Sodium in PDB 8bty: Structure of the Active Form of Scpb, the C5A-Peptidase From Streptococcus Agalactiae.

The structure of Structure of the Active Form of Scpb, the C5A-Peptidase From Streptococcus Agalactiae., PDB code: 8bty was solved by T.F.Kagawa, J.C.Cooney, T.Miclot, R.Cullen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.84 / 1.70
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	167.152, 167.152, 141.485, 90, 90, 120
R / Rfree (%)	18.8 / 21.6

The structure of Structure of the Active Form of Scpb, the C5A-Peptidase From Streptococcus Agalactiae. also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Structure of the Active Form of Scpb, the C5A-Peptidase From Streptococcus Agalactiae. (pdb code 8bty). 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 Structure of the Active Form of Scpb, the C5A-Peptidase From Streptococcus Agalactiae., PDB code: 8bty:

Sodium binding site 1 out of 1 in the Structure of the Active Form of Scpb, the C5A-Peptidase From Streptococcus Agalactiae.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Active Form of Scpb, the C5A-Peptidase From Streptococcus Agalactiae. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1104 b:28.4 occ:1.00 O A:ALA572 2.4 27.2 1.0 O A:ALA553 2.5 28.9 1.0 OG A:SER703 2.5 27.6 1.0 O A:MET550 2.5 25.3 1.0 O A:SER703 2.5 28.7 1.0 O A:SER551 2.9 27.1 1.0 C A:SER703 3.4 27.2 1.0 C A:ALA553 3.4 27.1 1.0 C A:SER551 3.5 25.9 1.0 N A:SER703 3.5 28.2 1.0 CB A:SER703 3.6 25.4 1.0 C A:ALA572 3.6 26.2 1.0 CA A:SER703 3.7 27.1 1.0 C A:MET550 3.7 24.1 1.0 N A:ALA553 3.7 24.0 1.0 CB A:ALA553 3.8 26.1 1.0 CA A:ALA553 3.8 26.8 1.0 CB A:ALA572 3.9 26.5 1.0 CA A:SER551 3.9 27.2 1.0 CA A:ALA572 4.2 28.7 1.0 N A:SER551 4.3 27.4 1.0 O A:HOH1335 4.3 28.6 1.0 C A:SER552 4.3 27.6 1.0 N A:SER552 4.4 26.7 1.0 N A:THR554 4.5 26.1 1.0 N A:ILE704 4.5 26.2 1.0 N A:GLY573 4.6 25.2 1.0 OE2 A:GLU700 4.6 29.0 1.0 C A:MET702 4.7 27.5 1.0 CA A:GLY573 4.8 25.5 1.0 CA A:MET550 4.9 24.5 1.0 CA A:SER552 4.9 26.1 1.0 N A:ALA555 4.9 28.9 1.0 O A:SER552 4.9 24.1 1.0

R.Cullen, M.Tecza, T.Miclot, S.Behan, M.Jain, M.K.Avink, J.C.Cooney, T.F.Kagawa. The 1.7 Angstrom Crystal Structure of the C5A Peptidase From Streptococcus Agalactiae (Scpb) Reveals An Active Site Competent For Catalysis. Proteins 2023.
ISSN: ESSN 1097-0134
PubMed: 37921533
DOI: 10.1002/PROT.26625