Magnesium in PDB 4pmw: Structure of Mouse DIS3L2 in Complex with Oligou Rna Substrate

The structure of Structure of Mouse DIS3L2 in Complex with Oligou Rna Substrate, PDB code: 4pmw was solved by C.R.Faehnle, J.Walleshauser, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.18 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.927, 96.075, 157.311, 90.00, 98.75, 90.00
R / Rfree (%)	20.2 / 25.1

The binding sites of Magnesium atom in the Structure of Mouse DIS3L2 in Complex with Oligou Rna Substrate (pdb code 4pmw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Mouse DIS3L2 in Complex with Oligou Rna Substrate, PDB code: 4pmw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Mouse DIS3L2 in Complex with Oligou Rna Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Mouse DIS3L2 in Complex with Oligou Rna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:37.9 occ:1.00 OD1 A:ASP381 2.2 50.4 1.0 OD2 A:ASP390 2.4 52.7 1.0 H A:ASP390 2.5 58.4 1.0 O A:HOH1002 2.6 20.0 1.0 OP1 C:U14 2.7 58.2 1.0 CG A:ASP390 2.8 51.0 1.0 O3' C:U13 3.0 47.0 1.0 OD1 A:ASP390 3.1 49.5 1.0 CG A:ASP381 3.1 49.2 1.0 H A:ASN389 3.1 50.8 1.0 OD2 A:ASP381 3.2 49.5 1.0 O A:ASP390 3.3 47.4 1.0 N A:ASP390 3.3 48.7 1.0 P C:U14 3.4 52.1 1.0 HA A:LEU388 3.7 55.6 1.0 N A:ASN389 3.7 42.4 1.0 CB A:ASP390 3.9 49.2 1.0 CA A:ASP390 3.9 47.9 1.0 HB3 A:LEU388 4.0 55.3 1.0 C A:ASP390 4.0 45.1 1.0 HB2 A:ASN389 4.0 52.1 1.0 O A:ILE380 4.1 41.1 1.0 HO2' C:U13 4.2 57.8 1.0 H4' C:U13 4.2 51.3 1.0 OP2 C:U14 4.2 47.3 1.0 H5'' C:U13 4.3 48.6 1.0 C3' C:U13 4.3 44.8 1.0 HB A:THR379 4.3 54.9 1.0 HB3 A:ASP390 4.4 59.1 1.0 C A:ASN389 4.4 46.3 1.0 CA A:LEU388 4.4 46.3 1.0 C A:LEU388 4.4 43.8 1.0 CA A:ASN389 4.5 42.6 1.0 CB A:ASP381 4.5 46.9 1.0 H A:ILE380 4.5 49.0 1.0 H5' C:U14 4.6 59.9 1.0 HB3 A:ASP381 4.6 56.2 1.0 C4' C:U13 4.6 42.8 1.0 O5' C:U14 4.7 48.6 1.0 HB2 A:ASP390 4.7 59.1 1.0 O2' C:U13 4.7 48.2 1.0 HD22 A:LEU388 4.7 52.6 1.0 CB A:LEU388 4.7 46.0 1.0 CB A:ASN389 4.7 43.4 1.0 C A:ILE380 4.9 40.7 1.0 HD22 A:ASN389 4.9 56.3 1.0 HA A:ASP390 4.9 57.5 1.0 H3' C:U13 4.9 53.8 1.0 C5' C:U13 5.0 40.5 1.0 HG22 A:THR379 5.0 57.3 1.0

Magnesium binding site 2 out of 2 in the Structure of Mouse DIS3L2 in Complex with Oligou Rna Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Mouse DIS3L2 in Complex with Oligou Rna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:51.5 occ:1.00 OD1 B:ASP381 2.0 54.8 1.0 OD2 B:ASP390 2.3 59.4 1.0 CG B:ASP390 2.7 60.4 1.0 O3' D:U13 2.7 53.1 1.0 OP1 D:U14 2.7 57.1 1.0 H B:ASP390 2.8 64.5 1.0 OD1 B:ASP390 2.8 61.0 1.0 CG B:ASP381 3.0 51.9 1.0 P D:U14 3.3 52.8 1.0 OD2 B:ASP381 3.4 50.9 1.0 H B:ASN389 3.5 52.1 1.0 O B:ASP390 3.5 56.1 1.0 N B:ASP390 3.6 53.8 1.0 O B:ILE380 3.6 41.2 1.0 HO2' D:U13 3.7 64.2 1.0 H4' D:U13 3.8 62.9 1.0 CB B:ASP390 3.9 57.6 1.0 C3' D:U13 4.0 51.9 1.0 HA B:LEU388 4.0 53.0 1.0 H5'' D:U13 4.1 62.9 1.0 CA B:ASP390 4.1 55.3 1.0 N B:ASN389 4.1 43.4 1.0 C B:ASP390 4.2 54.2 1.0 OP2 D:U14 4.2 51.9 1.0 O2' D:U13 4.2 53.5 1.0 C4' D:U13 4.3 52.4 1.0 H B:ILE380 4.3 53.5 1.0 HB2 B:ASN389 4.3 54.9 1.0 CB B:ASP381 4.3 48.9 1.0 HB3 B:LEU388 4.3 52.8 1.0 HB3 B:ASP390 4.4 69.1 1.0 HB B:THR379 4.4 67.1 1.0 HB3 B:ASP381 4.5 58.6 1.0 C B:ILE380 4.5 44.6 1.0 O5' D:U14 4.5 51.5 1.0 H5' D:U14 4.5 62.5 1.0 HB2 B:ASP390 4.6 69.1 1.0 HA B:ASP381 4.6 58.1 1.0 H3' D:U13 4.6 62.2 1.0 C B:ASN389 4.7 50.4 1.0 C2' D:U13 4.7 51.8 1.0 C5' D:U13 4.7 52.4 1.0 CA B:LEU388 4.7 44.2 1.0 C B:LEU388 4.8 42.1 1.0 HG11 B:VAL580 4.8 48.2 1.0 CA B:ASN389 4.8 46.0 1.0 HD22 B:LEU388 4.9 48.1 1.0 CA B:ASP381 4.9 48.4 1.0 N B:ILE380 5.0 44.6 1.0

C.R.Faehnle, J.Walleshauser, L.Joshua-Tor. Mechanism of DIS3L2 Substrate Recognition in the LIN28-Let-7 Pathway. Nature V. 514 252 2014.
ISSN: ESSN 1476-4687
PubMed: 25119025
DOI: 10.1038/NATURE13553