Sodium in PDB 8sm7: Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe

The structure of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe, PDB code: 8sm7 was solved by C.Liu, J.Rittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.78 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	127.369, 127.369, 217.84, 90, 90, 90
R / Rfree (%)	19.9 / 24.2

The structure of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Sodium atom in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe (pdb code 8sm7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe, PDB code: 8sm7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:46.4 occ:1.00 O B:HOH555 2.4 51.6 1.0 O B:GLY192 2.7 37.8 1.0 O B:SER194 2.9 34.1 1.0 OH G:TYR202 3.0 40.7 1.0 OH B:TYR202 3.2 44.4 1.0 CZ G:TYR202 3.5 40.7 1.0 CE1 G:TYR202 3.7 36.0 1.0 C B:GLY192 3.7 38.5 1.0 CA B:SER193 3.8 35.5 1.0 O B:GLY190 3.8 40.9 1.0 C B:SER193 3.8 35.5 1.0 N B:SER194 3.9 34.5 1.0 C B:SER194 4.0 35.8 1.0 N B:SER193 4.1 35.1 1.0 O B:SER193 4.4 35.5 1.0 O B:GLY191 4.4 36.4 1.0 CE2 G:TYR202 4.5 37.4 1.0 CZ B:TYR202 4.6 36.6 1.0 C B:GLY190 4.6 37.1 1.0 CA B:SER194 4.6 35.2 1.0 C B:GLY191 4.7 38.0 1.0 CD1 G:TYR202 4.8 33.5 1.0 O G:GLY190 4.8 38.9 1.0 CA B:GLY192 4.9 35.8 1.0 OG B:SER194 4.9 37.0 1.0 N B:GLY192 5.0 34.3 1.0

Sodium binding site 2 out of 3 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ G:Na403 b:51.8 occ:1.00 O G:LEU117 2.4 52.1 1.0 O G:HIS120 2.6 54.3 1.0 O G:PHE123 2.8 46.5 1.0 OD2 G:ASP149 3.4 52.7 1.0 OD1 G:ASP149 3.5 45.8 1.0 CG G:ASP149 3.5 46.2 1.0 C G:LEU117 3.6 46.2 1.0 C G:HIS120 3.6 54.4 1.0 CA G:LYS121 3.8 49.6 1.0 O G:LYS121 3.8 51.6 1.0 C G:PHE123 3.9 48.7 1.0 C G:LYS121 4.0 48.4 1.0 N G:LYS121 4.2 46.2 1.0 N G:PHE123 4.2 49.1 1.0 CB G:PHE123 4.3 42.5 1.0 CA G:LEU117 4.3 44.7 1.0 CA G:PHE123 4.3 45.7 1.0 CB G:ASP149 4.5 43.9 1.0 N G:GLY118 4.6 43.0 1.0 CB G:LEU117 4.7 41.6 1.0 CA G:GLY118 4.7 50.2 1.0 N G:HIS120 4.7 53.6 1.0 N G:ALA122 4.8 45.0 1.0 CA G:HIS120 4.8 50.6 1.0 NZ G:LYS124 4.9 41.5 1.0 CE G:LYS124 4.9 40.5 1.0

Sodium binding site 3 out of 3 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ G:Na404 b:49.8 occ:1.00 O G:HOH576 2.2 48.8 1.0 O G:HOH618 2.3 49.7 1.0 O G:HIS147 2.3 41.8 1.0 O G:ILE150 2.5 46.0 1.0 O G:GLY145 2.5 44.9 1.0 C G:HIS147 3.4 45.2 1.0 C G:GLY146 3.5 40.5 1.0 C G:ILE150 3.6 42.7 1.0 C G:GLY145 3.6 45.7 1.0 O G:GLY146 3.7 44.7 1.0 N G:HIS147 3.8 42.8 1.0 CA G:GLY146 3.9 38.4 1.0 CB G:ILE150 4.0 42.4 1.0 N G:ILE150 4.0 43.7 1.0 CA G:ILE150 4.1 38.8 1.0 CD2 G:LEU180 4.1 36.1 1.0 CA G:HIS147 4.2 40.9 1.0 N G:GLY146 4.2 42.0 1.0 N G:PRO148 4.3 47.9 1.0 CA G:PRO148 4.3 45.6 1.0 C G:PRO148 4.4 45.7 1.0 O G:PRO148 4.5 45.3 1.0 O G:HOH622 4.5 50.3 1.0 CG2 G:ILE150 4.7 42.7 1.0 N G:VAL151 4.7 38.5 1.0 CA G:GLY145 4.8 42.6 1.0 N G:ASP149 4.9 45.6 1.0

C.Liu, M.M.Powell, G.Rao, R.D.Britt, J.Rittle. Bioinformatic Discovery of A Cambialistic Monooxygenase. J.Am.Chem.Soc. V. 146 1783 2024.
ISSN: ESSN 1520-5126
PubMed: 38198693
DOI: 10.1021/JACS.3C12131