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

The structure of Crystal Structure of A Subtilisin-Like Protease, PDB code: 3lpd 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)	24.11 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.936, 45.655, 47.248, 98.00, 115.13, 113.41
R / Rfree (%)	18.2 / 23.7

The binding sites of Calcium atom in the Crystal Structure of A Subtilisin-Like Protease (pdb code 3lpd). 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: 3lpd:
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:Ca1 b:32.7 occ:1.00 OD1 A:ASP5 2.2 28.1 1.0 O A:VAL116 2.3 29.4 1.0 O A:ILE121 2.4 34.5 1.0 OD1 A:ASP49 2.4 28.0 1.0 OD1 A:ASN119 2.5 33.1 1.0 O A:VAL123 2.5 28.4 1.0 OD2 A:ASP49 2.5 25.4 1.0 CG A:ASP49 2.8 28.9 1.0 CG A:ASP5 3.2 32.2 1.0 N A:VAL123 3.4 29.1 1.0 C A:VAL116 3.5 29.2 1.0 CG A:ASN119 3.5 34.0 1.0 C A:VAL123 3.6 28.1 1.0 C A:ILE121 3.6 34.9 1.0 ND2 A:ASN119 3.8 32.0 1.0 CB A:ASP5 3.9 33.7 1.0 C A:GLY122 4.0 30.3 1.0 CA A:VAL123 4.1 28.0 1.0 OD2 A:ASP5 4.2 31.5 1.0 CA A:THR117 4.2 29.4 1.0 N A:THR117 4.3 29.3 1.0 CA A:GLY122 4.3 31.4 1.0 CB A:ASP49 4.4 28.6 1.0 N A:GLY122 4.4 33.7 1.0 CG1 A:ILE121 4.5 37.8 1.0 CA A:VAL116 4.6 27.8 1.0 N A:ILE121 4.6 37.7 1.0 CA A:ILE121 4.7 37.1 1.0 CB A:VAL116 4.8 28.5 1.0 N A:ALA124 4.8 27.6 1.0 O A:GLY122 4.8 30.2 1.0 N A:VAL116 4.8 26.0 1.0 N A:ASN119 4.8 36.2 1.0 CB A:ASN119 4.9 36.0 1.0 C A:THR117 4.9 31.7 1.0 N A:ASN118 4.9 32.9 1.0 CA A:ASP5 5.0 35.7 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:Ca341 b:31.9 occ:1.00 OD2 A:ASP69 2.2 37.3 1.0 O A:ASP76 2.3 33.8 1.0 O A:HOH405 2.3 10.1 1.0 OD2 A:ASP74 2.6 35.7 1.0 OD2 A:ASP59 2.7 30.5 1.0 OD1 A:ASP74 2.7 30.8 1.0 CG A:ASP74 3.0 35.3 1.0 C A:ASP76 3.4 33.6 1.0 CG A:ASP69 3.5 36.6 1.0 CG A:ASP59 3.5 26.2 1.0 CB A:ASP59 3.6 26.2 1.0 NH1 A:ARG136 4.0 25.8 1.0 CA A:CA342 4.1 35.1 1.0 CB A:ASP76 4.1 36.7 1.0 CA A:ASP76 4.2 35.0 1.0 CB A:ASP69 4.3 36.5 1.0 OD1 A:ASP69 4.3 37.3 1.0 N A:ASP76 4.4 35.3 1.0 OE1 A:GLU80 4.5 35.1 1.0 N A:PRO77 4.5 32.2 1.0 CB A:ASP74 4.5 37.4 1.0 O A:PHE78 4.7 29.6 1.0 OD1 A:ASP59 4.7 25.1 1.0 O A:HOH374 4.7 24.9 1.0 CG A:ASP76 4.7 36.7 1.0 N A:PHE78 4.8 30.4 1.0 CA A:PRO77 4.8 30.5 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:Ca342 b:35.1 occ:1.00 O A:GLY72 2.2 38.1 1.0 O A:HOH374 2.4 24.9 1.0 OD1 A:ASP71 2.4 43.1 1.0 O A:ASP71 2.4 40.2 1.0 OD1 A:ASP74 2.5 30.8 1.0 OD1 A:ASP69 2.6 37.3 1.0 OD2 A:ASP69 3.0 37.3 1.0 C A:ASP71 3.1 41.1 1.0 CG A:ASP69 3.2 36.6 1.0 C A:GLY72 3.3 37.9 1.0 CG A:ASP71 3.5 44.0 1.0 CG A:ASP74 3.6 35.3 1.0 N A:GLY72 3.8 40.7 1.0 OG A:SER67 3.9 34.3 1.0 CA A:GLY72 3.9 39.3 1.0 CA A:ASP71 4.0 43.1 1.0 OD2 A:ASP59 4.0 30.5 1.0 CA A:CA341 4.1 31.9 1.0 CB A:SER67 4.1 32.8 1.0 N A:ASP71 4.1 42.6 1.0 CB A:ASP74 4.2 37.4 1.0 CB A:ASP71 4.3 44.1 1.0 O A:ILE61 4.3 27.6 1.0 N A:ARG73 4.4 37.0 1.0 CG A:ASP59 4.4 26.2 1.0 N A:ASP74 4.4 35.9 1.0 OD2 A:ASP71 4.5 46.2 1.0 OD2 A:ASP74 4.5 35.7 1.0 C A:ARG73 4.6 36.9 1.0 CB A:ASP69 4.7 36.5 1.0 CA A:ARG73 4.7 35.9 1.0 OD1 A:ASP59 4.8 25.1 1.0 CA A:ASP74 5.0 36.7 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