Iron in PDB 7plb: Caulobacter Crescentus Xylonolactonase with D-Xylose

All present enzymatic activity of Caulobacter Crescentus Xylonolactonase with D-Xylose:
3.1.1.68;

The structure of Caulobacter Crescentus Xylonolactonase with D-Xylose, PDB code: 7plb was solved by J.Paakkonen, N.Hakulinen, J.Rouvinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.47 / 1.73
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	85.84, 170.95, 79.14, 90, 90, 90
R / Rfree (%)	18.1 / 21.8

The binding sites of Iron atom in the Caulobacter Crescentus Xylonolactonase with D-Xylose (pdb code 7plb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Caulobacter Crescentus Xylonolactonase with D-Xylose, PDB code: 7plb:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Caulobacter Crescentus Xylonolactonase with D-Xylose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Caulobacter Crescentus Xylonolactonase with D-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:20.2 occ:0.48 O A:HOH409 1.8 21.5 1.0 OE1 A:GLU18 1.9 22.7 0.5 O1 A:XYP303 2.0 25.6 1.0 OD1 A:ASP196 2.0 20.6 0.5 OD1 A:ASN146 2.2 21.0 1.0 HO1 A:XYP303 2.3 30.8 1.0 O A:HOH447 2.3 35.2 1.0 OD1 A:ASP196 2.7 25.2 0.5 CD A:GLU18 2.9 23.6 0.5 CG A:ASP196 3.0 22.8 0.5 CG A:ASN146 3.0 21.6 1.0 OE2 A:GLU18 3.0 22.8 0.5 OE1 A:GLU18 3.1 23.5 0.5 ND2 A:ASN146 3.2 18.4 1.0 C1 A:XYP303 3.2 30.4 1.0 OD2 A:ASP196 3.3 22.8 0.5 CD A:GLU18 3.3 23.1 0.5 H1 A:XYP303 3.4 36.5 1.0 OE2 A:GLU18 3.5 24.7 0.5 CG A:ASP196 3.6 22.7 0.5 ND2 A:ASN101 3.6 19.8 1.0 O5 A:XYP303 3.9 37.6 1.0 O A:HOH401 4.0 34.2 1.0 N A:GLY197 4.0 22.2 1.0 CG A:GLU18 4.1 21.6 0.5 OD2 A:ASP196 4.1 28.4 0.5 HO2 A:XYP303 4.2 27.4 1.0 OD1 A:ASP102 4.2 20.6 1.0 OD1 A:ASN101 4.2 19.3 1.0 O A:THR237 4.2 18.1 1.0 CG A:ASN101 4.3 22.0 1.0 C A:ASP196 4.3 20.6 0.5 C2 A:XYP303 4.3 23.3 1.0 CA A:GLY197 4.3 19.9 1.0 CB A:ASP196 4.4 20.1 0.5 C A:ASP196 4.4 20.7 0.5 CB A:ASN146 4.4 19.7 1.0 CB A:ASP102 4.4 18.8 1.0 CG A:ASP102 4.4 18.6 1.0 O2 A:XYP303 4.4 22.8 1.0 H2 A:XYP303 4.5 28.0 1.0 CG A:GLU18 4.6 22.5 0.5 CB A:ASP196 4.6 19.8 0.5 CA A:ASP196 4.7 19.6 0.5 CA A:ASP196 4.7 19.6 0.5 O A:HOH426 4.8 27.8 1.0 O A:ASP196 4.8 19.6 0.5

Iron binding site 2 out of 2 in the Caulobacter Crescentus Xylonolactonase with D-Xylose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Caulobacter Crescentus Xylonolactonase with D-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:21.5 occ:0.65 OE1 B:GLU18 1.9 30.6 1.0 OD1 B:ASP196 2.0 28.2 1.0 O B:HOH436 2.0 23.8 1.0 O1 B:XYP302 2.1 25.3 1.0 OD1 B:ASN146 2.1 23.5 1.0 O B:HOH530 2.2 29.6 1.0 HO1 B:XYP302 2.5 30.4 1.0 CD B:GLU18 2.9 29.1 1.0 CG B:ASN146 3.0 27.9 1.0 CG B:ASP196 3.0 29.4 1.0 C1 B:XYP302 3.3 36.0 1.0 ND2 B:ASN146 3.3 24.9 1.0 OE2 B:GLU18 3.3 29.2 1.0 H1 B:XYP302 3.4 43.1 1.0 OD2 B:ASP196 3.5 32.9 1.0 ND2 B:ASN101 3.7 21.9 1.0 O5 B:XYP302 3.9 54.6 1.0 HO2 B:XYP302 4.0 43.3 1.0 CG B:GLU18 4.1 26.5 1.0 N B:GLY197 4.1 23.1 1.0 OD1 B:ASN101 4.2 25.4 1.0 OD1 B:ASP102 4.2 20.4 1.0 CB B:ASP196 4.3 23.6 1.0 CG B:ASN101 4.4 28.6 1.0 CB B:ASN146 4.4 21.4 1.0 C B:ASP196 4.4 24.8 1.0 CG B:ASP102 4.4 24.6 1.0 CA B:GLY197 4.4 20.3 1.0 O B:THR237 4.4 20.3 1.0 C2 B:XYP302 4.4 36.9 1.0 CB B:ASP102 4.5 20.0 1.0 O2 B:XYP302 4.5 36.1 1.0 CA B:ASP196 4.7 24.3 1.0 O B:HOH457 4.7 31.2 1.0 H2 B:XYP302 4.7 44.3 1.0 O B:ASP196 5.0 20.6 1.0

J.Paakkonen, N.Hakulinen, M.Andberg, A.Koivula, J.Rouvinen. Three-Dimensional Structure of Xylonolactonase From Caulobacter Crescentus: A Mononuclear Iron Enzyme of the 6-Bladed Beta-Propeller Hydrolase Family. Protein Sci. 2021.
ISSN: ESSN 1469-896X
PubMed: 34761460
DOI: 10.1002/PRO.4229