Sodium in PDB 7bj3: Scpa From Streptococcus Pyogenes, S512A Active Site Mutant

All present enzymatic activity of Scpa From Streptococcus Pyogenes, S512A Active Site Mutant:
3.4.21.110;

The structure of Scpa From Streptococcus Pyogenes, S512A Active Site Mutant, PDB code: 7bj3 was solved by T.F.Kagawa, M.R.O'connell, J.C.Cooney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.24 / 2.60
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	167.39, 167.39, 141.84, 90, 90, 120
R / Rfree (%)	20.6 / 26.5

The structure of Scpa From Streptococcus Pyogenes, S512A Active Site Mutant also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Scpa From Streptococcus Pyogenes, S512A Active Site Mutant (pdb code 7bj3). 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 Scpa From Streptococcus Pyogenes, S512A Active Site Mutant, PDB code: 7bj3:

Sodium binding site 1 out of 1 in the Scpa From Streptococcus Pyogenes, S512A Active Site Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Scpa From Streptococcus Pyogenes, S512A Active Site Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:13.3 occ:1.00 OG A:SER703 2.4 17.0 1.0 O A:MET550 2.5 12.8 1.0 O A:ALA572 2.5 11.2 1.0 O A:SER703 2.5 20.5 1.0 O A:ALA553 2.5 18.6 1.0 O A:SER551 2.9 14.1 1.0 C A:SER703 3.4 16.6 1.0 C A:ALA553 3.5 16.6 1.0 C A:SER551 3.5 15.0 1.0 CB A:SER703 3.5 16.9 1.0 N A:SER703 3.6 12.7 1.0 C A:ALA572 3.6 13.8 1.0 C A:MET550 3.6 15.2 1.0 N A:ALA553 3.6 10.8 1.0 CA A:SER703 3.7 17.7 1.0 CB A:ALA553 3.8 11.5 1.0 CA A:ALA553 3.8 13.4 1.0 CA A:SER551 3.9 14.9 1.0 CB A:ALA572 4.0 13.1 1.0 N A:SER551 4.2 15.0 1.0 CA A:ALA572 4.3 12.8 1.0 C A:SER552 4.4 12.4 1.0 N A:SER552 4.4 12.1 1.0 N A:ILE704 4.6 14.0 1.0 N A:GLY573 4.6 12.4 1.0 OE2 A:GLU700 4.7 19.0 1.0 N A:THR554 4.7 11.4 1.0 C A:MET702 4.7 13.9 1.0 CA A:MET550 4.8 14.5 1.0 CA A:GLY573 4.9 13.8 1.0 CA A:SER552 4.9 11.0 1.0 N A:ALA555 4.9 16.1 1.0

M.Tecza, T.F.Kagawa, M.Jain, J.C.Cooney. Enzyme Kinetic and Binding Studies Identify Determinants of Specificity For the Immunomodulatory Enzyme Scpa, A C5A Inactivating Bacterial Protease Comput Struct Biotechnol J 2021.
ISSN: ESSN 2001-0370
DOI: 10.1016/J.CSBJ.2021.04.024