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Calcium in PDB 1wra: Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae

Enzymatic activity of Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae

All present enzymatic activity of Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae:
3.1.4.38;

Protein crystallography data

The structure of Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae, PDB code: 1wra was solved by G.Garau, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.84 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 98.302, 98.302, 172.600, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.4

Other elements in 1wra:

The structure of Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae (pdb code 1wra). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae, PDB code: 1wra:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1wra

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Calcium binding site 1 out of 4 in the Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae


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 Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:19.8
occ:1.00
 OD2 A:ASP62 2.3 18.3 1.0
OD1 A:ASP120 2.4 21.9 1.0
O A:GLY117 2.4 18.6 1.0
O A:HOH528 2.4 21.7 1.0
O A:HOH526 2.5 16.4 1.0
OE1 A:GLU121 2.6 24.6 1.0
OE2 A:GLU121 2.6 23.3 1.0
CD A:GLU121 3.0 24.1 1.0
CG A:ASP120 3.3 24.8 1.0
CG A:ASP62 3.3 18.2 1.0
OD2 A:ASP120 3.3 27.7 1.0
C A:GLY117 3.6 18.4 1.0
O A:HOH523 3.8 18.7 1.0
CB A:ASP62 3.9 19.6 1.0
OD1 A:ASP62 4.2 16.5 1.0
O A:HOH593 4.3 17.7 1.0
CA A:GLY117 4.5 18.9 1.0
CA A:ASN118 4.5 18.8 1.0
CG A:GLU121 4.5 24.6 1.0
N A:ASN118 4.5 19.0 1.0
O A:HOH564 4.5 21.1 1.0
O A:HOH565 4.6 23.5 1.0
CB A:ASP64 4.7 18.7 1.0
CB A:ASP120 4.7 23.8 1.0
O A:HOH521 4.8 20.2 1.0
N A:GLU121 4.8 22.9 1.0
N A:ASP120 4.8 21.7 1.0
OD2 A:ASP64 4.9 22.2 1.0
C A:ASN118 4.9 19.6 1.0
N A:VAL119 5.0 19.8 1.0

Calcium binding site 2 out of 4 in 1wra

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Calcium binding site 2 out of 4 in the Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae


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 Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:17.8
occ:1.00
 O A:HOH543 2.3 20.6 1.0
O A:ASP64 2.3 17.9 1.0
OE2 A:GLU61 2.3 21.1 1.0
O A:HOH590 2.4 16.9 1.0
OD1 A:ASP62 2.4 16.5 1.0
O A:HOH524 2.6 15.7 1.0
O A:ASP62 2.6 19.1 1.0
CG A:ASP62 3.4 18.2 1.0
CD A:GLU61 3.5 19.1 1.0
C A:ASP62 3.5 19.1 1.0
C A:ASP64 3.6 19.1 1.0
N A:ASP62 3.9 18.0 1.0
CA A:ASP62 4.1 18.3 1.0
OD2 A:ASP62 4.1 18.3 1.0
O A:HOH523 4.2 18.7 1.0
OD2 A:ASP149 4.2 20.2 1.0
O A:GLU80 4.2 22.8 1.0
CB A:SER113 4.2 16.7 1.0
CB A:PHE65 4.3 18.6 1.0
N A:ASP64 4.3 17.9 1.0
CG A:GLU61 4.3 18.1 1.0
OE1 A:GLU61 4.3 18.8 1.0
C A:TYR63 4.3 17.9 1.0
CB A:ASP62 4.4 19.6 1.0
N A:PHE65 4.4 19.8 1.0
O A:TYR63 4.5 16.9 1.0
CA A:PHE65 4.5 19.4 1.0
CA A:ASP64 4.6 18.7 1.0
N A:TYR63 4.6 18.7 1.0
OG A:SER113 4.7 16.3 1.0
O A:HOH521 4.8 20.2 1.0
O A:HOH527 4.9 22.4 1.0
CA A:TYR63 4.9 18.8 1.0
C A:GLU61 5.0 18.4 1.0

Calcium binding site 3 out of 4 in 1wra

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Calcium binding site 3 out of 4 in the Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae


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 Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:19.0
occ:1.00
 OD1 B:ASP62 2.3 16.5 1.0
OE2 B:GLU61 2.3 21.0 1.0
O B:HOH1516 2.3 17.4 1.0
O B:HOH1515 2.4 24.9 1.0
O B:ASP64 2.4 22.0 1.0
O B:HOH1514 2.5 18.0 1.0
O B:ASP62 2.6 22.8 1.0
CG B:ASP62 3.4 19.6 1.0
CD B:GLU61 3.4 21.1 1.0
C B:ASP62 3.5 21.2 1.0
C B:ASP64 3.6 23.0 1.0
N B:ASP62 3.8 21.0 1.0
CA B:ASP62 4.0 20.9 1.0
O B:HOH1534 4.1 22.8 1.0
OD2 B:ASP149 4.2 23.8 1.0
OD2 B:ASP62 4.2 21.0 1.0
CB B:SER113 4.2 18.4 1.0
O B:GLU80 4.2 24.3 1.0
OE1 B:GLU61 4.3 19.8 1.0
CG B:GLU61 4.3 20.7 1.0
N B:ASP64 4.3 22.5 1.0
CB B:PHE65 4.3 24.2 1.0
CB B:ASP62 4.3 20.7 1.0
C B:TYR63 4.4 22.2 1.0
O B:TYR63 4.5 22.1 1.0
N B:PHE65 4.5 23.1 1.0
N B:TYR63 4.5 22.3 1.0
CA B:PHE65 4.6 24.0 1.0
CA B:ASP64 4.6 22.8 1.0
OG B:SER113 4.7 18.7 1.0
O B:HOH1580 4.7 15.2 1.0
CA B:TYR63 4.9 22.3 1.0
C B:GLU61 4.9 20.2 1.0

Calcium binding site 4 out of 4 in 1wra

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Calcium binding site 4 out of 4 in the Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae


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 Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:21.1
occ:1.00
 OD2 B:ASP62 2.2 21.0 1.0
OD1 B:ASP120 2.3 23.3 1.0
O B:HOH1559 2.4 23.2 1.0
O B:GLY117 2.4 18.1 1.0
O B:HOH1560 2.4 20.5 1.0
OE2 B:GLU121 2.5 20.4 1.0
OE1 B:GLU121 2.5 23.1 1.0
CD B:GLU121 2.9 24.0 1.0
CG B:ASP120 3.2 25.1 1.0
CG B:ASP62 3.3 19.6 1.0
OD2 B:ASP120 3.3 29.9 1.0
C B:GLY117 3.6 19.2 1.0
O B:HOH1534 3.8 22.8 1.0
CB B:ASP62 3.8 20.7 1.0
OD1 B:ASP62 4.3 16.5 1.0
O B:HOH1583 4.3 18.1 1.0
CG B:GLU121 4.4 25.3 1.0
O B:HOH1535 4.4 19.3 1.0
CA B:ASN118 4.5 19.2 1.0
N B:ASN118 4.5 19.8 1.0
CA B:GLY117 4.5 19.0 1.0
CB B:ASP120 4.6 23.3 1.0
CB B:ASP64 4.7 23.4 1.0
N B:ASP120 4.7 21.7 1.0
N B:GLU121 4.7 24.1 1.0
C B:ASN118 4.8 19.2 1.0
O B:HOH1580 4.9 15.2 1.0
N B:VAL119 4.9 19.8 1.0
OD2 B:ASP64 5.0 27.8 1.0

Reference:

G.Garau, D.Lemaire, T.Vernet, O.Dideberg, A.M.Di Guilmi. Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline-Binding Protein E From Streptococcus Pneumoniae: New Structural Features Among the Metallo-Beta-Lactamase Superfamily J.Biol.Chem. V. 280 28591 2005.
ISSN: ISSN 0021-9258
PubMed: 15908436
DOI: 10.1074/JBC.M502744200
Page generated: Tue Jul 8 03:16:13 2025

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