Magnesium in PDB 8rzf: Rnase W From Sulfolobus Acidocaldarius

The structure of Rnase W From Sulfolobus Acidocaldarius, PDB code: 8rzf 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)	28.30 / 2.04
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	76.23, 76.23, 84.64, 90, 90, 90
R / Rfree (%)	19.2 / 21.4

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

Magnesium binding site 1 out of 2 in the Rnase W From Sulfolobus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rnase W From Sulfolobus Acidocaldarius within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:30.0 occ:1.00 OD1 A:ASP371 2.1 37.4 1.0 O A:HOH641 2.2 37.0 1.0 OD1 A:ASP367 2.2 23.4 1.0 OD1 A:ASN351 2.4 30.1 1.0 CG A:ASP371 3.0 35.9 1.0 CG A:ASP367 3.1 28.9 1.0 OD2 A:ASP371 3.2 44.0 1.0 OD2 A:ASP367 3.3 29.7 1.0 CG A:ASN351 3.4 26.5 1.0 O A:HOH601 3.8 38.3 1.0 ND2 A:ASN351 4.0 25.0 1.0 O A:HOH817 4.0 31.8 1.0 O A:GLU369 4.1 26.0 1.0 OH A:TYR349 4.2 38.1 1.0 O A:VAL370 4.2 24.7 1.0 O A:ILE352 4.2 23.3 1.0 N A:ILE352 4.3 23.6 1.0 NE2 A:HIS271 4.3 30.8 1.0 CA A:ASN351 4.4 21.2 1.0 CB A:ASN351 4.4 23.0 1.0 C A:GLU369 4.4 25.0 1.0 CB A:ASP371 4.5 25.4 1.0 N A:GLU369 4.5 21.8 1.0 CB A:ASP367 4.6 23.3 1.0 CA A:GLU369 4.6 26.3 1.0 CE1 A:TYR349 4.6 32.2 1.0 C A:ASN351 4.7 27.2 1.0 C A:VAL370 4.8 26.4 1.0 CZ A:TYR349 4.9 43.3 1.0 CD2 A:HIS271 5.0 27.9 1.0

Magnesium binding site 2 out of 2 in the Rnase W From Sulfolobus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rnase W From Sulfolobus Acidocaldarius within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.0 occ:1.00 O A:HOH601 2.6 38.3 1.0 O A:HOH817 2.8 31.8 1.0 O A:HOH627 3.1 34.6 1.0 OD2 A:ASP383 3.2 52.3 1.0 O A:HOH831 3.2 53.8 1.0 O A:HOH641 3.7 37.0 1.0 OD2 A:ASP371 3.9 44.0 1.0 CG A:ASP383 4.0 47.6 1.0 OH A:TYR349 4.2 38.1 1.0 OD1 A:ASP383 4.5 49.9 1.0 O A:GLU369 4.8 26.0 1.0 CB A:ASP383 5.0 29.3 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