Cobalt in PDB 2xjm: Crystal Structure of Streptococcus Suis Dpr with Cobalt

The structure of Crystal Structure of Streptococcus Suis Dpr with Cobalt, PDB code: 2xjm 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)	24.91 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.960, 137.420, 141.950, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 24

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

Chlorine	(Cl)	3 atoms
Calcium	(Ca)	8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of Streptococcus Suis Dpr with Cobalt (pdb code 2xjm). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 12 binding sites of Cobalt where determined in the Crystal Structure of Streptococcus Suis Dpr with Cobalt, PDB code: 2xjm:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1173 b:42.3 occ:1.00 OE2 A:GLU78 2.1 45.1 1.0 NE2 C:HIS47 2.2 35.3 1.0 OD2 A:ASP74 2.4 46.6 1.0 OD1 A:ASP74 2.4 46.2 1.0 O A:HOH2063 2.6 13.5 1.0 CG A:ASP74 2.7 43.5 1.0 CD A:GLU78 3.2 41.6 1.0 CD2 C:HIS47 3.2 33.1 1.0 CE1 C:HIS47 3.3 33.4 1.0 OE1 A:GLU78 3.7 41.2 1.0 CB A:ASP74 4.2 40.4 1.0 NE2 C:HIS59 4.2 39.4 1.0 OD1 C:ASP63 4.2 42.4 1.0 OD2 C:ASP63 4.3 46.3 1.0 CG A:GLU78 4.3 40.5 1.0 CG C:HIS47 4.3 31.9 1.0 ND1 C:HIS47 4.4 32.6 1.0 CE1 C:HIS59 4.4 38.3 1.0 NE1 C:TRP48 4.7 34.5 1.0 CG C:ASP63 4.7 40.3 1.0 O A:ASP74 4.8 39.4 1.0

Cobalt binding site 2 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1173 b:42.7 occ:1.00 OE2 B:GLU78 2.0 36.6 1.0 NE2 D:HIS47 2.2 25.9 1.0 OD1 B:ASP74 2.3 44.2 1.0 O B:HOH2093 2.5 22.8 1.0 O D:HOH2022 2.5 25.6 1.0 OD2 B:ASP74 2.7 40.4 1.0 CG B:ASP74 2.8 40.2 1.0 CD B:GLU78 3.0 33.6 1.0 CD2 D:HIS47 3.1 23.7 1.0 CE1 D:HIS47 3.2 24.2 1.0 OE1 B:GLU78 3.4 28.6 1.0 OD2 D:ASP63 4.0 43.5 1.0 NE2 D:HIS59 4.1 33.0 1.0 CG B:GLU78 4.2 30.0 1.0 CE1 D:HIS59 4.3 29.9 1.0 CB B:ASP74 4.3 35.3 1.0 CG D:HIS47 4.3 25.6 1.0 ND1 D:HIS47 4.3 28.0 1.0 OD1 D:ASP63 4.4 42.4 1.0 CG D:ASP63 4.6 37.0 1.0 NE1 D:TRP48 4.7 26.1 1.0 CD1 D:TRP48 5.0 25.4 1.0

Cobalt binding site 3 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ C:Co1173 b:48.5 occ:1.00 OE2 C:GLU78 2.1 41.6 1.0 NE2 A:HIS47 2.2 31.2 1.0 OD1 C:ASP74 2.3 47.1 1.0 OD2 C:ASP74 2.6 45.6 1.0 CG C:ASP74 2.7 45.0 1.0 O A:HOH2014 2.8 24.4 1.0 CD C:GLU78 3.1 40.1 1.0 CE1 A:HIS47 3.2 30.5 1.0 CD2 A:HIS47 3.2 30.8 1.0 OE1 C:GLU78 3.4 39.0 1.0 NE2 A:HIS59 4.0 30.5 1.0 OD2 A:ASP63 4.1 45.3 1.0 CE1 A:HIS59 4.1 26.7 1.0 CB C:ASP74 4.3 40.6 1.0 ND1 A:HIS47 4.3 32.9 1.0 CG A:HIS47 4.3 32.1 1.0 O A:HOH2019 4.4 26.9 1.0 CG C:GLU78 4.4 37.3 1.0 OD1 A:ASP63 4.5 44.3 1.0 NE1 A:TRP48 4.7 33.1 1.0 CG A:ASP63 4.7 38.8 1.0 CD1 A:TRP48 5.0 33.3 1.0

Cobalt binding site 4 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ D:Co1173 b:36.7 occ:1.00 OE2 D:GLU78 2.0 33.4 1.0 O D:HOH2088 2.0 20.9 1.0 NE2 B:HIS47 2.2 23.1 1.0 OD1 D:ASP74 2.4 40.5 1.0 OD2 D:ASP74 2.6 33.4 1.0 O D:HOH2089 2.6 18.3 1.0 CG D:ASP74 2.8 36.7 1.0 CD D:GLU78 3.0 31.0 1.0 CD2 B:HIS47 3.2 18.9 1.0 O B:HOH2024 3.2 32.1 1.0 CE1 B:HIS47 3.3 20.6 1.0 OE1 D:GLU78 3.4 30.9 1.0 NE2 B:HIS59 4.0 26.4 1.0 CE1 B:HIS59 4.2 21.8 1.0 CB D:ASP74 4.3 33.0 1.0 OD2 B:ASP63 4.3 39.3 1.0 CG D:GLU78 4.3 28.1 1.0 CG B:HIS47 4.3 22.9 1.0 OD1 B:ASP63 4.3 39.3 1.0 ND1 B:HIS47 4.3 22.4 1.0 NE1 B:TRP48 4.6 25.5 1.0 CG B:ASP63 4.8 32.7 1.0 CD1 B:TRP48 4.9 24.9 1.0 O D:ASP74 4.9 31.9 1.0

Cobalt binding site 5 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ E:Co1174 b:48.5 occ:1.00 OE2 E:GLU78 1.9 30.2 0.5 NE2 G:HIS47 2.1 36.1 1.0 OD1 E:ASP74 2.5 51.2 1.0 OD2 E:ASP74 2.7 51.2 1.0 O E:HOH2022 2.8 28.8 1.0 CG E:ASP74 2.9 49.3 1.0 CD2 G:HIS47 3.0 35.1 1.0 CD E:GLU78 3.1 31.9 0.5 CE1 G:HIS47 3.1 36.2 1.0 OE2 E:GLU78 3.3 35.4 0.5 OE1 E:GLU78 3.6 29.7 0.5 NE2 G:HIS59 4.1 37.9 1.0 OD2 G:ASP63 4.1 47.5 1.0 CG G:HIS47 4.2 35.8 1.0 ND1 G:HIS47 4.2 38.0 1.0 CD E:GLU78 4.3 34.6 0.5 CG E:GLU78 4.3 34.2 0.5 CE1 G:HIS59 4.3 37.4 1.0 OD1 G:ASP63 4.3 44.6 1.0 CG E:GLU78 4.4 35.5 0.5 CB E:ASP74 4.4 45.8 1.0 CG G:ASP63 4.7 41.7 1.0 NE1 G:TRP48 4.8 34.2 1.0 CD1 G:TRP48 5.0 35.1 1.0

Cobalt binding site 6 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ F:Co1173 b:33.5 occ:1.00 OE2 F:GLU78 2.0 21.3 0.5 NE2 H:HIS47 2.1 25.5 1.0 OD1 F:ASP74 2.3 44.1 1.0 OD2 F:ASP74 2.6 44.1 1.0 CG F:ASP74 2.8 40.7 1.0 CD F:GLU78 3.0 22.0 0.5 CD2 H:HIS47 3.1 23.3 1.0 OE2 F:GLU78 3.1 28.7 0.5 CE1 H:HIS47 3.2 23.1 1.0 OE1 F:GLU78 3.4 20.0 0.5 OD2 H:ASP63 3.9 44.6 1.0 CD F:GLU78 4.0 26.3 0.5 NE2 H:HIS59 4.2 30.3 1.0 CG H:HIS47 4.2 26.7 1.0 ND1 H:HIS47 4.2 27.5 1.0 CG F:GLU78 4.3 24.2 0.5 CB F:ASP74 4.3 36.0 1.0 CG F:GLU78 4.3 27.6 0.5 CE1 H:HIS59 4.4 29.8 1.0 O H:HOH2018 4.5 25.5 1.0 NE1 H:TRP48 4.6 29.1 1.0 CG H:ASP63 4.7 38.3 1.0 OD1 H:ASP63 4.7 42.4 1.0 CD1 H:TRP48 4.9 28.4 1.0 OE1 F:GLU78 4.9 24.3 0.5 O F:ASP74 5.0 34.2 1.0 CE1 H:HIS44 5.0 31.9 1.0

Cobalt binding site 7 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ G:Co1173 b:49.1 occ:1.00 OE2 G:GLU78 2.1 51.5 1.0 O G:HOH2052 2.1 31.0 1.0 NE2 E:HIS47 2.3 35.1 1.0 OD2 G:ASP74 2.4 46.9 1.0 OD1 G:ASP74 2.4 49.3 1.0 O G:HOH2022 2.6 19.2 1.0 CG G:ASP74 2.8 46.4 1.0 CD G:GLU78 3.2 48.3 1.0 CE1 E:HIS47 3.2 33.6 1.0 CD2 E:HIS47 3.3 32.7 1.0 OE1 G:GLU78 3.7 47.6 1.0 NE2 E:HIS59 4.1 33.5 1.0 OD2 E:ASP63 4.1 44.7 1.0 CB G:ASP74 4.3 42.9 1.0 CE1 E:HIS59 4.3 34.3 1.0 ND1 E:HIS47 4.3 33.0 1.0 CG G:GLU78 4.4 43.4 1.0 CG E:HIS47 4.4 32.1 1.0 OD1 E:ASP63 4.5 43.8 1.0 CG E:ASP63 4.8 40.3 1.0 NE1 E:TRP48 4.8 34.6 1.0

Cobalt binding site 8 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ H:Co1173 b:42.2 occ:1.00 OE2 H:GLU78 2.1 39.7 1.0 OD1 H:ASP74 2.2 42.0 1.0 NE2 F:HIS47 2.3 26.4 1.0 OD2 H:ASP74 2.6 38.8 1.0 CG H:ASP74 2.7 39.7 1.0 O F:HOH2017 2.8 30.8 1.0 CD H:GLU78 3.1 36.5 1.0 CD2 F:HIS47 3.2 23.6 1.0 CE1 F:HIS47 3.4 23.2 1.0 OE1 H:GLU78 3.4 35.9 1.0 NE2 F:HIS59 4.2 28.4 1.0 OD2 F:ASP63 4.2 41.3 1.0 CE1 F:HIS59 4.2 25.5 1.0 CB H:ASP74 4.2 36.1 1.0 CG H:GLU78 4.4 32.2 1.0 CG F:HIS47 4.4 24.5 1.0 ND1 F:HIS47 4.4 24.4 1.0 OD1 F:ASP63 4.6 39.0 1.0 NE1 F:TRP48 4.7 27.2 1.0 CG F:ASP63 4.8 35.4 1.0 CD1 F:TRP48 5.0 26.6 1.0

Cobalt binding site 9 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ I:Co1174 b:47.0 occ:1.00 OE2 I:GLU78 2.0 39.5 1.0 NE2 K:HIS47 2.3 23.5 1.0 OD1 I:ASP74 2.5 41.9 1.0 OD2 I:ASP74 2.5 39.3 1.0 O I:HOH2027 2.8 14.0 1.0 CG I:ASP74 2.8 39.8 1.0 CD I:GLU78 3.1 37.4 1.0 CD2 K:HIS47 3.3 22.9 1.0 CE1 K:HIS47 3.3 23.8 1.0 OE1 I:GLU78 3.6 34.5 1.0 OD2 K:ASP63 4.1 45.7 1.0 NE2 K:HIS59 4.1 29.8 1.0 OD1 K:ASP63 4.2 43.6 1.0 CE1 K:HIS59 4.2 29.1 1.0 CG I:GLU78 4.2 35.6 1.0 CB I:ASP74 4.3 36.3 1.0 ND1 K:HIS47 4.4 26.3 1.0 CG K:HIS47 4.4 25.6 1.0 CG K:ASP63 4.6 39.7 1.0 NE1 K:TRP48 4.7 29.5 1.0 CD1 K:TRP48 4.9 27.4 1.0

Cobalt binding site 10 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ J:Co1174 b:50.2 occ:1.00 OE2 J:GLU78 2.2 42.4 1.0 OD1 J:ASP74 2.2 43.8 1.0 NE2 L:HIS47 2.2 30.6 1.0 OD2 J:ASP74 2.6 42.5 1.0 CG J:ASP74 2.7 40.3 1.0 O J:HOH2035 2.9 19.6 1.0 CE1 L:HIS47 3.1 27.2 1.0 CD2 L:HIS47 3.2 29.6 1.0 CD J:GLU78 3.2 41.5 1.0 OE1 J:GLU78 3.7 43.1 1.0 NE2 L:HIS59 4.1 29.9 1.0 OD1 L:ASP63 4.1 47.5 1.0 CB J:ASP74 4.2 37.5 1.0 OD2 L:ASP63 4.2 46.4 1.0 CE1 L:HIS59 4.2 27.4 1.0 ND1 L:HIS47 4.3 28.8 1.0 CG L:HIS47 4.3 30.0 1.0 CG J:GLU78 4.4 39.1 1.0 NE1 L:TRP48 4.5 31.1 1.0 CG L:ASP63 4.6 41.3 1.0 CD1 L:TRP48 4.8 31.1 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