Magnesium in PDB 6f3h: Crystal Structure of DSS1 Exoribonuclease Active Site Mutant D477N From Candida Glabrata

The structure of Crystal Structure of DSS1 Exoribonuclease Active Site Mutant D477N From Candida Glabrata, PDB code: 6f3h was solved by M.Razew, E.Nowak, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.21 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	73.370, 83.230, 110.370, 106.21, 106.56, 90.93
R / Rfree (%)	19.6 / 24

The binding sites of Magnesium atom in the Crystal Structure of DSS1 Exoribonuclease Active Site Mutant D477N From Candida Glabrata (pdb code 6f3h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of DSS1 Exoribonuclease Active Site Mutant D477N From Candida Glabrata, PDB code: 6f3h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of DSS1 Exoribonuclease Active Site Mutant D477N From Candida Glabrata


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of DSS1 Exoribonuclease Active Site Mutant D477N From Candida Glabrata within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:0.9 occ:1.00 OD1 A:ASP469 1.8 0.3 1.0 O A:HOH1102 2.0 0.8 1.0 O A:HOH1101 2.0 0.5 1.0 CG A:ASP469 2.2 0.1 1.0 OD2 A:ASP469 2.2 0.6 1.0 OD1 A:ASP478 2.3 1.0 1.0 OD2 A:ASP478 2.8 0.7 1.0 CG A:ASP478 2.9 95.2 1.0 O3' C:A4 3.0 43.5 1.0 OP1 C:C5 3.4 45.2 1.0 CB A:ASP469 3.5 93.3 1.0 O A:ILE468 3.5 62.5 1.0 O2' C:A4 3.6 45.0 1.0 P C:C5 3.9 42.5 1.0 C A:ILE468 4.0 55.5 1.0 C3' C:A4 4.1 42.1 1.0 CA A:ASP469 4.1 78.5 1.0 C5' C:C5 4.2 47.9 1.0 N A:ASP469 4.3 66.5 1.0 C4' C:A4 4.3 45.4 1.0 O A:HOH1115 4.4 47.6 1.0 C2' C:A4 4.4 44.8 1.0 O A:ASP478 4.4 55.2 1.0 CG2 A:ILE476 4.4 50.3 1.0 CB A:ASP478 4.4 66.8 1.0 O5' C:C5 4.6 49.0 1.0 N A:ILE468 4.6 50.6 1.0 N A:ASP478 4.8 50.4 1.0 N A:ASN477 4.9 48.2 1.0 OH A:TYR595 4.9 46.8 1.0 C A:CYS467 5.0 53.2 1.0 CA A:ILE476 5.0 53.5 1.0 CA A:ILE468 5.0 49.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of DSS1 Exoribonuclease Active Site Mutant D477N From Candida Glabrata


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of DSS1 Exoribonuclease Active Site Mutant D477N From Candida Glabrata within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:0.7 occ:1.00 O B:HOH1104 2.1 99.5 1.0 OD1 B:ASP469 2.1 96.7 1.0 OD1 B:ASP478 2.2 80.9 1.0 OD2 B:ASP469 2.4 96.1 1.0 CG B:ASP469 2.6 91.2 1.0 O3' D:G4 2.9 53.8 1.0 OP1 D:A5 3.0 48.3 1.0 CG B:ASP478 3.3 71.5 1.0 P D:A5 3.5 48.9 1.0 OD2 B:ASP478 3.7 75.8 1.0 O2' D:G4 3.9 53.2 1.0 C3' D:G4 4.0 47.6 1.0 C5' D:A5 4.0 49.5 1.0 O B:ASP478 4.1 52.5 1.0 CB B:ASP469 4.1 81.0 1.0 N B:ASP478 4.2 47.1 1.0 N B:ASN477 4.3 42.4 1.0 O5' D:A5 4.3 51.2 1.0 O B:ILE468 4.3 61.4 1.0 C4' D:G4 4.4 50.6 1.0 CG2 B:ILE476 4.4 53.3 1.0 C2' D:G4 4.6 51.0 1.0 CB B:ASP478 4.6 55.8 1.0 O B:HOH1119 4.6 54.0 1.0 CA B:ILE476 4.7 49.7 1.0 OP2 D:A5 4.8 56.2 1.0 CA B:ASP478 4.8 50.1 1.0 C B:ILE468 4.8 58.1 1.0 CA B:ASP469 4.8 69.6 1.0 C B:ASP478 4.8 50.0 1.0 C B:ILE476 5.0 42.8 1.0

M.Razew, Z.Warkocki, M.Taube, A.Kolondra, M.Czarnocki-Cieciura, E.Nowak, K.Labedzka-Dmoch, A.Kawinska, J.Piatkowski, P.Golik, M.Kozak, A.Dziembowski, M.Nowotny. Structural Analysis of Mtexo Mitochondrial Rna Degradosome Reveals Tight Coupling of Nuclease and Helicase Components. Nat Commun V. 9 97 2018.
ISSN: ESSN 2041-1723
PubMed: 29311576
DOI: 10.1038/S41467-017-02570-5