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Calcium in PDB 3dr2: Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways

Enzymatic activity of Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways

All present enzymatic activity of Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways:
3.1.1.17;

Protein crystallography data

The structure of Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways, PDB code: 3dr2 was solved by C.-N.Chen, K.-H.Chin, A.H.-J.Wang, S.H.Chou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.78 / 1.67
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.541, 89.741, 85.228, 90.00, 127.71, 90.00
R / Rfree (%) 21.1 / 23.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways (pdb code 3dr2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways, PDB code: 3dr2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3dr2

Go back to Calcium Binding Sites List in 3dr2
Calcium binding site 1 out of 6 in the Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:4.3
occ:1.00
 O A:HOH992 2.2 21.9 1.0
O A:HOH838 2.4 23.7 1.0
O A:HOH1013 2.5 27.3 1.0
O A:HOH839 2.5 19.3 1.0
O A:HOH840 2.5 26.9 1.0
O A:HOH991 2.5 25.7 1.0
O A:HOH866 2.7 17.8 1.0
O A:HOH843 2.7 19.6 1.0
O A:HOH867 4.3 19.0 1.0
CG2 A:ILE137 4.3 18.5 1.0
O A:PHE244 4.4 15.4 1.0
O A:LEU136 4.4 13.5 1.0
O A:HOH787 4.4 30.0 1.0
OG1 A:THR283 4.5 14.4 1.0
O A:PRO50 4.5 16.0 1.0
O A:HOH837 4.6 13.6 1.0
OD2 A:ASP135 4.7 16.3 1.0
O A:CYS282 4.8 14.6 1.0
O A:HOH767 4.8 28.5 1.0
OD1 A:ASN281 4.9 13.6 1.0
O A:LEU193 4.9 14.4 1.0
CB A:THR283 4.9 13.3 1.0
O A:ASN91 4.9 12.5 1.0

Calcium binding site 2 out of 6 in 3dr2

Go back to Calcium Binding Sites List in 3dr2
Calcium binding site 2 out of 6 in the Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca707

b:1.0
occ:1.00
 OD1 A:ASN191 2.4 12.9 1.0
O A:HOH836 2.4 14.5 1.0
OD1 A:ASP242 2.4 15.2 1.0
OD1 A:ASN134 2.4 15.1 1.0
O A:HOH865 2.4 13.5 1.0
O A:HOH1002 2.5 24.6 1.0
OE2 A:GLU48 2.5 27.6 1.0
O A:HOH864 2.5 16.9 1.0
CG A:ASN191 3.5 13.0 1.0
CG A:ASN134 3.5 15.0 1.0
CG A:ASP242 3.6 15.3 1.0
CD A:GLU48 3.6 23.9 1.0
OE1 A:GLU48 3.9 24.6 1.0
ND2 A:ASN134 3.9 15.1 1.0
ND2 A:ASN191 4.0 14.4 1.0
OD2 A:ASP242 4.2 17.4 1.0
OD1 A:ASN89 4.4 17.9 1.0
O A:HOH888 4.5 22.5 1.0
O A:HOH898 4.5 25.5 1.0
OD1 A:ASP135 4.5 14.6 1.0
CB A:ASP135 4.6 13.2 1.0
C A:ASP242 4.6 16.3 1.0
ND2 A:ASN89 4.6 11.1 1.0
ND2 A:ASN281 4.6 14.1 1.0
O A:ASP242 4.7 16.4 1.0
N A:GLY243 4.7 15.0 1.0
CB A:ASN191 4.7 10.9 1.0
CB A:ASP242 4.7 15.4 1.0
O A:ASN134 4.7 13.1 1.0
C A:ASN191 4.7 14.5 1.0
CB A:ASN134 4.8 14.0 1.0
O A:SER280 4.8 11.5 1.0
O A:ASN191 4.8 15.5 1.0
CG A:ASP135 4.9 15.6 1.0
CG A:GLU48 4.9 21.1 1.0
CG A:ASN89 4.9 15.3 1.0
C A:ASN134 4.9 14.0 1.0
N A:GLY192 5.0 13.0 1.0
CA A:ASP242 5.0 14.6 1.0

Calcium binding site 3 out of 6 in 3dr2

Go back to Calcium Binding Sites List in 3dr2
Calcium binding site 3 out of 6 in the Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:13.3
occ:1.00
 O B:HOH938 2.6 38.7 1.0
O A:HOH904 3.1 28.0 1.0
CA B:GLY105 3.6 17.9 1.0
CD1 B:PHE87 3.8 13.7 1.0
CE1 B:PHE87 3.9 16.7 1.0
CB B:ALA86 3.9 15.6 1.0
CA B:ALA86 4.0 14.5 1.0
C B:GLY105 4.0 19.6 1.0
NH2 B:ARG67 4.1 15.3 1.0
OD2 A:ASP83 4.2 19.6 1.0
O B:GLY105 4.2 18.7 1.0
C B:ALA86 4.5 15.1 1.0
O B:ALA86 4.7 15.2 1.0
O B:HOH905 4.7 27.8 1.0
N B:ARG106 4.7 18.9 1.0
N B:GLY105 4.8 15.7 1.0
SG B:CYS160 4.9 30.1 1.0
O A:HOH940 5.0 30.2 1.0

Calcium binding site 4 out of 6 in 3dr2

Go back to Calcium Binding Sites List in 3dr2
Calcium binding site 4 out of 6 in the Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:1.0
occ:1.00
 O B:HOH875 2.3 18.2 1.0
OD1 B:ASN191 2.3 18.0 1.0
OD1 B:ASP242 2.4 15.9 1.0
O B:HOH725 2.4 24.4 1.0
OD1 B:ASN134 2.4 15.3 1.0
O B:HOH840 2.4 17.1 1.0
O B:HOH874 2.5 17.9 1.0
CG B:ASN191 3.5 16.6 1.0
CG B:ASN134 3.5 15.4 1.0
CG B:ASP242 3.6 18.6 1.0
O B:HOH726 3.9 33.3 1.0
ND2 B:ASN134 4.0 16.1 1.0
ND2 B:ASN191 4.1 15.2 1.0
OD2 B:ASP242 4.1 17.9 1.0
OE1 B:GLU48 4.2 27.1 1.0
OE2 B:GLU48 4.5 24.7 1.0
O B:HOH724 4.5 23.7 1.0
O B:HOH980 4.5 20.6 1.0
OD1 B:ASP135 4.5 15.1 1.0
OD1 B:ASN89 4.6 18.1 1.0
C B:ASP242 4.6 18.2 1.0
CB B:ASP135 4.6 14.7 1.0
ND2 B:ASN281 4.6 17.1 1.0
CB B:ASN191 4.6 16.6 1.0
N B:GLY243 4.6 15.9 1.0
C B:ASN191 4.7 15.4 1.0
CD B:GLU48 4.7 23.4 1.0
CB B:ASP242 4.7 17.3 1.0
ND2 B:ASN89 4.7 12.3 1.0
O B:ASN134 4.7 13.6 1.0
O B:ASP242 4.7 18.5 1.0
O B:ASN191 4.7 16.2 1.0
O B:SER280 4.8 12.6 1.0
CB B:ASN134 4.8 14.7 1.0
N B:GLY192 4.9 15.8 1.0
CG B:ASP135 4.9 16.9 1.0
O B:HOH841 4.9 21.1 1.0
CA B:GLY243 4.9 13.9 1.0
CA B:ASN191 5.0 15.5 1.0
C B:ASN134 5.0 13.4 1.0
CA B:ASP242 5.0 17.3 1.0

Calcium binding site 5 out of 6 in 3dr2

Go back to Calcium Binding Sites List in 3dr2
Calcium binding site 5 out of 6 in the Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca708

b:17.3
occ:1.00
 NH2 B:ARG68 2.8 19.5 1.0
O A:HOH875 3.4 22.6 1.0
OD2 B:ASP83 3.4 20.8 1.0
CE1 A:PHE87 3.7 14.0 1.0
OD1 B:ASP83 3.8 17.6 1.0
CZ B:ARG68 3.8 18.8 1.0
CG B:ASP83 3.8 19.1 1.0
NE B:ARG68 4.1 17.5 1.0
CB A:CYS160 4.1 26.8 1.0
NH2 A:ARG67 4.5 17.7 1.0
CB B:CYS5 4.5 30.2 1.0
CD1 A:PHE87 4.6 15.2 1.0
SG B:CYS5 4.6 32.0 1.0
CZ A:PHE87 4.6 15.7 1.0
O A:GLY159 4.6 16.4 1.0
C A:GLY159 4.7 19.2 1.0
N A:CYS160 4.7 20.8 1.0
CA A:CYS160 4.8 22.6 1.0
NH1 A:ARG67 5.0 16.4 1.0

Calcium binding site 6 out of 6 in 3dr2

Go back to Calcium Binding Sites List in 3dr2
Calcium binding site 6 out of 6 in the Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structural and Functional Analyses of XC5397 From Xanthomonas Campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca709

b:8.7
occ:1.00
 O B:HOH845 2.4 24.8 1.0
O B:HOH920 2.4 31.1 1.0
O B:HOH848 2.4 25.3 1.0
O B:HOH844 2.5 21.8 1.0
O B:HOH846 2.6 22.6 1.0
O B:HOH814 2.6 26.1 1.0
O B:HOH842 4.2 17.2 1.0
CG2 B:ILE137 4.4 18.1 1.0
O B:PHE244 4.4 17.0 1.0
O B:LEU136 4.4 16.5 1.0
O B:PRO50 4.6 16.6 1.0
O B:HOH944 4.6 26.4 1.0
O B:HOH843 4.6 17.5 1.0
OD2 B:ASP135 4.7 14.6 1.0
O B:HOH894 4.7 24.5 1.0
O B:LEU193 4.8 17.0 1.0
OG1 B:THR283 4.8 19.3 1.0
O B:CYS282 4.9 16.0 1.0
O B:ASN91 4.9 17.3 1.0
OD1 B:ASN281 4.9 17.1 1.0

Reference:

C.-N.Chen, K.-H.Chin, A.H.-J.Wang, S.-H.Chou. The First Crystal Structure of Gluconolactonase Important in the Glucose Secondary Metabolic Pathways J.Mol.Biol. V. 384 604 2008.
ISSN: ISSN 0022-2836
PubMed: 18848569
DOI: 10.1016/J.JMB.2008.09.055
Page generated: Tue Jul 8 11:41:55 2025

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