Calcium in PDB 3ti9: Crystal Structure of the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus

The structure of Crystal Structure of the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus, PDB code: 3ti9 was solved by W.Wong, J.C.Whisstock, C.J.Porter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.38 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.462, 90.514, 44.060, 90.00, 109.99, 90.00
R / Rfree (%)	15.7 / 20.7

The structure of Crystal Structure of the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus (pdb code 3ti9). 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 the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus, PDB code: 3ti9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus


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 the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca353 b:8.0 occ:1.00 OD1 A:ASP5 2.3 6.5 1.0 O A:VAL116 2.3 7.0 1.0 O A:VAL121 2.4 8.2 1.0 O A:VAL123 2.4 6.5 1.0 OD1 A:ASN119 2.5 7.1 1.0 OD1 A:ASP49 2.5 7.3 1.0 OD2 A:ASP49 2.6 9.1 1.0 CG A:ASP49 2.9 7.2 1.0 CG A:ASP5 3.3 7.7 1.0 C A:VAL116 3.5 7.1 1.0 CG A:ASN119 3.5 9.1 1.0 C A:VAL123 3.5 6.3 1.0 N A:VAL123 3.6 6.1 1.0 C A:VAL121 3.6 9.9 1.0 CB A:ASP5 3.9 8.0 1.0 ND2 A:ASN119 3.9 6.9 1.0 C A:GLY122 4.1 7.6 1.0 CA A:VAL123 4.2 6.2 1.0 CA A:THR117 4.2 8.1 1.0 N A:THR117 4.3 7.7 1.0 OD2 A:ASP5 4.3 7.1 1.0 CB A:ASP49 4.4 7.0 1.0 CA A:GLY122 4.4 8.0 1.0 N A:GLY122 4.4 9.3 1.0 CG1 A:VAL121 4.5 13.6 1.0 N A:VAL121 4.5 10.3 1.0 CA A:VAL121 4.6 10.6 1.0 CA A:VAL116 4.6 6.7 1.0 N A:ALA124 4.7 6.3 1.0 O A:GLY122 4.7 7.8 1.0 N A:ASN119 4.8 9.3 1.0 CB A:ASN119 4.8 9.6 1.0 CB A:VAL116 4.8 6.3 1.0 C A:THR117 4.8 8.6 1.0 N A:VAL116 4.9 6.2 1.0 N A:ASN118 4.9 8.8 1.0 CA A:ASP5 4.9 8.0 1.0 CA A:ALA124 5.0 6.4 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus


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 the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca354 b:7.2 occ:1.00 O A:ASN76 2.4 7.2 1.0 O A:HOH514 2.4 8.1 1.0 O A:HOH506 2.4 8.0 1.0 OD2 A:ASP69 2.4 4.7 1.0 OD2 A:ASP59 2.4 8.4 1.0 OD2 A:ASP74 2.5 7.0 1.0 OD1 A:ASP74 2.6 7.1 1.0 CG A:ASP74 2.9 7.5 1.0 CG A:ASP59 3.4 9.0 1.0 C A:ASN76 3.5 6.8 1.0 CG A:ASP69 3.5 8.3 1.0 CB A:ASP59 3.6 6.5 1.0 CA A:CA355 3.9 8.2 1.0 CB A:ASN76 4.1 8.2 1.0 CB A:ASP69 4.1 7.9 1.0 NH1 A:ARG136 4.2 6.9 1.0 CA A:ASN76 4.2 7.5 1.0 CB A:ASP74 4.4 7.3 1.0 N A:ASN76 4.5 7.7 1.0 OD1 A:ASP59 4.5 6.9 1.0 O A:HOH533 4.5 5.2 1.0 OD1 A:ASP69 4.6 7.9 1.0 CG A:ASN76 4.6 6.7 1.0 N A:PRO77 4.6 5.7 1.0 O A:HOH502 4.6 9.5 1.0 N A:ALA78 4.6 6.7 1.0 OD1 A:ASP71 4.7 12.7 1.0 OE2 A:GLU80 4.8 11.2 1.0 O A:ALA78 4.8 6.2 1.0 CA A:PRO77 4.8 6.1 1.0 ND2 A:ASN76 4.9 10.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus


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 the Basic Protease Bprb From the Ovine Footrot Pathogen, Dichelobacter Nodosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca355 b:8.2 occ:1.00 O A:GLN72 2.3 9.8 1.0 OD1 A:ASP71 2.4 12.7 1.0 OD1 A:ASP74 2.4 7.1 1.0 O A:HOH502 2.4 9.5 1.0 OD2 A:ASP69 2.5 4.7 1.0 O A:ASP71 2.5 10.5 1.0 OD1 A:ASP69 2.5 7.9 1.0 CG A:ASP69 2.8 8.3 1.0 C A:ASP71 3.2 10.6 1.0 C A:GLN72 3.4 10.1 1.0 CG A:ASP71 3.5 13.6 1.0 CG A:ASP74 3.5 7.5 1.0 N A:GLN72 3.9 10.4 1.0 CB A:ALA67 3.9 7.6 1.0 CA A:CA354 3.9 7.2 1.0 CA A:GLN72 4.0 11.2 1.0 CA A:ASP71 4.0 11.0 1.0 N A:ASP71 4.1 10.6 1.0 OD2 A:ASP59 4.2 8.4 1.0 CB A:ASP74 4.2 7.3 1.0 CB A:ASP69 4.3 7.9 1.0 CB A:ASP71 4.3 10.7 1.0 OD2 A:ASP71 4.4 11.6 1.0 CG A:ASP59 4.5 9.0 1.0 N A:ARG73 4.5 8.8 1.0 O A:ILE61 4.5 9.3 1.0 OD2 A:ASP74 4.5 7.0 1.0 N A:ASP74 4.7 6.9 1.0 C A:ARG73 4.7 7.0 1.0 CA A:ARG73 4.7 7.5 1.0 OD1 A:ASP59 4.7 6.9 1.0 O A:HOH514 4.8 8.1 1.0 C A:ASP69 5.0 8.9 1.0

W.Wong, L.C.Wijeyewickrema, R.M.Kennan, S.B.Reeve, D.L.Steer, C.Reboul, A.I.Smith, R.N.Pike, J.I.Rood, J.C.Whisstock, C.J.Porter. S1 Pocket of A Bacterially Derived Subtilisin-Like Protease Underpins Effective Tissue Destruction. J.Biol.Chem. V. 286 42180 2011.
ISSN: ISSN 0021-9258
PubMed: 21990366
DOI: 10.1074/JBC.M111.298711