Sodium in PDB 7ehf: Crystal Structure of the Aminoglycoside Resistance Methyltransferase NPMB1

The structure of Crystal Structure of the Aminoglycoside Resistance Methyltransferase NPMB1, PDB code: 7ehf was solved by A.Kawai, Y.Doi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.84 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.738, 65.798, 65.806, 90, 90, 90
R / Rfree (%)	16.6 / 19.4

The structure of Crystal Structure of the Aminoglycoside Resistance Methyltransferase NPMB1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase NPMB1 (pdb code 7ehf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase NPMB1, PDB code: 7ehf:

Sodium binding site 1 out of 1 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase NPMB1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase NPMB1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:23.3 occ:0.95 O A:LEU32 2.8 17.9 1.0 OD1 A:ASP31 2.8 16.4 1.0 N A:ASN105 2.8 14.4 1.0 O A:HOH440 3.1 17.3 1.0 O A:HOH526 3.2 21.5 0.7 O A:GLY33 3.5 16.7 1.0 CG A:ASP31 3.5 15.9 1.0 O A:ASN105 3.6 17.2 1.0 C A:LEU32 3.7 18.9 1.0 OD2 A:ASP31 3.7 17.4 1.0 CB A:ASN105 3.7 15.7 1.0 CA A:VAL104 3.7 14.3 1.0 CA A:ASN105 3.7 15.6 1.0 C A:GLY33 3.7 13.9 1.0 C A:VAL104 3.7 15.2 1.0 O A:THR103 3.8 15.5 1.0 ND2 A:ASN105 3.9 17.9 1.0 N A:LEU32 4.0 14.2 1.0 CG A:ASN105 4.1 18.3 1.0 C A:ASN105 4.1 17.7 1.0 N A:THR34 4.1 14.4 1.0 CA A:THR34 4.2 14.6 1.0 CA A:GLY33 4.3 15.5 1.0 C A:THR103 4.3 15.3 1.0 N A:VAL104 4.3 14.5 1.0 N A:GLY33 4.4 15.5 1.0 C A:ASP31 4.4 13.4 1.0 CA A:LEU32 4.5 14.6 1.0 CB A:ASP31 4.7 14.5 1.0 CA A:ASP31 4.8 13.2 1.0 OG1 A:THR103 4.9 17.1 1.0 O A:VAL104 4.9 16.3 1.0 CB A:VAL104 4.9 14.6 1.0 OD1 A:ASN105 5.0 19.3 1.0

A.Kawai, M.Suzuki, K.Tsukamoto, Y.Minato, Y.Doi. Functional and Structural Characterization of Acquired Pan-Aminoglycoside Resistance 16S Rrna Methyltransferase NPMB1. Antimicrob.Agents Chemother. 00921 2021.
ISSN: ESSN 1098-6596
PubMed: 34310216
DOI: 10.1128/AAC.01009-21