Iron in PDB 7plc: Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group

All present enzymatic activity of Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group:
3.1.1.68;

The structure of Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group, PDB code: 7plc 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)	157.81 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.776, 82.207, 159.24, 90, 97.69, 90
R / Rfree (%)	19.8 / 25

The binding sites of Iron atom in the Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group (pdb code 7plc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group, PDB code: 7plc:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group


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, P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe304 b:28.6 occ:0.85 O A:HOH422 1.9 22.2 1.0 O1 A:XYP301 2.0 29.8 1.0 OD1 A:ASN146 2.1 30.0 1.0 OD1 A:ASP196 2.2 32.2 1.0 OE1 A:GLU18 2.2 32.2 1.0 O A:HOH490 2.4 30.5 1.0 CD A:GLU18 2.9 28.0 1.0 OE2 A:GLU18 3.1 30.1 1.0 CG A:ASN146 3.1 24.9 1.0 C1 A:XYP301 3.2 32.8 1.0 CG A:ASP196 3.3 29.7 1.0 ND2 A:ASN146 3.5 21.5 1.0 ND2 A:ASN101 3.6 24.9 1.0 O5 A:XYP301 3.6 45.7 1.0 OD2 A:ASP196 3.7 30.6 1.0 CG A:GLU18 4.2 26.1 1.0 OD1 A:ASN101 4.3 25.6 1.0 N A:GLY197 4.3 24.9 1.0 CG A:ASN101 4.3 31.5 1.0 C2 A:XYP301 4.4 33.4 1.0 OD1 A:ASP102 4.4 23.9 1.0 O A:THR237 4.4 29.6 1.0 CB A:ASN146 4.5 21.4 1.0 CB A:ASP102 4.5 23.0 1.0 CG A:ASP102 4.5 23.2 1.0 CB A:ASP196 4.5 28.7 1.0 C A:ASP196 4.6 26.4 1.0 O2 A:XYP301 4.6 32.6 1.0 CA A:GLY197 4.6 21.9 1.0 O A:HOH460 4.7 26.5 1.0 CA A:ASP196 4.8 24.0 1.0 C5 A:XYP301 4.9 38.6 1.0 CA A:ASN146 5.0 26.8 1.0

Iron binding site 2 out of 4 in the Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group


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, P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:18.9 occ:0.83 O1 B:XYP301 2.0 15.1 1.0 O B:HOH469 2.0 22.3 1.0 OD1 B:ASN146 2.1 16.0 1.0 OD1 B:ASP196 2.2 20.3 1.0 OE1 B:GLU18 2.2 26.2 1.0 O B:HOH480 2.4 25.9 1.0 CD B:GLU18 3.0 25.2 1.0 CG B:ASN146 3.0 18.3 1.0 C1 B:XYP301 3.1 30.4 1.0 CG B:ASP196 3.3 29.3 1.0 OE2 B:GLU18 3.3 26.9 1.0 ND2 B:ASN146 3.4 18.8 1.0 O5 B:XYP301 3.7 30.8 1.0 OD2 B:ASP196 3.8 33.2 1.0 ND2 B:ASN101 3.9 18.0 1.0 N B:GLY197 4.1 18.5 1.0 O B:THR237 4.2 20.6 1.0 C2 B:XYP301 4.3 25.9 1.0 CG B:GLU18 4.3 23.2 1.0 CA B:GLY197 4.4 22.5 1.0 C B:ASP196 4.4 17.6 1.0 CB B:ASN146 4.4 18.2 1.0 OD1 B:ASN101 4.4 20.8 1.0 O2 B:XYP301 4.4 30.4 1.0 OD2 B:ASP102 4.4 25.9 1.0 CB B:ASP196 4.5 21.7 1.0 CG B:ASN101 4.5 23.4 1.0 CB B:ASP102 4.6 22.1 1.0 CG B:ASP102 4.6 24.6 1.0 O B:HOH489 4.6 24.5 1.0 CA B:ASP196 4.7 22.3 1.0 O B:ASP196 4.9 18.4 1.0 C5 B:XYP301 4.9 33.0 1.0 CA B:ASN146 5.0 17.5 1.0

Iron binding site 3 out of 4 in the Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe304 b:27.8 occ:0.93 OD1 C:ASP196 2.0 20.6 1.0 O1 C:XYP301 2.0 24.5 1.0 O C:HOH416 2.0 23.9 1.0 OE1 C:GLU18 2.2 25.6 1.0 OD1 C:ASN146 2.2 22.2 1.0 O C:HOH506 2.5 26.3 1.0 CD C:GLU18 2.9 23.3 1.0 CG C:ASN146 3.1 17.9 1.0 CG C:ASP196 3.1 24.5 1.0 OE2 C:GLU18 3.2 23.1 1.0 C1 C:XYP301 3.2 31.3 1.0 ND2 C:ASN146 3.5 22.1 1.0 OD2 C:ASP196 3.6 26.3 1.0 O5 C:XYP301 3.6 51.1 1.0 ND2 C:ASN101 3.7 24.2 1.0 N C:GLY197 4.2 20.5 1.0 OD1 C:ASN101 4.2 21.3 1.0 CG C:GLU18 4.2 19.4 1.0 O C:THR237 4.3 17.9 1.0 OD1 C:ASP102 4.3 26.2 1.0 CG C:ASN101 4.3 28.1 1.0 CB C:ASP196 4.4 22.2 1.0 CB C:ASN146 4.4 17.5 1.0 C C:ASP196 4.5 23.2 1.0 C2 C:XYP301 4.5 30.6 1.0 CG C:ASP102 4.5 26.0 1.0 CA C:GLY197 4.5 13.8 1.0 CB C:ASP102 4.6 17.9 1.0 O C:HOH447 4.7 28.5 1.0 CA C:ASP196 4.7 21.7 1.0 O2 C:XYP301 4.7 36.2 1.0 C5 C:XYP301 4.9 39.4 1.0 CA C:ASN146 5.0 24.6 1.0

Iron binding site 4 out of 4 in the Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Caulobacter Crescentus Xylonolactonase with D-Xylose, P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe303 b:24.8 occ:0.79 O D:HOH447 2.0 25.5 1.0 O1 D:XYP302 2.0 21.7 1.0 OE1 D:GLU18 2.1 31.6 1.0 OD1 D:ASP196 2.2 30.6 1.0 OD1 D:ASN146 2.2 26.7 1.0 O D:HOH477 2.4 29.9 1.0 CD D:GLU18 2.9 28.4 1.0 C1 D:XYP302 3.1 32.8 1.0 CG D:ASN146 3.2 21.6 1.0 CG D:ASP196 3.2 36.6 1.0 OE2 D:GLU18 3.3 29.6 1.0 ND2 D:ASN146 3.5 24.4 1.0 OD2 D:ASP196 3.6 37.5 1.0 O5 D:XYP302 3.7 42.1 1.0 ND2 D:ASN101 3.7 27.8 1.0 OD1 D:ASN101 4.2 34.8 1.0 CG D:GLU18 4.2 27.9 1.0 N D:GLY197 4.3 24.5 1.0 CG D:ASN101 4.3 33.0 1.0 O D:THR237 4.4 24.8 1.0 O D:HOH461 4.4 29.2 1.0 C2 D:XYP302 4.4 30.8 1.0 CB D:ASP196 4.6 28.0 1.0 CB D:ASN146 4.6 21.9 1.0 O2 D:XYP302 4.6 34.8 1.0 OD2 D:ASP102 4.6 27.9 1.0 CA D:GLY197 4.6 21.8 1.0 C D:ASP196 4.6 25.4 1.0 CG D:ASP102 4.6 28.5 1.0 CB D:ASP102 4.7 24.1 1.0 CA D:ASP196 4.9 25.7 1.0 C5 D:XYP302 4.9 32.1 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