Calcium in PDB 6vjb: Crystal Structure of A Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes

The structure of Crystal Structure of A Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes, PDB code: 6vjb was solved by E.Malito, S.Rouse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.51 / 2.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.500, 121.750, 106.640, 90.00, 111.78, 90.00
R / Rfree (%)	19 / 24.4

The binding sites of Calcium atom in the Crystal Structure of A Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes (pdb code 6vjb). 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 Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes, PDB code: 6vjb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes


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 Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1705 b:48.9 occ:1.00 O A:ASN1196 2.3 41.2 1.0 OD1 A:ASN1192 2.3 57.6 1.0 O A:HOH1898 2.4 44.8 1.0 OD1 A:ASP1198 2.4 46.0 1.0 O A:SER1190 2.5 55.3 1.0 OD1 A:ASP1194 2.6 54.3 1.0 OG A:SER1190 2.9 62.7 1.0 C A:ASN1196 3.4 43.8 1.0 CG A:ASP1194 3.4 52.4 1.0 CG A:ASN1192 3.4 62.1 1.0 CB A:SER1190 3.5 54.4 1.0 C A:SER1190 3.6 55.2 1.0 CG A:ASP1198 3.6 46.5 1.0 OD2 A:ASP1194 3.6 50.4 1.0 O A:LYS1197 3.8 42.9 1.0 C A:LYS1197 3.9 44.3 1.0 ND2 A:ASN1192 4.0 46.0 1.0 CA A:SER1190 4.1 51.4 1.0 N A:ASP1198 4.1 40.9 1.0 N A:ASN1196 4.2 41.6 1.0 N A:ASN1192 4.2 51.3 1.0 CA A:ASP1198 4.2 41.4 1.0 CA A:ASN1196 4.2 40.4 1.0 N A:LYS1197 4.3 41.6 1.0 CB A:ASP1198 4.4 43.2 1.0 N A:ASP1194 4.5 47.4 1.0 OD2 A:ASP1198 4.5 47.6 1.0 N A:SER1190 4.5 51.2 1.0 CA A:LYS1197 4.6 41.0 1.0 CB A:ASN1192 4.6 48.7 1.0 CB A:ASN1196 4.6 36.2 1.0 CB A:ASP1194 4.6 47.9 1.0 O A:GLY1381 4.7 45.7 1.0 N A:GLU1193 4.7 52.2 1.0 CA A:ASN1192 4.8 50.6 1.0 N A:PRO1191 4.8 51.5 1.0 C A:ASN1192 4.9 55.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes


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 Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1706 b:35.2 occ:1.00 O A:SER908 2.3 33.8 1.0 OD1 A:ASP916 2.4 29.5 1.0 OD1 A:ASP912 2.4 37.2 1.0 O A:ASN914 2.4 30.5 1.0 OD1 A:ASN910 2.4 30.3 1.0 OG A:SER908 2.6 30.4 1.0 CG A:ASP912 3.2 40.8 1.0 CG A:ASN910 3.3 46.4 1.0 OD2 A:ASP912 3.4 52.7 1.0 CB A:SER908 3.5 30.0 1.0 C A:SER908 3.5 33.2 1.0 ND2 A:ASN910 3.5 33.1 1.0 C A:ASN914 3.5 32.3 1.0 CG A:ASP916 3.6 34.6 1.0 CA A:SER908 4.0 28.9 1.0 N A:ASN914 4.1 29.8 1.0 N A:ASP916 4.2 31.1 1.0 N A:ASN910 4.2 35.3 1.0 C A:GLN915 4.2 33.9 1.0 CA A:ASN914 4.2 28.7 1.0 CA A:ASP916 4.3 30.5 1.0 O A:GLN915 4.3 34.9 1.0 OD2 A:ASP916 4.4 44.2 1.0 CB A:ASP916 4.5 31.1 1.0 N A:GLN915 4.5 29.7 1.0 N A:PRO909 4.5 32.0 1.0 CB A:ASN914 4.6 27.6 1.0 N A:ASP912 4.6 31.4 1.0 CB A:ASP912 4.6 31.7 1.0 N A:SER908 4.6 29.8 1.0 CB A:ASN910 4.6 30.2 1.0 CA A:PRO909 4.8 31.5 1.0 CA A:GLN915 4.8 29.9 1.0 CA A:ASN910 4.9 35.0 1.0 N A:ASN913 4.9 33.4 1.0 CA A:ASP912 4.9 30.1 1.0 N A:GLY911 5.0 34.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes


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 Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1707 b:59.1 occ:1.00 OD2 A:ASP1110 2.2 55.3 1.0 OD2 A:ASP1042 2.4 71.9 1.0 O A:GLN1019 2.5 41.1 1.0 OD1 A:ASP1042 2.6 64.8 1.0 OD1 A:ASP1017 2.6 47.0 1.0 OD2 A:ASP1017 2.6 50.6 1.0 CG A:ASP1042 2.8 66.6 1.0 CG A:ASP1017 2.9 46.7 1.0 O A:ARG1043 2.9 69.4 1.0 CG A:ASP1110 3.3 45.9 1.0 CB A:ASP1110 3.7 34.6 1.0 C A:GLN1019 3.7 40.1 1.0 C A:ARG1043 3.8 68.2 1.0 ND2 A:ASN1114 4.0 31.1 1.0 CA A:GLY1044 4.2 60.2 1.0 CB A:ASP1042 4.3 64.5 1.0 N A:GLY1044 4.4 61.8 1.0 CB A:ASP1017 4.4 36.0 1.0 N A:ARG1043 4.4 65.8 1.0 OD1 A:ASP1110 4.4 47.3 1.0 CA A:GLN1019 4.5 36.7 1.0 C A:LYS1020 4.6 43.4 1.0 N A:GLN1019 4.7 36.5 1.0 CB A:ALA1046 4.7 45.1 1.0 CB A:GLN1019 4.7 38.5 1.0 C A:GLY1044 4.7 60.6 1.0 N A:LYS1020 4.7 35.0 1.0 N A:PRO1021 4.7 41.4 1.0 CA A:ARG1043 4.8 66.0 1.0 CB A:ASN1114 4.8 29.8 1.0 CG A:ASN1114 4.8 43.6 1.0 CA A:LYS1020 4.9 35.7 1.0 O A:LYS1020 4.9 43.1 1.0 C A:ASP1042 5.0 68.1 1.0 CG A:PRO1021 5.0 46.4 1.0 N A:ALA1046 5.0 46.1 1.0

S.Mckenna, E.Malito, S.L.Rouse, F.Abate, G.Bensi, E.Chiarot, F.Micoli, F.Mancini, D.Gomes Moriel, G.Grandi, D.Mossakowska, M.Pearson, Y.Xu, J.Pease, S.Sriskandan, I.Margarit, M.J.Bottomley, S.Matthews. Structure, Dynamics and Immunogenicity of A Catalytically Inactive Cxc Chemokine-Degrading Protease Spycep From Streptococcus Pyogenes. Comput Struct Biotechnol J V. 18 650 2020.
ISSN: ISSN 2001-0370
PubMed: 32257048
DOI: 10.1016/J.CSBJ.2020.03.004