Calcium in PDB 3lpa: Crystal Structure of A Subtilisin-Like Protease

The structure of Crystal Structure of A Subtilisin-Like Protease, PDB code: 3lpa was solved by C.J.Porter, W.Wong, J.C.Whisstock, J.I.Rood, R.M.Kennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.26 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.059, 45.980, 47.243, 97.79, 115.24, 113.86
R / Rfree (%)	17.7 / 23.3

The binding sites of Calcium atom in the Crystal Structure of A Subtilisin-Like Protease (pdb code 3lpa). 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 Subtilisin-Like Protease, PDB code: 3lpa:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A Subtilisin-Like Protease


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 Subtilisin-Like Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca360 b:20.3 occ:1.00 O A:HOH373 2.2 6.1 1.0 O A:ASP76 2.3 23.8 1.0 OD2 A:ASP59 2.3 18.1 1.0 O A:HOH398 2.4 6.6 1.0 OD2 A:ASP69 2.4 25.6 1.0 OD2 A:ASP74 2.5 26.7 1.0 OD1 A:ASP74 2.7 28.0 1.0 CG A:ASP74 2.9 26.1 1.0 CG A:ASP59 3.3 18.2 1.0 C A:ASP76 3.5 22.7 1.0 CG A:ASP69 3.6 24.9 1.0 CB A:ASP59 3.6 18.7 1.0 CA A:CA362 4.0 23.7 1.0 CB A:ASP69 4.1 24.0 1.0 NH1 A:ARG136 4.2 15.0 1.0 CA A:ASP76 4.2 23.9 1.0 CB A:ASP76 4.3 25.5 1.0 OD1 A:ASP59 4.4 16.3 1.0 N A:ASP76 4.4 24.2 1.0 CB A:ASP74 4.4 25.8 1.0 OE2 A:GLU80 4.5 23.3 1.0 N A:PRO77 4.6 21.3 1.0 OD1 A:ASP69 4.6 23.8 1.0 O A:HOH347 4.6 6.0 1.0 N A:PHE78 4.7 20.9 1.0 CG A:ASP76 4.7 25.4 1.0 CA A:PRO77 4.8 20.0 1.0 O A:PHE78 4.8 21.8 1.0 O A:HOH469 4.9 13.4 1.0 CD A:ARG136 5.0 15.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A Subtilisin-Like Protease


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 Subtilisin-Like Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca361 b:21.4 occ:1.00 OD1 A:ASP5 2.2 25.3 1.0 O A:VAL116 2.3 20.9 1.0 OD1 A:ASN119 2.4 24.7 1.0 O A:ILE121 2.4 22.0 1.0 OD1 A:ASP49 2.5 19.9 1.0 O A:VAL123 2.5 20.5 1.0 OD2 A:ASP49 2.6 18.1 1.0 CG A:ASP49 2.9 21.5 1.0 CG A:ASP5 3.3 25.7 1.0 CG A:ASN119 3.5 24.9 1.0 C A:VAL116 3.5 20.6 1.0 N A:VAL123 3.6 21.7 1.0 C A:VAL123 3.6 20.5 1.0 C A:ILE121 3.6 23.9 1.0 ND2 A:ASN119 3.9 23.7 1.0 CB A:ASP5 4.0 25.5 1.0 C A:GLY122 4.1 23.1 1.0 OD2 A:ASP5 4.2 26.9 1.0 CA A:VAL123 4.2 20.1 1.0 CA A:THR117 4.2 20.3 1.0 N A:THR117 4.3 20.9 1.0 CA A:GLY122 4.4 22.3 1.0 CB A:ASP49 4.4 20.0 1.0 N A:GLY122 4.5 23.1 1.0 N A:ILE121 4.5 25.9 1.0 CG1 A:ILE121 4.5 27.5 1.0 CA A:VAL116 4.6 19.1 1.0 CA A:ILE121 4.6 25.6 1.0 N A:ALA124 4.7 21.2 1.0 N A:ASN119 4.7 26.1 1.0 O A:GLY122 4.8 24.3 1.0 CB A:VAL116 4.8 18.1 1.0 CB A:ASN119 4.8 25.9 1.0 C A:THR117 4.9 22.1 1.0 N A:ASN118 4.9 24.2 1.0 N A:VAL116 5.0 18.9 1.0 C A:ASN119 5.0 26.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A Subtilisin-Like Protease


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 Subtilisin-Like Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca362 b:23.7 occ:1.00 O A:GLY72 2.2 24.4 1.0 O A:HOH347 2.4 6.0 1.0 OD1 A:ASP71 2.4 29.4 1.0 OD1 A:ASP74 2.4 28.0 1.0 OD2 A:ASP69 2.4 25.6 1.0 O A:ASP71 2.5 26.1 1.0 OD1 A:ASP69 2.5 23.8 1.0 CG A:ASP69 2.8 24.9 1.0 C A:ASP71 3.2 26.8 1.0 C A:GLY72 3.3 23.5 1.0 CG A:ASP74 3.5 26.1 1.0 CG A:ASP71 3.5 31.1 1.0 N A:GLY72 3.8 24.9 1.0 OG A:SER67 3.8 25.1 1.0 CA A:GLY72 3.9 23.9 1.0 CA A:ASP71 4.0 28.4 1.0 CA A:CA360 4.0 20.3 1.0 OD2 A:ASP59 4.1 18.1 1.0 CB A:ASP74 4.1 25.8 1.0 N A:ASP71 4.1 27.8 1.0 CB A:SER67 4.2 23.2 1.0 CB A:ASP71 4.3 29.8 1.0 OD2 A:ASP71 4.3 33.0 1.0 CB A:ASP69 4.3 24.0 1.0 O A:ILE61 4.4 19.2 1.0 CG A:ASP59 4.4 18.2 1.0 N A:ARG73 4.4 23.4 1.0 OD2 A:ASP74 4.4 26.7 1.0 N A:ASP74 4.5 23.8 1.0 C A:ARG73 4.6 23.7 1.0 OD1 A:ASP59 4.6 16.3 1.0 CA A:ARG73 4.7 22.7 1.0 O A:HOH398 4.9 6.6 1.0 CA A:ASP74 4.9 24.4 1.0 CB A:ASP59 5.0 18.7 1.0

R.M.Kennan, W.Wong, O.P.Dhungyel, X.Han, D.Wong, D.Parker, C.J.Rosado, R.H.P.Law, S.Mcgowan, S.B.Reeve, V.Levina, G.A.Powers, R.N.Pike, S.P.Bottomley, A.I.Smith, I.Marsh, R.J.Whittington, J.C.Whisstock, C.J.Porter, J.I.Rood. The Subtilisin-Like Protease APRV2 Is Required For Virulence and Uses A Novel Disulphide-Tethered Exosite to Bind Substrates Plos Pathog. V. 6 E1001 2010.
ISSN: ISSN 1553-7366
PubMed: 21124876
DOI: 10.1371/JOURNAL.PPAT.1001210