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Iron 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:

Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1wra

Go back to Iron Binding Sites List in 1wra
Iron 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 Iron with other atoms in the Fe 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:Fe401

b:19.9
occ:1.00
 O A:HOH508 2.1 18.1 1.0
OD1 A:ASN208 2.1 16.8 1.0
O4 A:PC501 2.2 18.3 1.0
ND1 A:HIS112 2.2 19.6 1.0
OD2 A:ASP228 2.3 15.1 1.0
NE2 A:HIS110 2.4 15.2 1.0
CE1 A:HIS112 3.1 19.5 1.0
CG A:ASN208 3.1 18.2 1.0
P1 A:PC501 3.2 28.1 1.0
CG A:ASP228 3.2 14.3 1.0
CD2 A:HIS110 3.2 15.9 1.0
CG A:HIS112 3.3 18.5 1.0
FE A:FE402 3.4 19.2 1.0
CE1 A:HIS110 3.4 16.8 1.0
ND2 A:ASN208 3.5 16.7 1.0
O1 A:PC501 3.6 24.0 1.0
CB A:ASP228 3.6 15.7 1.0
CB A:HIS112 3.6 17.1 1.0
O2 A:PC501 3.7 28.0 1.0
NE2 A:HIS115 4.1 19.6 1.0
CD2 A:HIS115 4.2 19.5 1.0
NE2 A:HIS112 4.3 15.7 1.0
OD1 A:ASP228 4.3 15.0 1.0
CD2 A:HIS112 4.4 15.8 1.0
CG A:HIS110 4.4 14.4 1.0
O A:HOH509 4.5 27.7 1.0
CB A:ASN208 4.5 15.9 1.0
ND1 A:HIS110 4.5 14.5 1.0
O3 A:PC501 4.6 21.1 1.0
OD1 A:ASP114 4.6 16.7 1.0
CD2 A:HIS253 4.7 19.2 1.0
NE2 A:HIS253 4.8 18.0 1.0
CA A:ASN208 4.8 16.4 1.0
OD1 A:ASP206 4.9 14.4 1.0
OD2 A:ASP114 4.9 16.6 1.0
N A:ASN208 5.0 16.5 1.0

Iron binding site 2 out of 4 in 1wra

Go back to Iron Binding Sites List in 1wra
Iron 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 Iron with other atoms in the Fe 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:Fe402

b:19.2
occ:1.00
 NE2 A:HIS115 2.1 19.6 1.0
O A:HOH508 2.2 18.1 1.0
OD2 A:ASP114 2.2 16.6 1.0
OD2 A:ASP228 2.2 15.1 1.0
O1 A:PC501 2.2 24.0 1.0
NE2 A:HIS254 2.2 18.4 1.0
CD2 A:HIS115 3.0 19.5 1.0
CG A:ASP228 3.1 14.3 1.0
CD2 A:HIS254 3.1 19.6 1.0
CE1 A:HIS115 3.2 22.2 1.0
CG A:ASP114 3.2 17.3 1.0
OD1 A:ASP228 3.2 15.0 1.0
CE1 A:HIS254 3.3 20.4 1.0
FE A:FE401 3.4 19.9 1.0
OD1 A:ASP114 3.5 16.7 1.0
P1 A:PC501 3.5 28.1 1.0
O A:HOH517 3.9 18.0 1.0
O4 A:PC501 3.9 18.3 1.0
O2 A:PC501 4.1 28.0 1.0
CG A:HIS115 4.2 18.8 1.0
ND1 A:HIS115 4.2 20.7 1.0
CG A:HIS254 4.3 16.7 1.0
ND1 A:HIS254 4.3 19.4 1.0
NE2 A:HIS110 4.4 15.2 1.0
CD2 A:HIS253 4.4 19.2 1.0
CE1 A:HIS110 4.5 16.8 1.0
CB A:ASP228 4.5 15.7 1.0
CB A:ASP114 4.6 17.1 1.0
O3 A:PC501 4.7 21.1 1.0
O A:GLY42 4.9 18.7 1.0
O A:HOH642 4.9 14.2 1.0
NE2 A:HIS253 4.9 18.0 1.0

Iron binding site 3 out of 4 in 1wra

Go back to Iron Binding Sites List in 1wra
Iron 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 Iron with other atoms in the Fe 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:Fe401

b:19.9
occ:1.00
 OD1 B:ASN208 2.1 16.9 1.0
O3 B:PC501 2.2 22.3 1.0
ND1 B:HIS112 2.2 18.8 1.0
OD2 B:ASP228 2.2 12.8 1.0
O B:HOH1513 2.2 22.1 1.0
NE2 B:HIS110 2.3 16.2 1.0
CE1 B:HIS112 3.0 22.4 1.0
CG B:ASN208 3.1 17.8 1.0
CG B:ASP228 3.2 17.6 1.0
P1 B:PC501 3.3 27.9 1.0
CD2 B:HIS110 3.3 17.3 1.0
CG B:HIS112 3.3 20.5 1.0
CE1 B:HIS110 3.3 17.8 1.0
FE B:FE402 3.4 19.6 1.0
ND2 B:ASN208 3.5 18.9 1.0
CB B:ASP228 3.6 17.1 1.0
CB B:HIS112 3.7 18.8 1.0
O2 B:PC501 3.7 29.7 1.0
O4 B:PC501 3.7 25.2 1.0
NE2 B:HIS115 4.2 16.0 1.0
NE2 B:HIS112 4.2 18.0 1.0
CD2 B:HIS115 4.3 17.3 1.0
OD1 B:ASP228 4.4 15.8 1.0
CD2 B:HIS112 4.4 21.4 1.0
CB B:ASN208 4.5 17.5 1.0
O B:HOH1521 4.5 32.8 1.0
ND1 B:HIS110 4.5 14.3 1.0
CG B:HIS110 4.5 14.9 1.0
O1 B:PC501 4.5 20.4 1.0
CD2 B:HIS253 4.5 19.6 1.0
OD1 B:ASP114 4.6 19.1 1.0
CA B:ASN208 4.7 17.9 1.0
NE2 B:HIS253 4.8 16.1 1.0
OD1 B:ASP206 4.9 21.0 1.0
OD2 B:ASP114 4.9 17.5 1.0
N B:ASN208 5.0 17.6 1.0

Iron binding site 4 out of 4 in 1wra

Go back to Iron Binding Sites List in 1wra
Iron 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 Iron with other atoms in the Fe 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:Fe402

b:19.6
occ:1.00
 O B:HOH1513 1.9 22.1 1.0
OD2 B:ASP114 2.1 17.5 1.0
NE2 B:HIS115 2.2 16.0 1.0
NE2 B:HIS254 2.2 19.6 1.0
OD2 B:ASP228 2.2 12.8 1.0
O4 B:PC501 2.3 25.2 1.0
CD2 B:HIS115 3.0 17.3 1.0
CG B:ASP114 3.1 19.9 1.0
CG B:ASP228 3.1 17.6 1.0
CD2 B:HIS254 3.1 18.6 1.0
CE1 B:HIS254 3.2 21.4 1.0
CE1 B:HIS115 3.3 17.1 1.0
OD1 B:ASP228 3.3 15.8 1.0
OD1 B:ASP114 3.4 19.1 1.0
FE B:FE401 3.4 19.9 1.0
P1 B:PC501 3.5 27.9 1.0
O B:HOH1528 3.7 21.8 1.0
O3 B:PC501 3.9 22.3 1.0
O2 B:PC501 4.1 29.7 1.0
CG B:HIS115 4.3 17.3 1.0
CG B:HIS254 4.3 18.6 1.0
ND1 B:HIS254 4.3 18.9 1.0
ND1 B:HIS115 4.3 18.1 1.0
CD2 B:HIS253 4.4 19.6 1.0
NE2 B:HIS110 4.5 16.2 1.0
CB B:ASP114 4.5 19.0 1.0
CE1 B:HIS110 4.5 17.8 1.0
CB B:ASP228 4.6 17.1 1.0
O1 B:PC501 4.7 20.4 1.0
O B:GLY42 4.9 21.0 1.0
O B:HOH1532 4.9 15.1 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: Sun Dec 13 14:35:17 2020

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