Sodium in PDB 9f8x: Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase

All present enzymatic activity of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase:
1.7.2.4;

The structure of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase, PDB code: 9f8x was solved by O.Einsle, A.Pomowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.50 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	65.26, 69.375, 153.188, 81.38, 77.92, 88.61
R / Rfree (%)	13 / 15.2

The structure of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase also contains other interesting chemical elements:

Calcium	(Ca)	8 atoms
Chlorine	(Cl)	4 atoms
Copper	(Cu)	24 atoms

The binding sites of Sodium atom in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase (pdb code 9f8x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase, PDB code: 9f8x:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na706 b:26.3 occ:1.00 O B:HOH1447 2.3 32.4 1.0 OD2 B:ASP353 2.3 21.9 1.0 O B:HOH1381 2.3 25.6 1.0 O B:HOH1402 2.7 27.6 1.0 CG B:ASP353 3.3 20.2 1.0 NA B:NA707 3.6 25.2 1.0 CB B:ASP353 3.7 18.0 1.0 O B:HOH946 4.0 29.1 1.0 O B:HOH1278 4.0 34.8 1.0 O B:HOH1009 4.0 24.4 1.0 O B:HOH1431 4.4 30.7 1.0 O B:HOH1133 4.4 19.8 1.0 OD1 B:ASP353 4.5 19.8 1.0 O B:HOH1481 4.5 29.3 1.0 O B:HOH1542 4.6 39.3 1.0 O B:HOH1092 4.8 19.3 1.0

Sodium binding site 2 out of 3 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na707 b:25.2 occ:1.00 O B:HOH1402 2.5 27.6 1.0 O B:HOH1009 2.5 24.4 1.0 O B:HOH1609 2.5 26.4 1.0 NA B:NA708 3.6 26.5 1.0 NA B:NA706 3.6 26.3 1.0 OD2 B:ASP353 3.9 21.9 1.0 O B:HOH1259 4.0 26.0 1.0 O B:HOH1481 4.0 29.3 1.0 O B:HOH1431 4.3 30.7 1.0 O B:HOH1307 4.5 31.3 1.0

Sodium binding site 3 out of 3 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na708 b:26.5 occ:1.00 O B:HOH1625 2.3 44.1 1.0 O B:HOH1481 2.4 29.3 1.0 O B:HOH846 2.4 24.4 1.0 O B:HOH1009 2.4 24.4 1.0 O B:HOH1307 2.7 31.3 1.0 NA B:NA707 3.6 25.2 1.0 O B:HOH1477 4.0 51.4 1.0 NZ B:LYS250 4.2 19.6 1.0 OE1 B:GLU282 4.5 31.1 1.0 OD2 B:ASP353 4.5 21.9 1.0 O B:HOH1613 4.5 46.9 1.0 O B:HOH1259 4.5 26.0 1.0 OE2 B:GLU282 4.5 33.7 1.0 CD B:LYS250 4.6 18.0 1.0 O B:HOH1396 4.7 27.4 1.0 O B:HOH1609 4.8 26.4 1.0 CD B:GLU282 4.9 24.4 1.0 CE B:LYS250 4.9 17.2 1.0

A.Pomowski, S.Dell'acqua, A.Wust, S.R.Pauleta, I.Moura, O.Einsle. Revisiting the Metal Sites of Nitrous Oxide Reductase in A Low-Dose Structure From Marinobacter Nauticus. J.Biol.Inorg.Chem. V. 29 279 2024.
ISSN: ESSN 1432-1327
PubMed: 38720157
DOI: 10.1007/S00775-024-02056-Y