Sodium in PDB 7yzx: Scpa From Streptococcus Pyogenes, D783A Mutant.

All present enzymatic activity of Scpa From Streptococcus Pyogenes, D783A Mutant.:
3.4.21.110;

The structure of Scpa From Streptococcus Pyogenes, D783A Mutant., PDB code: 7yzx was solved by T.F.Kagawa, J.C.Cooney, M.Jain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 1.90
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.417, 169.417, 141.83, 90, 90, 120
R / Rfree (%)	19.8 / 22.9

The structure of Scpa From Streptococcus Pyogenes, D783A Mutant. also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Scpa From Streptococcus Pyogenes, D783A Mutant. (pdb code 7yzx). 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, D783A Mutant., PDB code: 7yzx:

Sodium binding site 1 out of 1 in the Scpa From Streptococcus Pyogenes, D783A 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, D783A Mutant. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:31.9 occ:1.00 O A:ALA572 2.4 32.5 1.0 OG A:SER703 2.4 35.5 1.0 O A:SER703 2.5 34.4 1.0 O A:ALA553 2.5 34.0 1.0 O A:MET550 2.5 32.8 1.0 O A:SER551 2.9 29.1 1.0 C A:SER703 3.4 36.3 1.0 C A:ALA553 3.4 32.1 1.0 C A:ALA572 3.5 32.6 1.0 CB A:SER703 3.6 30.5 1.0 C A:SER551 3.6 35.3 1.0 N A:SER703 3.6 33.0 1.0 CA A:SER703 3.7 32.0 1.0 N A:ALA553 3.7 28.8 1.0 C A:MET550 3.7 32.2 1.0 CB A:ALA553 3.8 27.8 1.0 CA A:ALA553 3.8 29.5 1.0 CB A:ALA572 3.9 31.0 1.0 CA A:SER551 4.0 31.6 1.0 CA A:ALA572 4.2 32.4 1.0 O A:HOH1322 4.3 37.1 1.0 N A:SER551 4.3 31.4 1.0 C A:SER552 4.4 33.3 1.0 N A:SER552 4.5 29.6 1.0 N A:THR554 4.5 33.1 1.0 N A:ILE704 4.5 31.8 1.0 N A:GLY573 4.5 33.5 1.0 OE2 A:GLU700 4.7 34.9 1.0 CA A:GLY573 4.8 31.3 1.0 C A:MET702 4.8 31.5 1.0 CA A:MET550 4.9 32.8 1.0 N A:ALA555 4.9 32.4 1.0 CA A:SER552 5.0 30.1 1.0

T.F.Kagawa, M.Jain, J.C.Cooney. X-Ray Diffraction Data For the C5A-Peptidase Mutant with Modified Activity and Specificity. Data Brief V. 46 08778 2023.
ISSN: ESSN 2352-3409
PubMed: 36478677
DOI: 10.1016/J.DIB.2022.108778