Calcium in PDB 3ipk: Crystal Structure of A3VP1 of Agi/II of Streptococcus Mutans

The structure of Crystal Structure of A3VP1 of Agi/II of Streptococcus Mutans, PDB code: 3ipk was solved by M.R.Larson, K.R.Rajashankar, M.Patel, R.Robinette, P.Crowley, S.M.Michalek, L.J.Brady, C.C.Deivanayagam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.72 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.031, 164.146, 67.733, 90.00, 91.03, 90.00
R / Rfree (%)	18.1 / 22.2

The binding sites of Calcium atom in the Crystal Structure of A3VP1 of Agi/II of Streptococcus Mutans (pdb code 3ipk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A3VP1 of Agi/II of Streptococcus Mutans, PDB code: 3ipk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A3VP1 of Agi/II of Streptococcus Mutans


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 A3VP1 of Agi/II of Streptococcus Mutans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:26.3 occ:1.00 O A:SER697 2.2 8.7 1.0 OD1 A:ASN699 2.3 10.0 1.0 OG A:SER697 2.4 9.8 1.0 O A:HOH1108 2.4 11.5 1.0 O A:HOH979 2.5 9.7 1.0 OE1 A:GLU706 2.6 9.8 1.0 CB A:SER697 3.2 8.6 1.0 C A:SER697 3.3 9.2 1.0 CD A:GLU706 3.4 13.6 1.0 OE2 A:GLU706 3.5 15.1 1.0 CG A:ASN699 3.5 8.2 1.0 O A:HOH1054 3.7 21.3 1.0 CA A:SER697 3.8 9.1 1.0 O A:HOH1056 4.0 27.9 1.0 O A:TRP816 4.1 8.7 1.0 N A:ASN699 4.2 8.3 1.0 ND2 A:ASN699 4.4 9.0 1.0 N A:LEU698 4.4 7.9 1.0 CB A:ASN699 4.5 7.6 1.0 OD2 A:ASP760 4.5 15.3 1.0 O A:HOH919 4.6 13.2 1.0 C2 A:PMS900 4.8 39.1 1.0 CE3 A:TRP816 4.8 18.2 1.0 O A:HOH912 4.8 8.6 1.0 CA A:LEU698 4.8 8.8 1.0 OD1 A:ASP760 4.9 12.8 1.0 CG A:GLU706 4.9 13.2 1.0 O A:ALA696 4.9 12.0 1.0 CA A:ASN699 5.0 8.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A3VP1 of Agi/II of Streptococcus Mutans


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 A3VP1 of Agi/II of Streptococcus Mutans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca905 b:23.4 occ:1.00 OG B:SER697 2.2 9.7 1.0 O B:SER697 2.2 9.5 1.0 OD1 B:ASN699 2.3 11.8 1.0 O B:HOH1313 2.4 12.8 1.0 O B:HOH1362 2.4 13.6 1.0 OE1 B:GLU706 2.6 11.5 1.0 CB B:SER697 3.1 11.1 1.0 C B:SER697 3.3 9.3 1.0 CD B:GLU706 3.4 13.8 1.0 OE2 B:GLU706 3.5 15.7 1.0 CG B:ASN699 3.5 11.3 1.0 O B:HOH1707 3.7 30.7 1.0 O B:HOH1534 3.7 27.8 1.0 CA B:SER697 3.7 9.2 1.0 O B:TRP816 3.9 10.0 1.0 N B:ASN699 4.2 9.8 1.0 OD2 B:ASP760 4.3 16.8 1.0 O B:HOH1393 4.4 11.5 1.0 ND2 B:ASN699 4.4 11.0 1.0 N B:LEU698 4.4 8.0 1.0 CB B:ASN699 4.4 11.2 1.0 CE3 B:TRP816 4.5 21.3 1.0 OD1 B:ASP760 4.7 12.6 1.0 C2 B:PMS901 4.8 39.9 1.0 O B:HOH1321 4.8 11.2 1.0 CZ3 B:TRP816 4.8 22.2 1.0 CA B:LEU698 4.8 9.7 1.0 CG B:GLU706 4.8 11.3 1.0 CG B:ASP760 4.9 16.5 1.0 O B:ALA696 4.9 8.8 1.0 CA B:ASN699 5.0 10.6 1.0

M.R.Larson, K.R.Rajashankar, M.H.Patel, R.A.Robinette, P.J.Crowley, S.Michalek, L.J.Brady, C.Deivanayagam. Elongated Fibrillar Structure of A Streptococcal Adhesin Assembled By the High-Affinity Association of Alpha- and Ppii-Helices. Proc.Natl.Acad.Sci.Usa V. 107 5983 2010.
ISSN: ISSN 0027-8424
PubMed: 20231452
DOI: 10.1073/PNAS.0912293107