Iron in PDB 7pld: Caulobacter Crescentus Xylonolactonase with (R)-4-Hydroxy-2- Pyrrolidone

All present enzymatic activity of Caulobacter Crescentus Xylonolactonase with (R)-4-Hydroxy-2- Pyrrolidone:
3.1.1.68;

The structure of Caulobacter Crescentus Xylonolactonase with (R)-4-Hydroxy-2- Pyrrolidone, PDB code: 7pld 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)	78.14 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	87.747, 171.729, 79.254, 90, 90, 90
R / Rfree (%)	19.4 / 23.4

The binding sites of Iron atom in the Caulobacter Crescentus Xylonolactonase with (R)-4-Hydroxy-2- Pyrrolidone (pdb code 7pld). 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 (R)-4-Hydroxy-2- Pyrrolidone, PDB code: 7pld:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Caulobacter Crescentus Xylonolactonase with (R)-4-Hydroxy-2- Pyrrolidone


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 (R)-4-Hydroxy-2- Pyrrolidone within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:22.3 occ:0.47 O A:HOH481 1.8 23.3 1.0 OE1 A:GLU18 2.0 27.6 1.0 O A:HOH532 2.0 32.0 1.0 OD1 A:ASN146 2.2 21.7 1.0 OD1 A:ASP196 2.3 27.9 1.0 O A:HOH417 2.5 35.2 1.0 CD A:GLU18 2.9 27.6 1.0 CG A:ASN146 3.1 20.6 1.0 ND2 A:ASN146 3.3 21.1 1.0 OE2 A:GLU18 3.3 28.5 1.0 CG A:ASP196 3.4 29.2 1.0 ND2 A:ASN101 3.7 25.8 1.0 OD2 A:ASP196 4.0 34.3 1.0 N A:GLY197 4.1 21.0 1.0 OD1 A:ASN101 4.2 24.8 1.0 CG A:GLU18 4.2 23.2 1.0 O A:THR237 4.2 19.0 1.0 O A:HOH407 4.3 36.2 1.0 CG A:ASN101 4.3 27.2 1.0 O A:HOH506 4.4 31.9 1.0 OD1 A:ASP102 4.4 23.7 1.0 O A:HOH436 4.4 34.3 1.0 CB A:ASN146 4.5 19.5 1.0 C A:ASP196 4.5 21.2 1.0 CA A:GLY197 4.5 21.7 1.0 CB A:ASP196 4.5 16.8 1.0 CG A:ASP102 4.6 21.6 1.0 CB A:ASP102 4.6 21.0 1.0 CA A:ASP196 4.8 18.5 1.0

Iron binding site 2 out of 2 in the Caulobacter Crescentus Xylonolactonase with (R)-4-Hydroxy-2- Pyrrolidone


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 (R)-4-Hydroxy-2- Pyrrolidone within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe305 b:20.3 occ:0.63 O01 B:7UK301 1.9 24.8 0.3 O B:HOH462 1.9 23.8 1.0 O01 B:7UK301 2.0 25.0 0.3 OD1 B:ASP196 2.0 26.4 1.0 OE1 B:GLU18 2.1 24.7 1.0 O B:HOH490 2.2 25.6 1.0 OD1 B:ASN146 2.3 20.8 1.0 C02 B:7UK301 2.8 26.4 0.3 C02 B:7UK301 2.8 26.4 0.3 CD B:GLU18 3.0 27.6 1.0 CG B:ASN146 3.1 24.0 1.0 CG B:ASP196 3.1 28.9 1.0 ND2 B:ASN146 3.3 22.4 1.0 OE2 B:GLU18 3.4 27.4 1.0 H031 B:7UK301 3.4 36.4 0.3 OD2 B:ASP196 3.6 31.2 1.0 C03 B:7UK301 3.6 30.3 0.3 H071 B:7UK301 3.7 36.5 0.3 N07 B:7UK301 3.7 30.4 0.3 ND2 B:ASN101 3.7 20.7 1.0 N07 B:7UK301 3.9 25.6 0.3 H032 B:7UK301 4.0 31.5 0.3 C03 B:7UK301 4.0 26.3 0.3 H032 B:7UK301 4.0 36.4 0.3 H071 B:7UK301 4.1 30.8 0.3 N B:GLY197 4.1 19.3 1.0 CG B:GLU18 4.2 27.8 1.0 OD1 B:ASN101 4.2 22.5 1.0 OD1 B:ASP102 4.3 21.8 1.0 CG B:ASN101 4.3 24.6 1.0 O B:THR237 4.4 21.5 1.0 CB B:ASP196 4.4 21.6 1.0 C B:ASP196 4.4 21.8 1.0 H031 B:7UK301 4.5 31.5 0.3 CG B:ASP102 4.5 25.1 1.0 CA B:GLY197 4.5 18.5 1.0 CB B:ASN146 4.5 19.2 1.0 CB B:ASP102 4.6 22.2 1.0 CA B:ASP196 4.7 19.7 1.0 O B:HOH449 4.7 31.4 1.0 C06 B:7UK301 4.9 31.4 0.3 C06 B:7UK301 4.9 29.7 0.3 C04 B:7UK301 5.0 31.4 0.3

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