Magnesium in PDB 8wzc: Nyn Domain of Human Khnyn Complex with Rna

The structure of Nyn Domain of Human Khnyn Complex with Rna, PDB code: 8wzc was solved by S.Hong, J.Choe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.73 / 1.93
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	111.197, 111.197, 111.197, 90, 90, 90
R / Rfree (%)	18 / 20.9

The binding sites of Magnesium atom in the Nyn Domain of Human Khnyn Complex with Rna (pdb code 8wzc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Nyn Domain of Human Khnyn Complex with Rna, PDB code: 8wzc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Nyn Domain of Human Khnyn Complex with Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nyn Domain of Human Khnyn Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:27.4 occ:1.00 OD2 A:ASP566 2.1 37.7 1.0 O A:HOH821 2.1 59.2 1.0 OP1 D:A6 2.2 37.4 1.0 OD2 A:ASP584 2.2 34.4 1.0 OP2 D:U3 2.2 123.1 1.0 O D:HOH101 2.5 59.6 1.0 OH A:TYR564 3.0 44.6 1.0 CG A:ASP584 3.1 37.2 1.0 CG A:ASP566 3.2 33.2 1.0 OD1 A:ASP584 3.2 41.4 1.0 P D:U3 3.5 157.6 1.0 P D:A6 3.5 44.3 1.0 OD1 A:ASP566 3.6 32.8 1.0 O5' D:A6 3.9 47.1 1.0 CZ A:TYR564 3.9 42.0 1.0 O5' D:U3 3.9 160.4 1.0 CE1 A:TYR564 4.1 38.2 1.0 O A:HOH825 4.1 28.5 1.0 C5' D:A6 4.2 52.5 1.0 MG A:MG705 4.2 16.7 1.0 OP2 D:A6 4.3 43.7 1.0 CB A:ASP566 4.4 32.1 1.0 CB A:ASP584 4.5 32.9 1.0 OD1 A:ASP588 4.6 50.2 1.0 CD1 A:PHE586 4.6 39.4 1.0 O3' D:U5 4.7 42.6 1.0 OP1 D:U3 4.7 159.1 1.0 CE1 A:PHE586 4.8 39.2 1.0 OD2 A:ASP588 4.9 55.0 1.0 O A:HOH862 5.0 31.2 1.0

Magnesium binding site 2 out of 2 in the Nyn Domain of Human Khnyn Complex with Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nyn Domain of Human Khnyn Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:16.7 occ:1.00 OD1 A:ASP566 2.2 32.8 1.0 O A:HOH862 2.2 31.2 1.0 O3' D:U5 2.4 42.6 1.0 O A:HOH811 2.4 25.4 1.0 O A:HOH825 2.5 28.5 1.0 OD1 A:ASP565 2.5 26.9 1.0 OP1 D:A6 2.6 37.4 1.0 P D:A6 3.0 44.3 1.0 CG A:ASP566 3.3 33.2 1.0 CG A:ASP565 3.5 30.4 1.0 C3' D:U5 3.7 45.6 1.0 OD2 A:ASP565 3.8 28.1 1.0 OD2 A:ASP566 3.8 37.7 1.0 O5' D:A6 3.9 47.1 1.0 C4' D:U5 4.0 55.4 1.0 O2' D:U5 4.1 47.7 1.0 OD2 A:ASP584 4.2 34.4 1.0 MG A:MG704 4.2 27.4 1.0 OP2 D:A6 4.3 43.7 1.0 N A:ASP566 4.4 26.5 1.0 C2' D:U5 4.5 46.5 1.0 O A:HOH819 4.5 41.5 1.0 CB A:ASP566 4.5 32.1 1.0 OD1 A:ASP484 4.6 23.1 1.0 C5' D:U5 4.6 65.4 1.0 CE A:MET569 4.6 31.0 1.0 OD2 A:ASP484 4.6 25.9 1.0 CE1 A:TYR564 4.6 38.2 1.0 O A:HOH897 4.7 33.9 1.0 CA A:ASP566 4.8 27.5 1.0 CB A:ASP565 4.9 25.7 1.0 CG A:ASP484 5.0 24.8 1.0

S.Hong, J.Choe. Crystal Structure of Nyn Domain of Human Khnyn in Complex with Single Strand Rna. Biochem.Biophys.Res.Commun. V. 738 50545 2024.
ISSN: ESSN 1090-2104
PubMed: 39167961
DOI: 10.1016/J.BBRC.2024.150545