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

Protein crystallography data

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

Other elements in 2xjo:

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

Nickel (Ni) 12 atoms
Calcium (Ca) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Streptococcus Suis Dpr with Nickel, PDB code: 2xjo:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 2xjo

Go back to Chlorine Binding Sites List in 2xjo
Chlorine binding site 1 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1176

b:16.2
occ:1.00
 N B:LYS171 3.1 38.6 1.0
O L:HOH2028 3.1 3.1 1.0
CA B:LYS171 3.4 42.9 1.0
CA L:GLY84 3.5 37.2 1.0
CB B:ALA169 3.7 35.1 1.0
CD B:PRO170 3.7 34.2 1.0
N B:PRO170 3.9 33.8 1.0
N L:GLY84 4.2 37.1 1.0
C B:PRO170 4.2 36.0 1.0
O L:HOH2029 4.3 15.4 1.0
C B:ALA169 4.4 33.3 1.0
O J:HOH2010 4.5 6.9 1.0
N B:LEU172 4.5 43.8 1.0
C B:LYS171 4.5 43.1 1.0
CG B:LYS171 4.5 46.5 1.0
CA B:PRO170 4.5 34.4 1.0
CB B:LYS171 4.5 42.9 1.0
CB B:PRO170 4.6 32.9 1.0
CA B:ALA169 4.6 34.0 1.0
CG B:PRO170 4.6 33.5 1.0
C L:GLY84 4.7 37.9 1.0
C L:LEU83 4.8 37.0 1.0
O B:HOH2090 4.9 22.0 1.0
O L:LEU83 4.9 38.9 1.0
O L:GLY84 4.9 37.9 1.0

Chlorine binding site 2 out of 6 in 2xjo

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Chlorine binding site 2 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1174

b:26.2
occ:1.00
 O D:HOH2017 2.8 19.4 1.0
N D:ILE111 3.3 43.5 1.0
CG1 D:ILE111 3.7 44.3 1.0
O I:HOH2010 3.7 12.6 1.0
CB D:THR110 3.8 46.9 1.0
CB D:ILE111 3.8 44.1 1.0
O D:ARG51 3.9 40.5 1.0
CA D:GLY52 3.9 39.6 1.0
CA D:THR110 4.1 45.9 1.0
O D:HOH2065 4.1 9.0 1.0
CA D:ILE111 4.2 43.7 1.0
C D:THR110 4.2 44.7 1.0
OG1 D:THR110 4.6 47.7 1.0
OE1 D:GLU112 4.6 54.6 1.0
N D:ARG53 4.6 38.2 1.0
C D:GLY52 4.7 38.8 1.0
C D:ARG51 4.8 39.6 1.0
CG2 D:THR110 4.8 47.1 1.0
N D:GLY52 4.8 39.3 1.0
CA D:CA1175 5.0 38.5 1.0

Chlorine binding site 3 out of 6 in 2xjo

Go back to Chlorine Binding Sites List in 2xjo
Chlorine binding site 3 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1174

b:36.2
occ:1.00
 O A:HOH2027 3.1 28.2 1.0
N E:LYS171 3.3 57.2 1.0
CA A:GLY84 3.4 50.8 1.0
CB E:ALA169 3.7 56.3 1.0
CA E:LYS171 3.7 60.0 1.0
CD E:PRO170 3.8 53.1 1.0
N E:PRO170 4.0 52.9 1.0
O C:HOH2006 4.0 15.5 1.0
N A:GLY84 4.1 49.3 1.0
C E:PRO170 4.4 55.0 1.0
C E:ALA169 4.5 53.3 1.0
CG E:PRO170 4.5 52.6 1.0
CA E:PRO170 4.6 53.0 1.0
N E:LEU172 4.6 59.6 1.0
CA E:ALA169 4.6 54.6 1.0
CB E:PRO170 4.7 52.2 1.0
CG E:LYS171 4.7 62.2 1.0
C E:LYS171 4.7 60.1 1.0
C A:GLY84 4.7 51.0 1.0
C A:LEU83 4.7 49.6 1.0
CB E:LYS171 4.8 60.8 1.0
O A:LEU83 4.8 50.8 1.0
O A:HOH2026 4.9 27.2 1.0
O A:GLY84 4.9 51.3 1.0

Chlorine binding site 4 out of 6 in 2xjo

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Chlorine binding site 4 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1175

b:23.3
occ:1.00
 N G:LYS171 3.0 47.0 1.0
O B:HOH2037 3.1 4.8 1.0
CA G:LYS171 3.3 50.2 1.0
CA B:GLY84 3.4 43.0 1.0
CD G:PRO170 3.8 41.6 1.0
CB G:ALA169 3.8 42.3 1.0
N G:PRO170 4.0 41.4 1.0
N B:GLY84 4.0 41.8 1.0
C G:PRO170 4.1 44.4 1.0
CG G:LYS171 4.1 51.7 1.0
CB G:LYS171 4.3 51.0 1.0
C G:LYS171 4.4 51.2 1.0
N G:LEU172 4.4 51.9 1.0
CA G:PRO170 4.4 41.9 1.0
CB G:PRO170 4.5 41.8 1.0
C G:ALA169 4.5 41.7 1.0
CG G:PRO170 4.6 40.3 1.0
C B:LEU83 4.6 41.7 1.0
O B:HOH2038 4.6 20.1 1.0
C B:GLY84 4.7 44.0 1.0
CA G:ALA169 4.7 41.7 1.0
O B:LEU83 4.7 43.0 1.0
O B:THR82 4.9 41.0 1.0

Chlorine binding site 5 out of 6 in 2xjo

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Chlorine binding site 5 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1174

b:22.1
occ:1.00
 O I:HOH2007 2.7 16.9 1.0
O I:HOH2012 2.9 9.2 1.0
O I:HOH2041 3.2 10.6 1.0
N I:ILE111 3.2 44.8 1.0
O I:HOH2011 3.6 18.1 1.0
CB I:THR110 3.8 47.8 1.0
CA I:THR110 3.8 46.7 1.0
O I:ARG51 3.9 42.4 1.0
CA I:GLY52 3.9 40.0 1.0
CB I:ILE111 4.0 44.5 1.0
CG1 I:ILE111 4.0 44.9 1.0
C I:THR110 4.0 45.5 1.0
CA I:ILE111 4.2 44.2 1.0
O D:HOH2043 4.4 14.7 1.0
CG2 I:THR110 4.6 50.2 1.0
C I:GLY52 4.7 39.8 1.0
N I:ARG53 4.7 40.0 1.0
CA I:CA1175 4.7 38.5 1.0
C I:ARG51 4.8 41.1 1.0
OG1 I:THR110 4.8 47.7 1.0
N I:GLY52 4.9 40.6 1.0
N I:GLU112 4.9 45.2 1.0

Chlorine binding site 6 out of 6 in 2xjo

Go back to Chlorine Binding Sites List in 2xjo
Chlorine binding site 6 out of 6 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1174

b:20.0
occ:1.00
 O J:HOH2011 2.9 6.0 1.0
O F:HOH2014 3.5 9.5 1.0
N J:ILE111 3.5 36.4 1.0
OE1 J:GLU112 3.7 28.9 0.5
CB J:THR110 3.7 38.8 1.0
CA J:GLY52 3.9 31.1 1.0
CA J:THR110 4.0 38.0 1.0
O J:ARG51 4.0 33.4 1.0
CB J:ILE111 4.1 37.3 1.0
CG1 J:ILE111 4.1 39.1 1.0
CG2 J:THR110 4.1 41.0 1.0
C J:THR110 4.3 36.7 1.0
CA J:ILE111 4.4 36.4 1.0
O J:HOH2041 4.5 13.2 1.0
N J:ARG53 4.6 30.5 1.0
O B:HOH2034 4.7 16.8 1.0
C J:GLY52 4.7 30.8 1.0
CD J:GLU112 4.8 35.4 0.5
C J:ARG51 4.9 32.8 1.0
N J:GLY52 4.9 32.2 1.0
OG1 J:THR110 4.9 35.5 1.0

Reference:

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
Page generated: Sat Dec 12 09:26:00 2020

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