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

The structure of Crystal Structure of A Subtilisin-Like Protease, PDB code: 3lpc 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)	20.38 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.675, 45.821, 45.746, 98.40, 113.98, 114.61
R / Rfree (%)	13.5 / 17.6

The binding sites of Calcium atom in the Crystal Structure of A Subtilisin-Like Protease (pdb code 3lpc). 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: 3lpc:
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:11.0 occ:1.00 O A:GLY72 2.3 11.2 1.0 OD1 A:ASP71 2.3 12.8 1.0 OD1 A:ASP74 2.3 11.6 1.0 O A:HOH420 2.3 8.6 1.0 OD1 A:ASP69 2.5 10.1 1.0 O A:ASP71 2.5 10.8 1.0 OD2 A:ASP69 2.5 10.7 1.0 CG A:ASP69 2.8 12.8 1.0 C A:ASP71 3.2 12.0 1.0 C A:GLY72 3.4 10.4 1.0 CG A:ASP74 3.4 10.0 1.0 CG A:ASP71 3.5 17.6 1.0 N A:GLY72 3.8 12.3 1.0 CA A:CA362 3.9 9.9 1.0 CA A:GLY72 4.0 11.4 1.0 CA A:ASP71 4.0 12.1 1.0 OG A:SER67 4.0 12.2 1.0 CB A:ASP74 4.0 9.6 1.0 N A:ASP71 4.1 11.6 1.0 OD2 A:ASP59 4.1 10.7 1.0 CB A:SER67 4.2 10.2 1.0 O A:HOH554 4.3 20.6 1.0 CB A:ASP71 4.3 12.1 1.0 CB A:ASP69 4.3 10.6 1.0 OD2 A:ASP71 4.4 20.9 1.0 OD2 A:ASP74 4.4 10.4 1.0 O A:ILE61 4.4 9.2 1.0 CG A:ASP59 4.4 9.0 1.0 N A:ARG73 4.5 9.3 1.0 N A:ASP74 4.6 10.3 1.0 C A:ARG73 4.6 9.6 1.0 OD1 A:ASP59 4.7 8.1 1.0 CA A:ARG73 4.7 8.3 1.0 O A:HOH512 4.9 10.3 1.0 CA A:ASP74 5.0 9.7 1.0 O A:ASP69 5.0 11.7 1.0 C A:ASP69 5.0 10.7 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:Ca361 b:12.1 occ:1.00 OD1 A:ASP5 2.3 12.4 1.0 O A:VAL116 2.4 10.8 1.0 O A:ILE121 2.4 14.3 1.0 O A:VAL123 2.4 9.2 1.0 OD1 A:ASN119 2.4 14.7 1.0 OD1 A:ASP49 2.5 10.1 1.0 OD2 A:ASP49 2.6 11.8 1.0 CG A:ASP49 2.9 8.8 1.0 CG A:ASP5 3.3 13.9 1.0 CG A:ASN119 3.5 12.4 1.0 N A:VAL123 3.5 11.4 1.0 C A:VAL116 3.5 10.5 1.0 C A:VAL123 3.5 10.2 1.0 C A:ILE121 3.6 14.4 1.0 ND2 A:ASN119 3.9 12.9 1.0 CB A:ASP5 3.9 13.6 1.0 C A:GLY122 4.0 13.6 1.0 CA A:VAL123 4.1 10.1 1.0 CA A:THR117 4.2 11.0 1.0 N A:THR117 4.3 12.0 1.0 OD2 A:ASP5 4.3 15.1 1.0 CA A:GLY122 4.4 13.3 1.0 CB A:ASP49 4.4 8.8 1.0 N A:GLY122 4.4 13.4 1.0 CG1 A:ILE121 4.5 17.8 1.0 N A:ILE121 4.6 16.5 1.0 CA A:VAL116 4.6 9.1 1.0 CA A:ILE121 4.6 14.8 1.0 N A:ALA124 4.7 10.2 1.0 O A:GLY122 4.7 13.8 1.0 N A:ASN119 4.8 14.8 1.0 N A:VAL116 4.8 9.4 1.0 CB A:VAL116 4.8 7.9 1.0 CB A:ASN119 4.8 12.9 1.0 C A:THR117 4.9 13.5 1.0 N A:ASN118 4.9 15.9 1.0 CA A:ASP5 5.0 14.6 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:9.9 occ:1.00 OD2 A:ASP69 2.3 10.7 1.0 O A:ASP76 2.3 9.2 1.0 OD2 A:ASP59 2.4 10.7 1.0 O A:HOH512 2.4 10.3 1.0 O A:HOH407 2.4 8.2 1.0 OD2 A:ASP74 2.5 10.4 1.0 OD1 A:ASP74 2.6 11.6 1.0 CG A:ASP74 2.9 10.0 1.0 CG A:ASP59 3.3 9.0 1.0 CG A:ASP69 3.5 12.8 1.0 C A:ASP76 3.5 9.9 1.0 CB A:ASP59 3.6 7.1 1.0 CA A:CA360 3.9 11.0 1.0 CB A:ASP69 4.1 10.6 1.0 CB A:ASP76 4.1 11.7 1.0 NH1 A:ARG136 4.2 7.3 1.0 CA A:ASP76 4.2 11.0 1.0 O A:HOH554 4.3 20.6 1.0 OD1 A:ASP59 4.4 8.1 1.0 CB A:ASP74 4.4 9.6 1.0 N A:ASP76 4.4 9.0 1.0 OE2 A:GLU80 4.5 11.1 1.0 O A:HOH420 4.5 8.6 1.0 OD1 A:ASP69 4.5 10.1 1.0 N A:PRO77 4.6 11.1 1.0 O A:HOH557 4.6 23.6 1.0 CG A:ASP76 4.7 16.3 1.0 CA A:PRO77 4.8 10.1 1.0 O A:HOH552 4.8 20.6 1.0 N A:PHE78 4.8 9.4 1.0 O A:PHE78 4.8 9.6 1.0 OD1 A:ASP71 5.0 12.8 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