Magnesium in PDB 8rza: Ribonuclease W

The structure of Ribonuclease W, PDB code: 8rza was solved by M.Vayssieres, M.Blaud, N.Leulliot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 2.10
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.62, 120.62, 93.84, 90, 90, 120
R / Rfree (%)	21.2 / 24.4

The binding sites of Magnesium atom in the Ribonuclease W (pdb code 8rza). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ribonuclease W, PDB code: 8rza:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ribonuclease W


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ribonuclease W within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:83.5 occ:1.00 OP2 B:U3 2.4 59.0 1.0 OD2 A:ASP437 2.6 85.0 1.0 OD1 A:ASP364 2.8 57.3 1.0 OD2 A:ASP364 3.3 59.5 1.0 O3' B:A2 3.4 70.8 1.0 CG A:ASP364 3.4 56.1 1.0 O B:HOH105 3.4 58.4 1.0 P B:U3 3.4 59.4 1.0 OD2 A:ASP424 3.7 53.3 1.0 CG A:ASP437 3.7 79.2 1.0 OP1 B:U3 4.1 57.5 1.0 OD1 A:ASP437 4.2 95.5 1.0 O B:HOH103 4.3 61.6 1.0 O5' B:U3 4.8 51.1 1.0 C3' B:A2 4.8 65.7 1.0 CG A:ASP424 4.9 44.6 1.0 CB A:ASP364 4.9 52.6 1.0 CB A:ASP437 4.9 59.5 1.0

Magnesium binding site 2 out of 2 in the Ribonuclease W


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ribonuclease W within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:43.0 occ:1.00 O5' B:U3 2.0 51.1 1.0 O A:HOH604 2.2 45.7 1.0 OD1 A:ASP424 2.2 43.1 1.0 OD1 A:ASP420 2.2 40.4 1.0 OD1 A:ASN404 2.3 38.7 1.0 CG A:ASN404 3.0 36.2 1.0 CG A:ASP420 3.1 41.6 1.0 OD2 A:ASP420 3.2 39.2 1.0 CG A:ASP424 3.3 44.6 1.0 ND2 A:ASN404 3.4 34.1 1.0 P B:U3 3.4 59.4 1.0 OD2 A:ASP424 3.7 53.3 1.0 OP2 B:U3 3.7 59.0 1.0 CE1 A:HIS326 4.0 45.9 1.0 O A:GLU422 4.1 49.5 1.0 OP1 B:U3 4.1 57.5 1.0 CB A:ASN404 4.2 36.0 1.0 O A:VAL423 4.3 34.9 1.0 O A:ILE405 4.3 33.7 1.0 CA A:ASN404 4.4 33.7 1.0 N A:ILE405 4.4 33.1 1.0 C A:GLU422 4.4 44.6 1.0 O3' B:A2 4.5 70.8 1.0 N A:GLU422 4.5 38.6 1.0 CB A:ASP420 4.5 39.8 1.0 CE1 A:PHE402 4.5 40.2 1.0 NE2 A:HIS326 4.5 45.9 1.0 CB A:ASP424 4.6 42.1 1.0 CA A:GLU422 4.6 43.6 1.0 CZ A:PHE402 4.7 44.9 1.0 C A:VAL423 4.8 41.0 1.0 C3' B:A2 4.9 65.7 1.0 O A:HOH677 4.9 43.2 1.0 C A:ASN404 5.0 34.5 1.0

M.Vayssieres, M.Juttner, K.Haas, A.Ancelin, A.Marchfelder, N.Leulliot, S.Ferreira-Cerca, M.Blaud. Rnase W, A Conserved Ribonuclease Family with A Novel Active Site. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 39445822
DOI: 10.1093/NAR/GKAE907