Calcium in PDB 5xyr: Crystal Structure of A Serine Protease From Streptococcus Species

The structure of Crystal Structure of A Serine Protease From Streptococcus Species, PDB code: 5xyr was solved by C.Jobichen, J.Sivaraman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.80
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	191.625, 191.625, 250.956, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 25.7

The structure of Crystal Structure of A Serine Protease From Streptococcus Species also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of A Serine Protease From Streptococcus Species (pdb code 5xyr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Serine Protease From Streptococcus Species, PDB code: 5xyr:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A Serine Protease From Streptococcus Species


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Serine Protease From Streptococcus Species within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1702 b:44.3 occ:1.00 ND2 A:ASN1192 2.3 57.9 1.0 O A:ASN1196 2.3 47.3 1.0 OD1 A:ASN1192 2.4 61.3 1.0 OD1 A:ASP1194 2.4 57.9 1.0 OD1 A:ASP1198 2.4 49.9 1.0 O A:SER1190 2.5 43.2 1.0 OG A:SER1190 2.5 46.2 1.0 CG A:ASN1192 2.6 55.1 1.0 CG A:ASP1194 2.9 53.5 1.0 OD2 A:ASP1194 3.0 48.2 1.0 CB A:SER1190 3.5 42.4 1.0 C A:ASN1196 3.5 45.6 1.0 C A:SER1190 3.6 46.8 1.0 CG A:ASP1198 3.6 46.8 1.0 O A:LYS1197 3.8 45.7 1.0 CA A:SER1190 4.1 42.7 1.0 C A:LYS1197 4.1 39.6 1.0 CB A:ASN1192 4.1 45.2 1.0 N A:ASN1196 4.1 46.1 1.0 O A:GLY1381 4.2 48.4 1.0 CA A:ASN1196 4.2 44.8 1.0 CB A:ASP1194 4.3 48.5 1.0 OD2 A:ASP1198 4.3 49.6 1.0 N A:ASN1192 4.4 48.8 1.0 N A:ASP1198 4.4 39.0 1.0 N A:ASP1194 4.4 52.5 1.0 CB A:ASN1196 4.5 41.3 1.0 CA A:ASP1198 4.5 36.4 1.0 N A:LYS1197 4.5 43.0 1.0 N A:SER1190 4.6 37.8 1.0 CB A:ASP1198 4.7 35.3 1.0 N A:PRO1191 4.7 49.2 1.0 CA A:ASN1192 4.7 47.0 1.0 CA A:LYS1197 4.7 39.8 1.0 CA A:ASP1194 4.8 55.3 1.0 C A:GLY1381 4.9 42.5 1.0 N A:GLY1195 5.0 45.0 1.0 C A:ASN1192 5.0 51.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A Serine Protease From Streptococcus Species


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Serine Protease From Streptococcus Species within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1703 b:91.5 occ:1.00 N A:VAL402 2.3 57.3 1.0 CA A:LEU401 2.5 53.3 1.0 C A:LEU401 2.5 55.3 1.0 C A:GLY400 2.6 61.1 1.0 CA A:ASN351 2.6 50.4 1.0 O A:GLY400 2.6 60.1 1.0 N A:LEU401 2.6 59.8 1.0 OD1 A:ASN351 3.1 61.4 1.0 CB A:ASN351 3.2 45.0 1.0 N A:ASN351 3.2 46.5 1.0 O A:VAL402 3.4 58.0 1.0 O A:LEU401 3.5 59.6 1.0 CA A:VAL402 3.5 52.0 1.0 CG A:ASN351 3.5 52.6 1.0 C A:ASN351 3.7 49.1 1.0 O A:LEU584 3.7 54.9 1.0 CA A:GLY400 3.7 52.8 1.0 C A:VAL402 3.8 53.5 1.0 CB A:LEU401 4.0 55.3 1.0 N A:GLY352 4.0 51.2 1.0 CG1 A:VAL402 4.0 52.8 1.0 CD2 A:LEU401 4.2 44.5 1.0 CB A:VAL402 4.3 53.1 1.0 C A:ALA350 4.6 47.6 1.0 O A:ASN351 4.6 51.0 1.0 CG A:LEU401 4.7 52.6 1.0 ND2 A:ASN351 4.8 51.6 1.0 N A:GLY400 4.9 53.6 1.0 C A:LEU584 4.9 51.1 1.0 O A:TRP582 4.9 56.2 1.0 O A:GLY352 4.9 57.2 1.0 N A:GLY403 5.0 50.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A Serine Protease From Streptococcus Species


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Serine Protease From Streptococcus Species within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1704 b:51.2 occ:1.00 ND2 A:ASN910 2.3 57.5 1.0 OG A:SER908 2.3 45.7 1.0 OD1 A:ASN910 2.3 52.8 1.0 OD1 A:ASP912 2.4 42.8 1.0 O A:ASN914 2.5 46.2 1.0 OD1 A:ASP916 2.5 51.0 1.0 CG A:ASN910 2.6 50.0 1.0 O A:SER908 2.6 43.9 1.0 OD2 A:ASP912 2.9 54.4 1.0 CG A:ASP912 3.0 47.4 1.0 CB A:SER908 3.2 47.1 1.0 C A:SER908 3.6 47.5 1.0 C A:ASN914 3.7 47.2 1.0 CG A:ASP916 3.7 50.6 1.0 CA A:SER908 4.0 44.9 1.0 CB A:ASN910 4.0 47.4 1.0 O A:GLN915 4.3 46.4 1.0 N A:ASN910 4.3 49.1 1.0 OD2 A:ASP916 4.3 46.9 1.0 N A:ASN914 4.4 53.3 1.0 C A:GLN915 4.4 45.5 1.0 CA A:ASN914 4.4 50.0 1.0 CB A:ASN914 4.5 46.0 1.0 CB A:ASP912 4.5 42.7 1.0 N A:ASP916 4.6 46.3 1.0 N A:SER908 4.6 42.9 1.0 OD1 A:ASN1114 4.6 50.7 1.0 N A:ASP912 4.7 47.7 1.0 CA A:ASP916 4.7 39.0 1.0 O A:ALA1112 4.7 49.3 1.0 CA A:ASN910 4.7 44.4 1.0 N A:GLN915 4.7 43.3 1.0 CB A:ASP916 4.8 41.3 1.0 N A:PRO909 4.8 50.3 1.0 N A:ASN913 4.9 44.6 1.0 C A:ASN910 5.0 51.7 1.0 CA A:ASP912 5.0 43.2 1.0

C.Jobichen, Y.C.Tan, M.T.Prabhakar, D.Nayak, D.Biswas, N.S.Pannu, E.Hanski, J.Sivaraman. Structure of Scpc, A Virulence Protease Fromstreptococcus Pyogenes, Reveals the Functional Domains and Maturation Mechanism. Biochem. J. V. 475 2847 2018.
ISSN: ESSN 1470-8728
PubMed: 30049896
DOI: 10.1042/BCJ20180145