Magnesium in PDB 5zw3: Crystal Structure of Trmr From B. Subtilis

The structure of Crystal Structure of Trmr From B. Subtilis, PDB code: 5zw3 was solved by J.Kim, H.Ryu, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.27
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	76.874, 116.738, 43.437, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26.6

The binding sites of Magnesium atom in the Crystal Structure of Trmr From B. Subtilis (pdb code 5zw3). 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 Trmr From B. Subtilis, PDB code: 5zw3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Trmr From B. Subtilis


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 Trmr From B. Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:33.5 occ:1.00 O A:HOH413 1.9 32.3 1.0 OD2 A:ASP159 2.1 35.3 1.0 O A:HOH406 2.1 34.5 1.0 OD1 A:ASP133 2.2 36.3 1.0 O A:HOH414 2.2 27.8 1.0 OD1 A:ASN160 2.3 42.0 1.0 CG A:ASP133 3.1 36.1 1.0 CG A:ASN160 3.1 42.9 1.0 CG A:ASP159 3.2 34.5 1.0 OD2 A:ASP133 3.3 37.6 1.0 ND2 A:ASN160 3.4 43.0 1.0 CB A:ASP159 3.7 34.5 1.0 O A:HOH421 3.9 43.9 1.0 O A:PRO36 4.1 36.2 1.0 O A:HOH408 4.2 33.5 1.0 OD1 A:ASP159 4.2 37.8 1.0 CB A:ASP133 4.5 34.5 1.0 CB A:ASN160 4.5 40.0 1.0 C A:ASP159 4.8 35.6 1.0 O A:ASP133 4.8 35.6 1.0 N A:ASN160 4.9 38.8 1.0 CA A:ASP159 4.9 34.4 1.0 CA A:ASP133 4.9 34.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Trmr From B. Subtilis


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 Trmr From B. Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:36.6 occ:1.00 O B:HOH408 2.1 31.9 1.0 O B:HOH404 2.1 31.2 1.0 OD2 B:ASP159 2.1 32.5 1.0 OD1 B:ASP133 2.2 34.0 1.0 O B:HOH421 2.2 26.3 1.0 OD1 B:ASN160 2.4 51.3 1.0 ND2 B:ASN160 2.6 42.8 1.0 CG B:ASN160 2.8 45.2 1.0 CG B:ASP159 3.2 34.0 1.0 CG B:ASP133 3.2 37.5 1.0 OD2 B:ASP133 3.5 36.0 1.0 CB B:ASP159 3.8 33.2 1.0 OD1 B:ASP159 4.2 35.4 1.0 O B:PRO36 4.2 33.0 1.0 CB B:ASN160 4.3 41.3 1.0 OD2 B:ASP208 4.4 67.3 1.0 O B:HOH406 4.5 38.8 1.0 N B:ASN160 4.6 36.5 1.0 CB B:ASP133 4.6 35.7 1.0 C B:ASP159 4.6 33.0 1.0 CA B:ASP159 4.9 32.6 1.0 O B:ASP133 4.9 36.8 1.0 CA B:ASN160 4.9 39.9 1.0 CA B:ASP133 4.9 34.4 1.0

H.Ryu, T.L.Grove, S.C.Almo, J.Kim. Identification of A Novel Trna Wobble Uridine Modifying Activity in the Biosynthesis of 5-Methoxyuridine. Nucleic Acids Res. V. 46 9160 2018.
ISSN: ESSN 1362-4962
PubMed: 29982645
DOI: 10.1093/NAR/GKY592