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

The structure of Crystal Structure of A Serine Protease From Streptococcus Species, PDB code: 5xxz 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)	19.98 / 3.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.134, 132.847, 151.989, 90.00, 100.69, 90.00
R / Rfree (%)	20.6 / 26.3

The binding sites of Calcium atom in the Crystal Structure of A Serine Protease From Streptococcus Species (pdb code 5xxz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of A Serine Protease From Streptococcus Species, PDB code: 5xxz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 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:74.5 occ:1.00 OG1 A:THR412 2.6 36.4 1.0 OG A:SER627 2.9 37.4 1.0 OG A:SER374 2.9 37.9 1.0 CB A:SER374 3.5 37.9 1.0 CB A:THR412 3.8 36.1 1.0 CB A:SER627 3.9 37.9 1.0 CA A:LYS651 4.0 37.0 1.0 CB A:LYS651 4.0 36.8 1.0 N A:LYS651 4.1 37.4 1.0 CG1 A:VAL650 4.1 45.6 1.0 CG2 A:THR412 4.2 36.0 1.0 CG2 A:VAL376 4.5 37.5 1.0 CD1 A:LEU654 4.5 37.1 1.0 CA A:SER374 4.5 37.9 1.0 CG A:LYS651 4.7 36.4 1.0 C A:VAL650 4.7 39.0 1.0 O A:ALA647 4.7 50.0 1.0 CB A:VAL650 4.8 44.9 1.0 CD A:LYS651 4.9 40.0 1.0 N A:VAL375 5.0 37.4 1.0

Calcium binding site 2 out of 7 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:37.1 occ:1.00 O A:ARG1043 2.0 46.3 1.0 O A:GLN1019 2.2 39.6 1.0 OD1 A:ASP1042 2.3 49.2 1.0 OD2 A:ASP1017 2.3 36.6 1.0 OD2 A:ASP1042 2.4 48.1 1.0 OD2 A:ASP1110 2.4 39.2 1.0 OD1 A:ASP1017 2.5 37.1 1.0 CG A:ASP1042 2.6 49.3 1.0 CG A:ASP1017 2.8 36.7 1.0 C A:ARG1043 3.2 47.0 1.0 C A:GLN1019 3.4 39.1 1.0 CG A:ASP1110 3.6 36.5 1.0 ND2 A:ASN1114 3.8 43.9 1.0 N A:ARG1043 3.9 53.1 1.0 CB A:ASP1042 4.1 53.2 1.0 CB A:GLN1019 4.1 38.2 1.0 CA A:GLN1019 4.1 38.2 1.0 CA A:ARG1043 4.1 50.1 1.0 N A:GLY1044 4.2 47.5 1.0 CB A:ASP1110 4.2 36.4 1.0 CA A:GLY1044 4.2 46.6 1.0 N A:GLN1019 4.2 37.9 1.0 CB A:ASP1017 4.3 36.5 1.0 C A:LYS1020 4.4 38.2 1.0 O A:LYS1020 4.5 46.3 1.0 N A:LYS1020 4.5 41.0 1.0 OD1 A:ASP1110 4.5 36.4 1.0 C A:GLY1044 4.5 46.8 1.0 C A:ASP1042 4.6 53.9 1.0 N A:PRO1021 4.6 38.0 1.0 CA A:LYS1020 4.7 38.3 1.0 CB A:ARG1043 4.7 51.5 1.0 CG A:ASN1114 4.8 37.3 1.0 CB A:ASN1114 4.8 43.2 1.0 CA A:ASP1042 4.8 57.6 1.0 N A:ALA1046 4.8 35.9 1.0 CB A:ALA1046 4.8 35.7 1.0 N A:LEU1045 4.9 44.7 1.0 O A:GLY1044 4.9 45.5 1.0 N A:GLY1047 4.9 35.8 1.0

Calcium binding site 3 out of 7 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:53.6 occ:1.00 ND2 A:ASN910 2.2 61.2 1.0 OD1 A:ASP912 2.4 56.8 1.0 OD1 A:ASP916 2.4 72.6 1.0 OG A:SER908 2.4 44.3 1.0 OD1 A:ASN910 2.5 63.6 1.0 O A:SER908 2.5 40.4 1.0 O A:ASN914 2.5 45.6 1.0 CG A:ASN910 2.5 62.2 1.0 OD2 A:ASP912 2.8 55.5 1.0 CG A:ASP912 2.8 55.9 1.0 CB A:SER908 3.4 41.9 1.0 CG A:ASP916 3.6 72.7 1.0 C A:SER908 3.6 42.4 1.0 C A:ASN914 3.7 45.9 1.0 CB A:ASN910 4.0 61.3 1.0 N A:ASN910 4.0 58.7 1.0 OD2 A:ASP916 4.1 74.8 1.0 CA A:SER908 4.1 40.3 1.0 N A:ASN914 4.1 41.6 1.0 CB A:ASP912 4.2 54.2 1.0 CA A:ASN914 4.3 43.4 1.0 N A:ASP912 4.3 53.9 1.0 O A:GLY1113 4.4 43.8 1.0 CB A:ASN914 4.4 45.0 1.0 O A:GLN915 4.5 53.9 1.0 CA A:ASN910 4.5 60.6 1.0 C A:GLN915 4.6 55.0 1.0 CA A:ASP912 4.7 53.1 1.0 N A:ASP916 4.7 65.7 1.0 N A:PRO909 4.8 45.0 1.0 CB A:ASP916 4.8 69.9 1.0 CA A:ASP916 4.8 67.5 1.0 N A:GLY911 4.8 56.4 1.0 N A:GLN915 4.8 48.1 1.0 N A:SER908 4.8 40.2 1.0 N A:ASN913 4.8 49.2 1.0 O A:ALA1112 4.9 45.4 1.0 C A:ASN910 5.0 61.1 1.0 OD1 A:ASN1114 5.0 37.5 1.0 C A:ASP912 5.0 52.0 1.0

Calcium binding site 4 out of 7 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:Ca1705 b:30.0 occ:1.00 OG A:SER1190 1.5 68.7 1.0 OD1 A:ASP1198 1.9 44.6 1.0 OD2 A:ASP1194 2.0 66.0 1.0 O A:ASN1196 2.2 50.4 1.0 OD1 A:ASP1194 2.2 67.1 1.0 CG A:ASP1194 2.3 66.3 1.0 O A:SER1190 2.6 72.9 1.0 OD1 A:ASN1192 2.6 54.4 1.0 CB A:SER1190 2.8 69.0 1.0 CG A:ASP1198 3.1 46.2 1.0 C A:ASN1196 3.4 51.0 1.0 C A:SER1190 3.5 71.2 1.0 CA A:SER1190 3.7 70.6 1.0 CG A:ASN1192 3.7 55.1 1.0 OD2 A:ASP1198 3.8 45.6 1.0 CB A:ASP1194 3.8 65.0 1.0 O A:GLY1381 4.1 47.6 1.0 C A:LYS1197 4.1 48.9 1.0 N A:ASN1196 4.1 52.9 1.0 O A:LYS1197 4.1 50.5 1.0 CA A:ASN1196 4.1 51.9 1.0 ND2 A:ASN1192 4.1 54.9 1.0 N A:ASP1198 4.2 48.6 1.0 CB A:ASP1198 4.3 46.6 1.0 CA A:ASP1198 4.3 46.7 1.0 N A:SER1190 4.3 71.1 1.0 CB A:ASN1196 4.4 51.5 1.0 N A:ASP1194 4.4 66.7 1.0 N A:LYS1197 4.4 49.6 1.0 N A:ASN1192 4.5 64.0 1.0 CA A:ASP1194 4.6 62.8 1.0 CA A:LYS1197 4.7 48.7 1.0 N A:PRO1191 4.7 67.5 1.0 C A:GLY1381 4.8 47.9 1.0 O A:ALA1380 5.0 56.0 1.0

Calcium binding site 5 out of 7 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 5 of Crystal Structure of A Serine Protease From Streptococcus Species within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1702 b:35.6 occ:1.00 OD2 B:ASP1110 2.2 36.4 1.0 OD1 B:ASP1042 2.3 58.7 1.0 O B:GLN1019 2.4 35.7 1.0 OD2 B:ASP1017 2.4 45.9 1.0 OD2 B:ASP1042 2.5 58.4 1.0 OD1 B:ASP1017 2.5 46.4 1.0 O B:ARG1043 2.6 53.0 1.0 CG B:ASP1042 2.8 58.2 1.0 CG B:ASP1017 2.8 45.1 1.0 CG B:ASP1110 3.3 37.2 1.0 C B:GLN1019 3.6 37.4 1.0 CB B:ASP1110 3.6 37.3 1.0 ND2 B:ASN1114 3.7 41.1 1.0 C B:ARG1043 3.8 54.4 1.0 CB B:ASP1017 4.2 42.2 1.0 CB B:ASP1042 4.3 58.7 1.0 OD1 B:ASP1110 4.3 38.0 1.0 CA B:GLN1019 4.4 38.6 1.0 N B:ARG1043 4.4 55.4 1.0 CB B:GLN1019 4.4 40.0 1.0 CB B:ALA1046 4.4 39.0 1.0 C B:LYS1020 4.4 41.0 1.0 N B:GLN1019 4.4 39.8 1.0 CB B:ASN1114 4.5 42.6 1.0 CG B:ASN1114 4.6 42.9 1.0 N B:PRO1021 4.6 41.7 1.0 N B:LYS1020 4.6 37.7 1.0 O B:LYS1020 4.6 41.8 1.0 CA B:GLY1044 4.6 50.3 1.0 N B:GLY1044 4.6 53.2 1.0 CA B:ARG1043 4.7 55.8 1.0 N B:GLY1047 4.7 41.8 1.0 CA B:LYS1020 4.7 40.2 1.0 N B:ALA1046 4.7 37.8 1.0 CD B:PRO1021 4.8 41.0 1.0 C B:GLY1044 4.8 46.3 1.0 CG B:PRO1021 4.9 39.9 1.0

Calcium binding site 6 out of 7 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 6 of Crystal Structure of A Serine Protease From Streptococcus Species within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1703 b:48.2 occ:1.00 OG B:SER1190 2.3 39.4 1.0 O B:ASN1196 2.3 38.7 1.0 OD1 B:ASN1192 2.4 51.4 1.0 OD1 B:ASP1194 2.4 50.7 1.0 OD1 B:ASP1198 2.5 35.0 1.0 O B:SER1190 2.5 41.9 1.0 OD2 B:ASP1194 2.7 49.8 1.0 CG B:ASP1194 2.8 50.4 1.0 CB B:SER1190 3.3 35.4 1.0 CG B:ASN1192 3.5 50.1 1.0 C B:SER1190 3.5 38.6 1.0 C B:ASN1196 3.5 39.9 1.0 CG B:ASP1198 3.7 36.3 1.0 CA B:SER1190 3.9 38.0 1.0 ND2 B:ASN1192 3.9 49.0 1.0 O B:GLY1381 4.0 45.2 1.0 O B:LYS1197 4.0 35.5 1.0 C B:LYS1197 4.1 39.0 1.0 CB B:ASP1194 4.2 52.5 1.0 N B:ASN1192 4.2 48.1 1.0 N B:ASN1196 4.2 35.8 1.0 N B:ASP1198 4.3 37.5 1.0 CA B:ASN1196 4.3 36.1 1.0 CA B:ASP1198 4.3 35.0 1.0 N B:ASP1194 4.4 59.1 1.0 N B:SER1190 4.4 39.7 1.0 CB B:ASN1196 4.5 36.3 1.0 N B:LYS1197 4.6 40.6 1.0 CB B:ASP1198 4.6 34.8 1.0 OD2 B:ASP1198 4.6 36.7 1.0 C B:GLY1381 4.7 43.5 1.0 N B:PRO1191 4.7 38.7 1.0 O B:ALA1380 4.7 42.9 1.0 CB B:ASN1192 4.8 52.2 1.0 CA B:LYS1197 4.8 40.6 1.0 CA B:ASP1194 4.8 54.6 1.0 OD1 B:ASN1382 4.9 41.9 1.0 CA B:ASN1192 4.9 52.5 1.0 N B:GLU1193 5.0 66.1 1.0

Calcium binding site 7 out of 7 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 7 of Crystal Structure of A Serine Protease From Streptococcus Species within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1704 b:43.2 occ:1.00 OD1 B:ASN910 2.2 50.9 1.0 O B:SER908 2.2 39.3 1.0 OG B:SER908 2.3 38.0 1.0 OD1 B:ASP916 2.4 43.6 1.0 OD1 B:ASP912 2.4 47.5 1.0 O B:ASN914 2.4 32.0 1.0 OD2 B:ASP912 2.8 46.3 1.0 CG B:ASP912 2.9 46.0 1.0 CG B:ASN910 3.1 51.4 1.0 CB B:SER908 3.3 38.5 1.0 C B:SER908 3.3 39.2 1.0 C B:ASN914 3.6 40.1 1.0 CG B:ASP916 3.6 43.7 1.0 N B:ASN910 3.8 47.7 1.0 CB B:ASN910 3.9 48.6 1.0 CA B:SER908 3.9 38.2 1.0 ND2 B:ASN910 4.1 54.0 1.0 O B:GLN915 4.1 37.3 1.0 N B:ASN914 4.2 46.0 1.0 C B:GLN915 4.3 35.9 1.0 CB B:ASP912 4.3 45.0 1.0 CA B:ASN914 4.3 41.5 1.0 OD2 B:ASP916 4.4 44.1 1.0 CB B:ASN914 4.4 32.3 1.0 CA B:ASN910 4.4 47.7 1.0 N B:PRO909 4.5 40.5 1.0 N B:ASP916 4.5 38.3 1.0 O B:GLY1113 4.5 45.8 1.0 N B:SER908 4.6 39.1 1.0 CA B:ASP916 4.6 39.1 1.0 N B:ASP912 4.6 46.5 1.0 N B:GLN915 4.6 37.5 1.0 CB B:ASP916 4.7 42.3 1.0 C B:PRO909 4.7 45.9 1.0 CA B:PRO909 4.8 42.3 1.0 O B:ALA1112 4.8 37.1 1.0 OD1 B:ASN1114 4.8 44.4 1.0 CA B:GLN915 4.9 34.6 1.0 CA B:ASP912 4.9 45.4 1.0 N B:ASN913 5.0 52.3 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