Calcium in PDB 2xjo: Crystal Structure of Streptococcus Suis Dpr with Nickel

The structure of Crystal Structure of Streptococcus Suis Dpr with Nickel, PDB code: 2xjo 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)	20.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.856, 137.459, 141.729, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.2

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

Nickel	(Ni)	12 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Calcium atom in the Crystal Structure of Streptococcus Suis Dpr with Nickel (pdb code 2xjo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Streptococcus Suis Dpr with Nickel, PDB code: 2xjo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


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 Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1175 b:28.6 occ:1.00 O B:HOH2057 2.3 7.7 1.0 OE2 B:GLU113 2.4 44.7 1.0 OE1 B:GLU113 2.4 39.4 1.0 O B:HOH2062 2.6 16.6 1.0 CD B:GLU113 2.7 41.5 1.0 CG B:GLU113 4.3 36.1 1.0 CG2 B:THR110 4.6 36.3 1.0 N B:THR110 4.7 33.8 1.0 O B:ASN108 4.7 43.1 1.0 CA B:VAL109 4.8 36.9 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


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 Nickel within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1175 b:38.5 occ:1.00 O D:HOH2062 2.4 16.4 1.0 O G:HOH2043 2.5 16.6 1.0 O D:HOH2065 2.9 9.0 1.0 O D:ASN108 4.4 50.1 1.0 CA D:ASN108 4.5 47.9 1.0 O D:TYR107 4.7 43.2 1.0 O G:GLY167 4.7 42.9 1.0 C D:ASN108 4.7 48.7 1.0 O D:ARG51 4.9 40.5 1.0 O D:VAL109 4.9 47.8 1.0 CL D:CL1174 5.0 26.2 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


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 Nickel within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1174 b:9.9 occ:1.00 O F:HOH2044 2.2 9.1 1.0 O F:HOH2073 2.2 7.1 1.0 O F:HOH2072 2.4 11.2 1.0 O F:LEU166 2.4 33.1 1.0 C F:LEU166 3.5 32.4 1.0 O F:HOH2069 4.1 2.0 1.0 NE2 F:GLN168 4.1 39.4 1.0 CA F:LEU166 4.2 31.7 1.0 OE1 F:GLU112 4.4 57.5 1.0 O F:HOH2074 4.4 10.4 1.0 CB F:LEU166 4.4 31.5 1.0 N F:GLY167 4.5 32.0 1.0 CA F:GLY167 4.7 33.3 1.0 CD F:GLU112 4.8 55.3 1.0 CG F:GLN168 5.0 35.5 1.0 CG F:GLU112 5.0 49.0 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


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 Nickel within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1175 b:29.6 occ:1.00 O F:HOH2042 2.5 14.2 1.0 O F:ASN108 4.0 47.7 1.0 C F:ASN108 4.5 46.4 1.0 O F:TYR107 4.5 45.7 1.0 O F:VAL109 4.6 40.2 1.0 CA F:ASN108 4.6 47.5 1.0 O J:GLY167 4.7 41.1 1.0 O F:ARG51 4.8 36.9 1.0 OD1 F:ASN108 5.0 52.4 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


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 Nickel within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca1175 b:38.5 occ:1.00 O I:HOH2039 2.3 15.2 1.0 O I:HOH2007 2.6 16.9 1.0 O I:ASN108 4.2 50.9 1.0 O D:HOH2043 4.5 14.7 1.0 C I:ASN108 4.7 50.0 1.0 CL I:CL1174 4.7 22.1 1.0 O I:TYR107 4.7 45.8 1.0 O I:VAL109 4.8 45.3 1.0 CA I:ASN108 4.8 50.5 1.0 O I:ARG51 4.9 42.4 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


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 Nickel within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca1175 b:36.3 occ:1.00 O B:HOH2086 2.5 5.8 1.0 O J:HOH2041 2.7 13.2 1.0 O J:HOH2039 2.7 20.9 1.0 O J:ASN108 4.4 43.9 1.0 O B:GLY167 4.4 35.9 1.0 O B:HOH2034 4.6 16.8 1.0 O J:TYR107 4.7 38.9 1.0 C J:ASN108 4.9 42.9 1.0 O J:ARG51 4.9 33.4 1.0 CA J:ASN108 4.9 43.7 1.0 O J:VAL109 4.9 40.8 1.0 CA B:GLY167 4.9 34.2 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ K:Ca1175 b:48.5 occ:1.00 O K:HOH2068 2.4 18.4 1.0 O K:GLY167 4.0 43.1 1.0 O H:HOH2009 4.3 13.7 1.0 O H:ASN108 4.3 58.7 1.0 CA K:GLY167 4.4 41.8 1.0 C K:GLY167 4.6 42.3 1.0 CB H:ARG51 4.8 43.2 1.0 O H:ARG51 4.9 43.3 1.0 O H:TYR107 5.0 51.4 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