Calcium in PDB 3pg2: The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment

The structure of The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment, PDB code: 3pg2 was solved by K.Vengadesan, S.V.L.Narayana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.15 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.872, 60.273, 80.370, 90.00, 101.58, 90.00
R / Rfree (%)	20 / 23.4

The binding sites of Calcium atom in the The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment (pdb code 3pg2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment, PDB code: 3pg2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:9.2 occ:1.00 OD1 A:ASP218 2.3 9.4 1.0 O A:HOH3 2.4 9.3 1.0 OD1 A:ASP211 2.4 9.2 1.0 O A:LYS210 2.4 7.6 1.0 O A:HOH4 2.4 13.8 1.0 OD2 A:ASP209 2.5 7.3 1.0 OD1 A:ASP209 2.6 8.2 1.0 CG A:ASP209 2.9 7.7 1.0 CG A:ASP218 3.2 9.8 1.0 C A:LYS210 3.4 7.5 1.0 OD2 A:ASP218 3.5 11.1 1.0 CG A:ASP211 3.6 8.4 1.0 N A:LYS210 4.1 7.0 1.0 N A:ASP211 4.1 7.6 1.0 CA A:ASP211 4.1 7.8 1.0 O A:HOH875 4.3 22.2 1.0 CA A:LYS210 4.4 7.3 1.0 CB A:ASP209 4.4 8.2 1.0 CB A:ASP211 4.5 7.8 1.0 NZ A:LYS233 4.5 7.6 1.0 OD2 A:ASP211 4.5 6.7 1.0 O A:HOH65 4.6 16.6 1.0 CB A:ASP218 4.6 8.0 1.0 O A:HOH185 4.7 19.7 1.0 O A:ASP319 4.7 10.4 1.0 O A:ARG374 4.8 12.1 1.0 C A:ASP209 4.8 7.3 1.0 O A:GLN217 4.9 7.4 1.0

Calcium binding site 2 out of 4 in the The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:14.3 occ:1.00 O A:ALA364 2.4 15.8 1.0 OD1 A:ASP358 2.4 11.1 1.0 OE1 A:GLU244 2.4 11.3 1.0 OG1 A:THR360 2.5 14.6 1.0 OD1 A:ASN366 2.5 14.6 1.0 O A:THR360 2.5 14.4 1.0 OD1 A:ASP362 2.5 14.3 1.0 OD2 A:ASP358 2.6 11.4 1.0 CG A:ASP358 2.9 10.9 1.0 CD A:GLU244 3.4 13.0 1.0 CG A:ASP362 3.5 16.6 1.0 C A:THR360 3.5 15.0 1.0 CG A:ASN366 3.6 16.4 1.0 C A:ALA364 3.6 16.0 1.0 CB A:THR360 3.6 14.8 1.0 OD2 A:ASP362 3.9 15.1 1.0 CA A:THR360 3.9 14.7 1.0 ND2 A:ASN366 4.0 17.5 1.0 N A:ALA364 4.1 17.2 1.0 N A:THR360 4.1 13.9 1.0 OE2 A:GLU244 4.2 13.1 1.0 N A:ASP362 4.2 17.1 1.0 N A:ASN366 4.2 14.6 1.0 CG A:GLU244 4.3 12.2 1.0 CA A:ALA364 4.3 16.4 1.0 CB A:ASP358 4.4 10.8 1.0 CB A:GLU244 4.4 11.1 1.0 O A:HOH39 4.4 14.4 1.0 O A:HOH175 4.6 18.0 1.0 N A:ASP365 4.6 15.4 1.0 N A:LYS363 4.7 17.4 1.0 CB A:ALA364 4.7 16.3 1.0 N A:PRO361 4.7 15.5 1.0 CB A:ASP362 4.7 17.0 1.0 CG2 A:THR360 4.8 15.7 1.0 CB A:ASN366 4.8 14.3 1.0 CA A:ASP362 4.9 17.4 1.0 CA A:ASP365 4.9 15.3 1.0 CA A:ASN366 5.0 14.3 1.0

Calcium binding site 3 out of 4 in the The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1 b:12.5 occ:1.00 OD1 B:ASP211 2.3 11.9 1.0 OD1 B:ASP218 2.3 15.6 1.0 O B:HOH4 2.4 14.6 1.0 O B:LYS210 2.4 11.9 1.0 OD2 B:ASP209 2.5 13.6 1.0 OD1 B:ASP209 2.5 10.8 1.0 O B:HOH3 2.6 21.3 1.0 CG B:ASP209 2.8 11.0 1.0 CG B:ASP218 3.3 16.0 1.0 C B:LYS210 3.3 11.8 1.0 CG B:ASP211 3.5 11.9 1.0 OD2 B:ASP218 3.6 18.3 1.0 N B:LYS210 4.0 11.2 1.0 N B:ASP211 4.0 11.6 1.0 CA B:ASP211 4.1 12.2 1.0 CB B:ASP209 4.3 11.5 1.0 CA B:LYS210 4.3 11.6 1.0 NH2 B:ARG374 4.4 24.4 1.0 OD2 B:ASP211 4.4 13.1 1.0 CB B:ASP211 4.4 11.9 1.0 O B:HOH556 4.6 19.3 1.0 CB B:ASP218 4.6 13.5 1.0 O B:ASP319 4.7 15.6 1.0 NZ B:LYS233 4.7 11.2 1.0 NH1 B:ARG374 4.8 26.1 1.0 C B:ASP209 4.8 11.3 1.0 O B:GLN217 4.9 12.7 1.0 O B:HOH166 4.9 24.6 1.0 CZ B:ARG374 4.9 26.1 1.0 OD1 B:ASP319 5.0 14.2 1.0

Calcium binding site 4 out of 4 in the The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of the Major Pilin GBS80 of Streptococcus Agalactiae 35 kDa C-Terminal Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:19.0 occ:1.00 OE1 B:GLU244 2.3 17.9 1.0 O B:THR360 2.4 19.8 1.0 O B:ALA364 2.5 22.5 1.0 OD1 B:ASP362 2.5 19.5 1.0 OD1 B:ASP358 2.5 14.3 1.0 OD2 B:ASP358 2.5 15.0 1.0 OD1 B:ASN366 2.5 25.0 1.0 OG1 B:THR360 2.6 18.1 1.0 CG B:ASP358 2.8 13.7 1.0 CD B:GLU244 3.3 16.2 1.0 C B:THR360 3.5 19.2 1.0 CG B:ASP362 3.6 23.2 1.0 CG B:ASN366 3.6 21.7 1.0 C B:ALA364 3.7 22.8 1.0 CB B:THR360 3.7 18.2 1.0 OD2 B:ASP362 4.0 23.3 1.0 CA B:THR360 4.0 18.2 1.0 ND2 B:ASN366 4.0 22.1 1.0 OE2 B:GLU244 4.0 19.6 1.0 N B:ALA364 4.1 23.7 1.0 N B:ASP362 4.2 22.9 1.0 N B:ASN366 4.2 20.7 1.0 CG B:GLU244 4.3 15.6 1.0 N B:THR360 4.3 17.8 1.0 CB B:ASP358 4.3 13.9 1.0 CB B:GLU244 4.4 13.7 1.0 CA B:ALA364 4.4 23.2 1.0 O B:HOH525 4.5 21.3 1.0 O B:HOH91 4.6 18.7 1.0 N B:LYS363 4.6 24.2 1.0 N B:PRO361 4.6 20.0 1.0 CB B:ALA364 4.7 22.9 1.0 N B:ASP365 4.7 22.6 1.0 CB B:ASP362 4.8 23.1 1.0 CB B:ASN366 4.8 20.6 1.0 CA B:ASP362 4.9 23.3 1.0 CA B:ASP365 4.9 22.2 1.0 CA B:ASN366 5.0 20.7 1.0

K.Vengadesan, X.Ma, P.Dwivedi, H.Ton-That, S.V.L.Narayana. A Model For Group B Streptococcus Pilus Type 1: the Structure of A 35-kDa C-Terminal Fragment of the Major Pilin GBS80. J.Mol.Biol. V. 407 731 2011.
ISSN: ISSN 0022-2836
PubMed: 21333654
DOI: 10.1016/J.JMB.2011.02.024