C5' U:U66 4.4 55.4 1.0 NZ B:LYS216 4.5 34.0 1.0 CG B:GLU209 4.5 21.4 1.0 C B:GLU214 4.6 21.4 1.0 CA B:LYS216 4.7 31.7 1.0 CG B:LYS216 4.7 30.6 1.0 O3' T:C65 4.9 51.1 1.0 CA B:GLU214 5.0 13.6 1.0

Manganese binding site 3 out of 3 in the SLFN11 Dimer Bound to Trna-Met-Cat


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of SLFN11 Dimer Bound to Trna-Met-Cat within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1003 b:52.0 occ:1.00 OE1 B:GLU209 2.3 33.5 1.0 O3' T:C65 3.1 51.1 1.0 OP1 U:U66 3.1 53.5 1.0 CD B:GLU209 3.4 28.2 1.0 OE2 B:GLU209 3.9 28.2 1.0 O B:THR138 4.0 25.5 1.0 MN B:MN1002 4.0 30.2 1.0 OD2 B:ASP252 4.3 52.8 1.0 P U:U66 4.3 56.5 1.0 C3' T:C65 4.3 50.6 1.0 OE1 B:GLU214 4.4 20.5 1.0 OE2 B:GLU214 4.5 18.7 1.0 C4' T:C65 4.6 51.0 1.0 CB B:THR138 4.6 17.2 1.0 CG B:GLU209 4.6 21.4 1.0 OG1 B:THR138 4.6 21.4 1.0 O2' T:C65 4.6 47.1 1.0 CB B:GLU209 4.7 18.0 1.0 C5' U:U66 4.7 55.4 1.0 O5' U:U66 4.7 56.3 1.0 OD1 B:ASP252 4.8 54.5 1.0 OP2 U:U66 4.8 54.4 1.0 CD B:GLU214 4.9 15.5 1.0 CG B:ASP252 5.0 51.4 1.0 C5' T:C65 5.0 48.8 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