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

The structure of Crystal Structure of A Serine Protease From Streptococcus Species, PDB code: 5xya 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)	19.90 / 3.00
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	190.530, 190.530, 248.668, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 27.8

The binding sites of Calcium atom in the Crystal Structure of A Serine Protease From Streptococcus Species (pdb code 5xya). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of A Serine Protease From Streptococcus Species, PDB code: 5xya:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 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:Ca1705 b:18.1 occ:1.00 OD1 A:ASN1192 2.2 28.7 1.0 OD2 A:ASP1194 2.2 19.1 1.0 ND2 A:ASN1192 2.3 27.1 1.0 O A:ASN1196 2.3 13.5 1.0 OG A:SER1190 2.5 18.7 1.0 CG A:ASN1192 2.6 24.6 1.0 OD2 A:ASP1198 2.6 19.5 1.0 O A:SER1190 2.6 15.5 1.0 OD1 A:ASP1194 2.8 20.9 1.0 CG A:ASP1194 2.8 22.5 1.0 CB A:SER1190 3.4 18.6 1.0 C A:ASN1196 3.5 11.6 1.0 C A:SER1190 3.7 16.8 1.0 CG A:ASP1198 3.9 16.4 1.0 O A:LYS1197 4.1 18.7 1.0 CB A:ASN1192 4.1 13.5 1.0 CA A:SER1190 4.1 15.6 1.0 O A:GLY1381 4.1 14.7 1.0 N A:ASN1196 4.2 15.1 1.0 CA A:ASN1196 4.2 14.1 1.0 C A:LYS1197 4.3 15.9 1.0 CB A:ASP1194 4.3 16.2 1.0 CB A:ASN1196 4.4 14.5 1.0 N A:ASN1192 4.5 17.6 1.0 OD1 A:ASP1198 4.6 14.9 1.0 N A:LYS1197 4.6 10.6 1.0 N A:ASP1198 4.6 14.1 1.0 N A:SER1190 4.6 15.2 1.0 N A:ASP1194 4.6 19.6 1.0 C A:GLY1381 4.7 14.0 1.0 CA A:ASP1198 4.8 9.8 1.0 CA A:ASN1192 4.8 13.3 1.0 CA A:LYS1197 4.8 11.3 1.0 N A:PRO1191 4.9 13.8 1.0 CA A:ASP1194 4.9 15.6 1.0 CB A:ASP1198 4.9 11.0 1.0

Calcium binding site 2 out of 4 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:Ca1706 b:24.4 occ:1.00 OD2 A:ASP1017 2.3 26.9 1.0 O A:GLN1019 2.4 27.3 1.0 OD1 A:ASP1017 2.5 23.7 1.0 O A:ARG1043 2.5 28.4 1.0 OD2 A:ASP1042 2.5 37.3 1.0 OD1 A:ASP1042 2.5 29.2 1.0 OD2 A:ASP1110 2.6 33.2 1.0 CG A:ASP1017 2.6 25.3 1.0 OD1 A:ASP1110 2.8 30.1 1.0 CG A:ASP1042 2.9 35.0 1.0 CG A:ASP1110 2.9 32.4 1.0 C A:GLN1019 3.6 23.4 1.0 C A:ARG1043 3.6 31.9 1.0 CB A:ASP1017 4.1 22.1 1.0 ND2 A:ASN1114 4.1 21.5 1.0 CB A:ASP1110 4.3 26.7 1.0 N A:ARG1043 4.3 28.9 1.0 N A:GLN1019 4.4 25.8 1.0 C A:LYS1020 4.4 28.9 1.0 CB A:ASP1042 4.4 39.6 1.0 CA A:GLN1019 4.4 24.5 1.0 CB A:ALA1046 4.5 22.0 1.0 N A:GLY1044 4.5 26.9 1.0 CA A:ARG1043 4.5 35.3 1.0 CA A:GLY1044 4.5 26.5 1.0 N A:PRO1021 4.5 29.4 1.0 N A:LYS1020 4.6 21.4 1.0 O A:LYS1020 4.6 32.6 1.0 CB A:GLN1019 4.6 31.7 1.0 CA A:LYS1020 4.6 26.5 1.0 CB A:ASN1114 4.8 28.8 1.0 C A:GLY1044 4.8 25.9 1.0 O A:GLY1044 4.9 36.0 1.0 CG A:ASN1114 4.9 27.6 1.0 CA A:ASP1110 4.9 25.8 1.0

Calcium binding site 3 out of 4 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:Ca1707 b:21.8 occ:1.00 OD1 A:ASN910 2.3 24.0 1.0 ND2 A:ASN910 2.3 24.4 1.0 OG A:SER908 2.3 17.7 1.0 O A:ASN914 2.3 14.1 1.0 O A:SER908 2.4 16.1 1.0 OD2 A:ASP912 2.5 25.1 1.0 CG A:ASN910 2.6 21.4 1.0 OD1 A:ASP916 2.7 23.6 1.0 OD1 A:ASP912 2.8 23.1 1.0 CG A:ASP912 3.0 23.0 1.0 CB A:SER908 3.4 18.4 1.0 C A:ASN914 3.5 17.4 1.0 C A:SER908 3.5 17.4 1.0 CG A:ASP916 4.0 25.2 1.0 CA A:SER908 4.0 16.5 1.0 CB A:ASN910 4.0 16.9 1.0 N A:ASN914 4.1 26.9 1.0 CA A:ASN914 4.2 21.9 1.0 O A:GLN915 4.2 17.7 1.0 CB A:ASN914 4.3 21.1 1.0 N A:ASN910 4.3 16.9 1.0 C A:GLN915 4.3 16.3 1.0 CB A:ASP912 4.4 22.6 1.0 N A:ASP916 4.5 16.4 1.0 OD1 A:ASN1114 4.6 32.1 1.0 N A:GLN915 4.6 20.9 1.0 CA A:ASP916 4.6 14.3 1.0 N A:PRO909 4.7 19.7 1.0 N A:ASP912 4.7 20.0 1.0 N A:SER908 4.7 15.4 1.0 CA A:ASN910 4.8 16.8 1.0 OD2 A:ASP916 4.8 25.6 1.0 O A:GLY1113 4.9 24.7 1.0 O A:ALA1112 4.9 26.1 1.0 CA A:GLN915 4.9 15.5 1.0 CB A:ASP916 4.9 18.5 1.0 CA A:ASP912 5.0 20.3 1.0

Calcium binding site 4 out of 4 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 4 of Crystal Structure of A Serine Protease From Streptococcus Species within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1708 b:57.7 occ:1.00 N A:HIS937 2.3 21.5 1.0 CB A:TYR936 2.5 16.8 1.0 CB A:ASP940 2.5 28.5 1.0 OD2 A:ASP940 2.7 28.1 1.0 CA A:TYR936 2.9 14.4 1.0 C A:TYR936 3.0 15.8 1.0 O A:HIS937 3.1 19.4 1.0 CG A:ASP940 3.1 26.2 1.0 CA A:HIS937 3.3 19.0 1.0 O A:ASN945 3.4 22.4 1.0 C A:HIS937 3.6 17.8 1.0 CG A:TYR936 3.6 17.2 1.0 CB A:HIS937 3.8 18.9 1.0 CD2 A:TYR936 3.8 21.0 1.0 CA A:ASP940 4.0 29.9 1.0 O A:TYR936 4.1 14.5 1.0 OD1 A:ASP940 4.3 22.3 1.0 N A:TYR936 4.3 13.3 1.0 N A:ASP940 4.4 29.7 1.0 C A:ASN945 4.4 18.4 1.0 O A:ASP940 4.6 23.0 1.0 CG A:LEU947 4.6 9.8 1.0 C A:ASP940 4.8 24.8 1.0 CD1 A:TYR936 4.9 12.9 1.0 N A:ALA938 4.9 16.6 1.0 N A:ASN945 5.0 25.5 1.0 CD2 A:LEU947 5.0 9.7 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