Atomistry » Calcium » PDB 3dcq-3dsw » 3dr2
Atomistry »
  Calcium »
    PDB 3dcq-3dsw »
      3dr2 »

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: Sat Dec 12 04:09:07 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy