Sodium in PDB 9azh: Native Nnha in P1

All present enzymatic activity of Native Nnha in P1:
3.5.99.9;

The structure of Native Nnha in P1, PDB code: 9azh was solved by T.S.Peat, J.Newman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.09 / 2.04
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.727, 117.377, 121.125, 117.14, 91.3, 101.38
R / Rfree (%)	15.6 / 17.9

The structure of Native Nnha in P1 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Native Nnha in P1 (pdb code 9azh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Native Nnha in P1, PDB code: 9azh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Native Nnha in P1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Native Nnha in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:26.3 occ:1.00 O A:HOH795 2.4 15.1 1.0 O A:GLN242 2.6 13.3 1.0 OD2 A:ASP281 2.8 23.2 1.0 OD1 A:ASP281 3.0 24.6 1.0 CG A:ASP281 3.3 20.0 1.0 O A:HOH737 3.3 28.9 1.0 CB A:ALA284 3.8 10.4 1.0 N A:ALA284 3.8 10.5 1.0 C A:GLN242 3.8 10.8 1.0 CG A:ARG244 3.8 23.8 1.0 CA A:ALA284 4.1 10.5 1.0 CB A:ASP283 4.2 16.2 1.0 CA A:LEU243 4.3 9.5 1.0 O A:HOH730 4.3 13.4 1.0 CD A:ARG244 4.4 29.4 1.0 N A:LEU243 4.5 9.6 1.0 C A:ASP283 4.5 11.6 1.0 C A:LEU243 4.7 9.8 1.0 CB A:ASP281 4.8 17.0 1.0 N A:ARG244 4.8 10.8 1.0 CA A:ASP283 4.8 13.5 1.0 NH1 C:ARG244 4.9 44.5 1.0 CA A:GLN242 4.9 11.4 1.0 O A:HOH503 4.9 21.1 1.0 O C:HOH540 4.9 23.6 1.0 N A:GLN242 5.0 9.4 1.0

Sodium binding site 2 out of 3 in the Native Nnha in P1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Native Nnha in P1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:44.0 occ:1.00 O B:HOH563 2.4 20.7 1.0 O B:HOH670 2.7 20.3 1.0 O B:ALA267 3.0 11.3 1.0 O B:HOH711 3.1 25.7 1.0 OD1 B:ASN266 3.2 18.5 1.0 N B:ALA267 3.3 9.9 1.0 CB B:LEU314 3.6 14.0 1.0 CB B:ALA267 3.7 10.3 1.0 CA B:ALA267 3.7 10.8 1.0 C B:ALA267 3.8 11.3 1.0 CG B:ASN266 3.9 16.7 1.0 CB B:ASN266 4.0 13.6 1.0 O B:MET203 4.1 12.4 1.0 CD2 B:LEU314 4.1 18.3 1.0 C B:ASN266 4.1 10.7 1.0 O B:HOH608 4.2 31.7 1.0 CA B:ASN266 4.3 11.5 1.0 CG B:LEU314 4.4 15.6 1.0 NZ B:LYS356 4.5 29.9 1.0 O B:HOH698 4.6 20.8 1.0 N B:LEU314 4.6 11.6 1.0 CA B:LEU314 4.8 13.5 1.0 CG2 B:ILE60 4.8 10.0 1.0 O B:VAL312 4.9 13.3 1.0

Sodium binding site 3 out of 3 in the Native Nnha in P1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Native Nnha in P1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:23.4 occ:1.00 O C:HOH764 2.5 23.1 1.0 O C:GLN242 2.7 14.1 1.0 OD2 C:ASP281 2.8 25.6 1.0 OD1 C:ASP281 3.1 28.1 1.0 CG C:ASP281 3.3 21.5 1.0 O C:HOH578 3.3 29.5 1.0 N C:ALA284 3.7 10.2 1.0 CB C:ALA284 3.7 10.2 1.0 C C:GLN242 3.8 13.0 1.0 CA C:ALA284 4.0 10.2 1.0 CB C:ASP283 4.1 16.1 1.0 CD C:ARG244 4.2 29.5 1.0 O C:HOH698 4.3 11.9 1.0 CA C:LEU243 4.4 12.2 1.0 O C:HOH664 4.4 28.8 1.0 CG C:ARG244 4.4 22.9 1.0 C C:ASP283 4.4 11.5 1.0 N C:LEU243 4.5 11.8 1.0 NE C:ARG244 4.7 37.9 1.0 CA C:ASP283 4.7 13.2 1.0 CB C:ASP281 4.8 17.3 1.0 C C:LEU243 4.8 12.2 1.0 NH1 A:ARG244 4.8 42.6 1.0 N C:ARG244 4.8 12.3 1.0 O C:HOH530 4.9 30.2 1.0 CA C:GLN242 4.9 14.1 1.0 N C:GLN242 5.0 11.9 1.0 O C:HOH502 5.0 21.9 1.0

F.H.Ahmed, J.W.Liu, S.Royan, A.C.Warden, L.Esquirol, G.Pandey, J.Newman, C.Scott, T.S.Peat. Structural Insights Into the Enzymatic Breakdown of Azomycin-Derived Antibiotics By 2-Nitroimdazole Hydrolase (Nnha). Commun Biol V. 7 1676 2024.
ISSN: ESSN 2399-3642
PubMed: 39702827
DOI: 10.1038/S42003-024-07336-6