Sodium in PDB 7r8p: Open Form of SAOUHSC_02373 in Complex with Adp, MG2+ and Na+

The structure of Open Form of SAOUHSC_02373 in Complex with Adp, MG2+ and Na+, PDB code: 7r8p was solved by J.L.Pederick, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.45 / 1.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.258, 70.581, 109.773, 90, 90, 90
R / Rfree (%)	19 / 21.5

The structure of Open Form of SAOUHSC_02373 in Complex with Adp, MG2+ and Na+ also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the Open Form of SAOUHSC_02373 in Complex with Adp, MG2+ and Na+ (pdb code 7r8p). 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 Open Form of SAOUHSC_02373 in Complex with Adp, MG2+ and Na+, PDB code: 7r8p:

Sodium binding site 1 out of 1 in the Open Form of SAOUHSC_02373 in Complex with Adp, MG2+ and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Open Form of SAOUHSC_02373 in Complex with Adp, MG2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:20.1 occ:0.81 O A:HOH651 2.3 23.7 1.0 OD1 A:ASP301 2.3 23.0 1.0 O A:HOH638 2.4 25.6 1.0 O A:HOH713 2.4 28.7 1.0 OD1 A:ASN303 2.5 21.5 1.0 O A:LEU302 2.6 20.7 1.0 CG A:ASP301 3.4 22.4 1.0 CG A:ASN303 3.4 20.3 1.0 C A:LEU302 3.4 17.9 1.0 O A:HOH501 3.4 24.7 1.0 OD2 A:ASP301 3.7 23.7 1.0 O A:HOH703 3.8 23.4 1.0 CA A:ASN303 3.9 16.4 1.0 NH2 A:ARG305 4.0 32.2 0.6 N A:ASN303 4.0 16.3 1.0 N A:LEU302 4.1 16.6 1.0 ND2 A:ASN303 4.1 22.4 1.0 CB A:ASN303 4.2 17.2 1.0 O A:HOH778 4.3 39.3 1.0 O A:HOH840 4.4 38.4 1.0 CA A:LEU302 4.4 16.6 1.0 CE A:LYS136 4.5 24.1 1.0 O A:ASN134 4.6 21.3 1.0 OD1 A:ASN134 4.6 18.2 1.0 O2B A:ADP401 4.6 29.0 1.0 C A:ASP301 4.6 17.1 1.0 CB A:ASP301 4.7 19.4 1.0 NE A:ARG305 4.7 29.6 0.6 CZ A:ARG305 4.8 33.9 0.6 CA A:ASP301 4.8 17.3 1.0

J.L.Pederick, A.J.Horsfall, B.Jovcevski, J.Klose, A.D.Abell, T.L.Pukala, J.B.Bruning. Discovery of An ʟ-Amino Acid Ligase Implicated in Staphylococcal Sulfur Amino Acid Metabolism. J.Biol.Chem. V. 298 02392 2022.
ISSN: ESSN 1083-351X
PubMed: 35988643
DOI: 10.1016/J.JBC.2022.102392