Calcium in PDB 2xkq: Crystal Structure of Streptococcus Suis Dpr with Manganese

The structure of Crystal Structure of Streptococcus Suis Dpr with Manganese, PDB code: 2xkq was solved by T.Haikarainen, A.Thanassoulas, P.Stavros, G.Nounesis, S.Haataja, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.222, 139.467, 143.827, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 24.5

The structure of Crystal Structure of Streptococcus Suis Dpr with Manganese also contains other interesting chemical elements:

Manganese	(Mn)	12 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Crystal Structure of Streptococcus Suis Dpr with Manganese (pdb code 2xkq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Streptococcus Suis Dpr with Manganese, PDB code: 2xkq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Manganese


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 Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1175 b:42.5 occ:1.00 OE2 B:GLU113 2.5 42.9 1.0 OE1 B:GLU113 2.5 42.9 1.0 CD B:GLU113 2.8 41.2 1.0 CG B:GLU113 4.3 36.2 1.0 CG2 B:THR110 4.7 34.6 1.0 N B:THR110 4.7 33.0 1.0 CA B:VAL109 4.9 33.5 1.0 O B:ASN108 4.9 36.3 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Manganese


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 Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1176 b:58.0 occ:1.00 O B:HOH2054 2.7 16.2 1.0 O J:HOH2032 2.7 19.3 1.0 O B:GLY167 4.3 33.5 1.0 CA B:GLY167 4.5 31.1 1.0 O J:HOH2033 4.8 2.0 1.0 C B:GLY167 4.8 32.1 1.0 O J:ARG51 4.9 30.2 1.0 O J:ASN108 5.0 41.2 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Manganese


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 Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1175 b:29.7 occ:1.00 OD2 D:ASP24 2.3 51.1 1.0 OE2 D:GLU139 2.7 49.6 1.0 CG D:ASP24 3.4 48.8 1.0 CD D:GLU139 3.6 48.0 1.0 CG D:GLU139 3.6 44.7 1.0 CB D:ASP24 4.0 45.2 1.0 O D:HOH2002 4.1 6.3 1.0 OD1 D:ASP24 4.4 49.5 1.0 OE1 D:GLU139 4.8 47.3 1.0 N D:ASP24 4.9 44.5 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Manganese


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1174 b:13.2 occ:1.00 O F:HOH2055 2.3 8.2 1.0 O F:HOH2039 2.3 3.1 1.0 O F:LEU166 2.4 28.5 1.0 O F:HOH2056 2.4 7.5 1.0 C F:LEU166 3.5 27.8 1.0 OE2 F:GLU112 4.1 56.1 1.0 NE2 F:GLN168 4.2 34.4 1.0 CA F:LEU166 4.2 27.6 1.0 CB F:LEU166 4.4 28.0 1.0 N F:GLY167 4.5 27.4 1.0 CA F:GLY167 4.7 28.2 1.0 CD F:GLU112 5.0 54.0 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Manganese


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1175 b:33.5 occ:1.00 O F:HOH2036 2.7 20.8 1.0 O F:ASN108 4.3 42.4 1.0 O J:GLY167 4.5 35.6 1.0 O F:ARG51 4.8 33.8 1.0 O F:TYR107 4.8 41.0 1.0 C F:ASN108 4.9 41.9 1.0 CA J:GLY167 4.9 32.9 1.0 CB F:ARG51 4.9 34.3 1.0 O F:VAL109 5.0 37.3 1.0 CA F:ASN108 5.0 42.9 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Manganese


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1174 b:26.3 occ:1.00 O G:ASN108 3.1 57.4 1.0 C G:ASN108 4.3 55.7 1.0 OE1 G:GLU113 4.7 53.6 1.0 CB G:ASN108 4.9 57.6 1.0

T.Haikarainen, A.Thanassoulas, P.Stavros, G.Nounesis, S.Haataja, A.C.Papageorgiou. Structural and Thermodynamic Characterization of Metal Ion Binding in Streptococcus Suis Dpr. J.Mol.Biol. V. 405 448 2011.
ISSN: ISSN 0022-2836
PubMed: 21056572
DOI: 10.1016/J.JMB.2010.10.058