Magnesium in PDB 9nyy: Nucleic Acid Bound Human SLFN14, State 1

The structure of Nucleic Acid Bound Human SLFN14, State 1 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Nucleic Acid Bound Human SLFN14, State 1 (pdb code 9nyy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Nucleic Acid Bound Human SLFN14, State 1, PDB code: 9nyy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Nucleic Acid Bound Human SLFN14, State 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nucleic Acid Bound Human SLFN14, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:19.1 occ:1.00 O A:THR136 2.9 44.0 1.0 OE1 A:GLU211 3.0 41.1 1.0 OE1 A:GLU206 3.2 51.8 1.0 OE2 A:GLU211 3.2 45.2 1.0 CD A:GLU211 3.5 41.1 1.0 OP1 D:C7 3.6 2.0 1.0 C5' D:U6 3.8 6.8 1.0 C A:THR136 3.9 40.3 1.0 OP2 D:C7 3.9 5.2 1.0 OG1 A:THR136 4.0 55.9 1.0 P D:C7 4.1 2.3 1.0 OP1 D:U6 4.2 6.6 1.0 CD A:GLU206 4.2 52.5 1.0 MG A:MG1003 4.2 25.9 1.0 O3' D:U6 4.3 4.5 1.0 CG2 A:THR136 4.4 40.6 1.0 CA A:SER137 4.4 35.2 1.0 OE2 A:GLU206 4.5 53.7 1.0 C4' D:U6 4.5 5.3 1.0 N A:SER137 4.6 33.2 1.0 CB A:THR136 4.7 51.2 1.0 O5' D:U6 4.7 6.2 1.0 C3' D:U6 4.9 4.7 1.0 CA A:THR136 4.9 43.0 1.0 CG A:GLU211 5.0 37.9 1.0 CB A:SER137 5.0 38.2 1.0

Magnesium binding site 2 out of 3 in the Nucleic Acid Bound Human SLFN14, State 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nucleic Acid Bound Human SLFN14, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:25.9 occ:1.00 O A:PHE212 2.0 46.9 1.0 OP1 D:C7 2.4 2.0 1.0 C A:PHE212 3.1 52.4 1.0 CE A:LYS213 3.2 43.2 1.0 OE2 A:GLU211 3.2 45.2 1.0 OE2 A:GLU206 3.3 53.7 1.0 CD A:GLU211 3.5 41.1 1.0 P D:C7 3.7 2.3 1.0 NZ A:LYS213 3.8 55.7 1.0 N A:PHE212 3.8 40.8 1.0 CG A:GLU211 4.0 37.9 1.0 CD A:LYS213 4.0 43.5 1.0 OE1 A:GLU211 4.1 41.1 1.0 N A:LYS213 4.1 50.2 1.0 CA A:PHE212 4.1 46.7 1.0 C5' D:C7 4.1 4.0 1.0 CG A:LYS213 4.1 51.0 1.0 OP2 D:C7 4.2 5.2 1.0 CD A:GLU206 4.2 52.5 1.0 MG A:MG1002 4.2 19.1 1.0 CA A:LYS213 4.3 49.8 1.0 O5' D:C7 4.3 2.7 1.0 OE1 A:GLU206 4.4 51.8 1.0 CD1 A:PHE212 4.4 59.4 1.0 C4' D:C7 4.5 5.4 1.0 CB A:LYS213 4.8 55.9 1.0 C A:GLU211 4.8 42.9 1.0 O3' D:U6 4.9 4.5 1.0 CE1 A:PHE212 5.0 62.2 1.0 CG A:PHE212 5.0 60.7 1.0

Magnesium binding site 3 out of 3 in the Nucleic Acid Bound Human SLFN14, State 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nucleic Acid Bound Human SLFN14, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:18.2 occ:1.00 OE2 B:GLU211 2.2 38.6 1.0 CD B:GLU211 3.1 38.6 1.0 OE1 B:GLU211 3.3 51.5 1.0 OG1 B:THR136 3.4 61.7 1.0 O B:THR136 3.6 54.0 1.0 OE1 B:GLU206 4.0 70.9 1.0 C B:THR136 4.1 48.6 1.0 OE2 B:GLU206 4.1 65.8 1.0 CD B:GLU206 4.2 66.9 1.0 N B:SER137 4.4 42.7 1.0 CG B:GLU211 4.5 34.3 1.0 OH B:TYR231 4.5 36.0 1.0 CA B:SER137 4.6 37.0 1.0 CB B:THR136 4.7 55.6 1.0 CA B:THR136 4.9 51.1 1.0

J.Van Riper, A.O.Martinez-Claros, L.Wang, H.E.Schneiderman, S.Maheshwari, M.C.Pillon. Cryoem Structure of the SLFN14 Endoribonuclease Reveals Insight Into Rna Binding and Cleavage Nat Commun V. 16 5848 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-025-61091-8