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

Protein crystallography data

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

Other elements in 2xjm:

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

Cobalt (Co) 12 atoms
Chlorine (Cl) 3 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 2xjm

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Calcium binding site 1 out of 8 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


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 Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1174

b:41.3
occ:1.00
 OE1 B:GLU113 2.3 41.0 1.0
O B:HOH2058 2.4 23.9 1.0
OE2 B:GLU113 2.6 45.8 1.0
CD B:GLU113 2.8 40.9 1.0
CG B:GLU113 4.3 33.3 1.0
CG2 B:THR110 4.6 33.3 1.0
CA B:VAL109 4.7 32.0 1.0
N B:THR110 4.7 30.3 1.0
O B:HOH2056 4.8 28.2 1.0
O B:ASN108 5.0 35.3 1.0
O B:HOH2062 5.0 20.6 1.0

Calcium binding site 2 out of 8 in 2xjm

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Calcium binding site 2 out of 8 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


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 Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1174

b:58.4
occ:1.00
 O L:HOH2050 2.5 42.9 1.0
O L:HOH2051 2.6 23.4 1.0
O L:HOH2049 2.7 35.6 1.0
O C:GLY167 4.3 44.2 1.0
O L:TYR107 4.3 44.0 1.0
O L:ASN108 4.4 47.0 1.0
CA L:ASN108 4.7 46.8 1.0
O L:ARG51 4.7 38.8 1.0
C L:ASN108 4.8 46.2 1.0
CA C:GLY167 4.8 41.7 1.0
CB L:ARG51 4.9 40.0 1.0
O L:VAL109 5.0 44.2 1.0
C C:GLY167 5.0 42.9 1.0

Calcium binding site 3 out of 8 in 2xjm

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Calcium binding site 3 out of 8 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


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 Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1175

b:53.1
occ:1.00
 OE2 E:GLU139 3.4 69.9 1.0
O E:ALA23 3.4 33.7 1.0
CG E:GLU139 4.0 62.8 1.0
CD E:GLU139 4.1 66.5 1.0
C E:ALA23 4.6 33.5 1.0
CB E:ASP24 4.7 62.0 1.0
CA E:ASP24 4.7 60.9 1.0
CG1 E:VAL135 5.0 54.2 1.0

Calcium binding site 4 out of 8 in 2xjm

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Calcium binding site 4 out of 8 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


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 Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1174

b:15.8
occ:1.00
 O F:HOH2065 2.2 16.2 1.0
O F:LEU166 2.4 25.2 1.0
O F:HOH2064 2.4 16.2 1.0
C F:LEU166 3.5 25.2 1.0
CA F:LEU166 4.2 25.0 1.0
NE2 F:GLN168 4.3 35.1 1.0
N F:GLY167 4.4 25.1 1.0
O F:HOH2066 4.4 11.5 1.0
CB F:LEU166 4.5 25.2 1.0
CA F:GLY167 4.5 26.3 1.0
C F:GLY167 5.0 27.3 1.0

Calcium binding site 5 out of 8 in 2xjm

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Calcium binding site 5 out of 8 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


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 Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1175

b:45.7
occ:1.00
 O F:HOH2037 2.5 27.4 1.0
O F:ASN108 4.3 40.5 1.0
O J:GLY167 4.5 34.9 1.0
O F:TYR107 4.5 38.9 1.0
C F:ASN108 4.6 39.4 1.0
CA F:ASN108 4.6 40.2 1.0
O F:VAL109 4.7 35.7 1.0
O F:ARG51 4.8 31.3 1.0
OD1 F:ASN108 4.9 42.7 1.0
CB F:ARG51 4.9 31.2 1.0

Calcium binding site 6 out of 8 in 2xjm

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Calcium binding site 6 out of 8 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


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 Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1176

b:45.8
occ:1.00
 O K:HOH2070 2.4 24.6 1.0
O H:ASN108 4.0 48.4 1.0
O K:HOH2071 4.2 19.6 1.0
O K:GLY167 4.4 37.6 1.0
C H:ASN108 4.7 46.5 1.0
O H:VAL109 4.7 41.4 1.0
CA H:ASN108 4.7 46.5 1.0
CA K:GLY167 4.8 36.3 1.0
O H:TYR107 4.9 43.9 1.0

Calcium binding site 7 out of 8 in 2xjm

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Calcium binding site 7 out of 8 in the Crystal Structure of Streptococcus Suis Dpr with Cobalt


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 Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca1176

b:42.0
occ:1.00
 O I:HOH2042 2.3 25.4 1.0
O I:HOH2043 2.9 31.2 1.0
O I:ASN108 3.8 42.4 1.0
C I:ASN108 4.3 41.7 1.0
CA I:ASN108 4.5 42.2 1.0
O I:VAL109 4.5 41.0 1.0
O I:TYR107 4.8 39.8 1.0
C I:VAL109 5.0 40.5 1.0
CG2 I:THR110 5.0 43.8 1.0

Calcium binding site 8 out of 8 in 2xjm

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Streptococcus Suis Dpr with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca1176

b:54.7
occ:1.00
 O J:HOH2019 2.3 28.0 1.0
O J:HOH2047 2.6 26.2 1.0
O B:HOH2087 2.7 19.0 1.0
O J:HOH2048 2.7 22.6 1.0
O B:GLY167 4.2 31.3 1.0
O J:ASN108 4.5 37.8 1.0
O J:TYR107 4.6 34.3 1.0
CA B:GLY167 4.7 29.8 1.0
CA J:ASN108 4.8 37.7 1.0
C J:ASN108 4.8 36.8 1.0
C B:GLY167 4.9 30.6 1.0
O J:ARG51 4.9 27.9 1.0
O J:VAL109 4.9 35.6 1.0
CB J:ARG51 4.9 28.3 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: Tue Jul 8 09:23:37 2025

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