Manganese 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:

Chlorine	(Cl)	4 atoms
Calcium	(Ca)	6 atoms

Pages:

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

Binding sites:

The binding sites of Manganese 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 Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of Streptococcus Suis Dpr with Manganese, PDB code: 2xkq:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1173 b:20.6 occ:1.00 OE2 A:GLU78 2.1 42.4 1.0 OD1 A:ASP74 2.2 45.7 1.0 NE2 C:HIS47 2.3 32.7 1.0 OD2 A:ASP74 2.7 44.7 1.0 CG A:ASP74 2.8 42.8 1.0 CD2 C:HIS47 3.2 32.9 1.0 CD A:GLU78 3.2 41.6 1.0 CE1 C:HIS47 3.3 32.6 1.0 OE1 A:GLU78 3.8 42.6 1.0 CB A:ASP74 4.3 40.8 1.0 OD2 C:ASP63 4.3 39.4 1.0 CG A:GLU78 4.4 39.2 1.0 CG C:HIS47 4.4 34.1 1.0 ND1 C:HIS47 4.4 34.2 1.0 CE1 C:HIS59 4.4 34.6 1.0 NE2 C:HIS59 4.5 36.1 1.0 OD1 C:ASP63 4.5 44.6 1.0 NE1 C:TRP48 4.6 33.9 1.0 CG C:ASP63 4.8 40.0 1.0 CD1 C:TRP48 5.0 32.9 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1174 b:14.7 occ:1.00 OE2 B:GLU78 2.0 37.5 1.0 OD1 B:ASP74 2.2 47.2 1.0 NE2 D:HIS47 2.3 30.8 1.0 O B:HOH2059 2.7 15.5 1.0 CG B:ASP74 2.9 43.0 1.0 OD2 B:ASP74 2.9 43.6 1.0 CD B:GLU78 3.2 34.8 1.0 CD2 D:HIS47 3.2 30.3 1.0 CE1 D:HIS47 3.4 30.2 1.0 OE1 B:GLU78 3.8 35.4 1.0 OD1 D:ASP63 4.2 40.6 1.0 CG B:GLU78 4.3 33.0 1.0 CB B:ASP74 4.3 39.3 1.0 CG D:HIS47 4.4 30.2 1.0 NE2 D:HIS59 4.5 34.0 1.0 ND1 D:HIS47 4.5 29.9 1.0 CE1 D:HIS59 4.5 31.9 1.0 OD2 D:ASP63 4.5 40.6 1.0 NE1 D:TRP48 4.6 29.5 1.0 CG D:ASP63 4.8 37.5 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1173 b:30.8 occ:1.00 OE2 C:GLU78 2.1 44.4 1.0 OD1 C:ASP74 2.2 49.3 1.0 NE2 A:HIS47 2.4 33.4 1.0 OD2 C:ASP74 2.9 49.1 1.0 CG C:ASP74 2.9 47.0 1.0 CD C:GLU78 3.3 42.9 1.0 CD2 A:HIS47 3.3 33.9 1.0 CE1 A:HIS47 3.4 32.0 1.0 OE1 C:GLU78 3.8 41.3 1.0 OD1 A:ASP63 4.1 43.7 1.0 NE2 A:HIS59 4.4 32.6 1.0 CB C:ASP74 4.4 44.2 1.0 CG C:GLU78 4.4 39.5 1.0 ND1 A:HIS47 4.4 33.4 1.0 CG A:HIS47 4.4 33.9 1.0 CE1 A:HIS59 4.4 30.9 1.0 OD2 A:ASP63 4.7 44.7 1.0 NE1 A:TRP48 4.8 38.1 1.0 O A:HOH2009 4.8 25.1 1.0 CG A:ASP63 4.9 41.0 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1174 b:20.1 occ:1.00 OE2 D:GLU78 2.1 38.6 1.0 NE2 B:HIS47 2.4 23.8 1.0 OD1 D:ASP74 2.5 42.3 1.0 OD2 D:ASP74 2.5 38.0 1.0 CG D:ASP74 2.8 38.6 1.0 CD2 B:HIS47 3.2 23.9 1.0 CD D:GLU78 3.3 34.9 1.0 CE1 B:HIS47 3.5 23.4 1.0 OE1 D:GLU78 3.8 36.3 1.0 OD1 B:ASP63 4.1 42.5 1.0 CB D:ASP74 4.3 35.7 1.0 NE2 B:HIS59 4.4 26.3 1.0 CG D:GLU78 4.4 32.8 1.0 CG B:HIS47 4.5 24.1 1.0 CE1 B:HIS59 4.5 24.3 1.0 ND1 B:HIS47 4.6 25.5 1.0 NE1 B:TRP48 4.7 29.1 1.0 CG B:ASP63 4.9 38.4 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1174 b:29.4 occ:1.00 OE2 E:GLU78 2.2 44.9 1.0 NE2 G:HIS47 2.3 36.3 1.0 OD1 E:ASP74 2.3 51.7 1.0 OD2 E:ASP74 3.0 50.1 1.0 CG E:ASP74 3.0 48.8 1.0 CE1 G:HIS47 3.2 36.2 1.0 CD2 G:HIS47 3.2 35.9 1.0 CD E:GLU78 3.4 43.0 1.0 OD1 G:ASP63 4.1 48.1 1.0 OE1 E:GLU78 4.1 41.2 1.0 ND1 G:HIS47 4.3 38.0 1.0 NE2 G:HIS59 4.3 37.5 1.0 CG G:HIS47 4.3 37.2 1.0 OD2 G:ASP63 4.4 47.8 1.0 CG E:GLU78 4.4 40.5 1.0 CB E:ASP74 4.4 45.5 1.0 CE1 G:HIS59 4.6 36.7 1.0 CG G:ASP63 4.7 43.8 1.0 NE1 G:TRP48 4.7 41.6 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1173 b:13.1 occ:1.00 OD1 F:ASP74 2.0 48.3 1.0 OE2 F:GLU78 2.2 39.9 1.0 NE2 H:HIS47 2.3 28.1 1.0 CG F:ASP74 2.9 43.8 1.0 CD2 H:HIS47 3.1 28.4 1.0 OD2 F:ASP74 3.2 45.5 1.0 CD F:GLU78 3.2 37.4 1.0 O F:HOH2024 3.4 14.2 1.0 CE1 H:HIS47 3.4 27.3 1.0 OE1 F:GLU78 3.8 34.8 1.0 OD1 H:ASP63 4.1 39.9 1.0 CB F:ASP74 4.3 39.3 1.0 CG H:HIS47 4.3 31.2 1.0 CG F:GLU78 4.4 34.5 1.0 NE2 H:HIS59 4.4 31.7 1.0 ND1 H:HIS47 4.4 30.4 1.0 CE1 H:HIS59 4.6 30.8 1.0 OD2 H:ASP63 4.6 41.5 1.0 NE1 H:TRP48 4.7 33.9 1.0 CG H:ASP63 4.7 38.2 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn1173 b:34.2 occ:1.00 OD1 G:ASP74 1.9 53.1 1.0 NE2 E:HIS47 2.3 36.1 1.0 OE2 G:GLU78 2.3 48.8 1.0 CG G:ASP74 2.8 48.0 1.0 OD2 G:ASP74 3.0 50.6 1.0 O G:HOH2014 3.1 18.2 1.0 CD2 E:HIS47 3.3 36.9 1.0 CE1 E:HIS47 3.3 36.1 1.0 CD G:GLU78 3.5 46.7 1.0 CB G:ASP74 4.3 44.8 1.0 OE1 G:GLU78 4.3 47.2 1.0 CG G:GLU78 4.4 42.2 1.0 CE1 E:HIS59 4.4 37.9 1.0 ND1 E:HIS47 4.4 37.2 1.0 CG E:HIS47 4.4 36.0 1.0 NE2 E:HIS59 4.4 37.9 1.0 OD2 E:ASP63 4.5 47.8 1.0 OD1 E:ASP63 4.6 45.0 1.0 NE1 E:TRP48 4.7 40.2 1.0 CD1 E:TRP48 5.0 38.6 1.0 CG E:ASP63 5.0 42.7 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn1173 b:24.6 occ:1.00 OD1 H:ASP74 2.0 42.6 1.0 OE2 H:GLU78 2.1 38.4 1.0 NE2 F:HIS47 2.3 28.2 1.0 CG H:ASP74 2.9 40.8 1.0 O F:HOH2014 3.1 17.4 1.0 OD2 H:ASP74 3.1 40.4 1.0 CE1 F:HIS47 3.2 24.0 1.0 CD H:GLU78 3.2 36.3 1.0 CD2 F:HIS47 3.3 27.2 1.0 O H:HOH2025 3.7 14.5 1.0 OE1 H:GLU78 3.8 35.8 1.0 OD1 F:ASP63 4.2 43.5 1.0 CB H:ASP74 4.3 38.6 1.0 ND1 F:HIS47 4.3 25.6 1.0 CG H:GLU78 4.3 33.7 1.0 NE2 F:HIS59 4.4 28.0 1.0 CG F:HIS47 4.4 26.7 1.0 CE1 F:HIS59 4.4 25.7 1.0 OD2 F:ASP63 4.8 43.0 1.0 NE1 F:TRP48 4.9 30.0 1.0 CG F:ASP63 4.9 38.5 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1173 b:26.2 occ:1.00 OE2 I:GLU78 2.2 39.3 1.0 NE2 K:HIS47 2.3 25.8 1.0 OD2 I:ASP74 2.5 42.8 1.0 OD1 I:ASP74 2.5 45.8 1.0 CG I:ASP74 2.9 42.4 1.0 CD2 K:HIS47 3.3 26.1 1.0 O K:HOH2014 3.3 12.2 1.0 CD I:GLU78 3.3 37.7 1.0 CE1 K:HIS47 3.3 24.8 1.0 O I:HOH2018 3.9 21.8 1.0 OE1 I:GLU78 3.9 38.0 1.0 OD1 K:ASP63 4.1 47.3 1.0 CG I:GLU78 4.3 36.2 1.0 OD2 K:ASP63 4.4 42.6 1.0 CB I:ASP74 4.4 38.8 1.0 ND1 K:HIS47 4.4 27.6 1.0 CG K:HIS47 4.4 28.3 1.0 NE2 K:HIS59 4.5 33.8 1.0 NE1 K:TRP48 4.5 33.6 1.0 CE1 K:HIS59 4.6 34.7 1.0 CG K:ASP63 4.7 42.8 1.0 CD1 K:TRP48 4.9 32.6 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Streptococcus Suis Dpr with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1173 b:17.4 occ:1.00 OD1 J:ASP74 2.0 46.7 1.0 OE2 J:GLU78 2.3 41.3 1.0 NE2 L:HIS47 2.4 29.2 1.0 CG J:ASP74 2.8 45.2 1.0 OD2 J:ASP74 2.8 47.1 1.0 CD2 L:HIS47 3.3 29.3 1.0 CD J:GLU78 3.3 40.2 1.0 CE1 L:HIS47 3.3 30.2 1.0 OE1 J:GLU78 3.9 40.3 1.0 OD1 L:ASP63 4.0 48.0 1.0 CB J:ASP74 4.2 42.6 1.0 OD2 L:ASP63 4.4 48.2 1.0 NE2 L:HIS59 4.4 26.9 1.0 CG J:GLU78 4.4 38.4 1.0 CE1 L:HIS59 4.4 28.1 1.0 ND1 L:HIS47 4.5 31.2 1.0 CG L:HIS47 4.5 30.8 1.0 CG L:ASP63 4.6 43.4 1.0 NE1 L:TRP48 4.7 34.7 1.0 CE1 L:HIS44 4.9 34.9 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