Zinc in PDB 1i8j: Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid

All present enzymatic activity of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid:
4.2.1.24;

The structure of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid, PDB code: 1i8j was solved by J.Kervinen, E.K.Jaffe, F.Stauffer, R.Neier, A.Wlodawer, A.Zdanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.90
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.741, 128.741, 142.760, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.7

The structure of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid (pdb code 1i8j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid, PDB code: 1i8j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:33.4 occ:1.00 O A:HOH685 2.3 27.5 1.0 SG A:CYS129 2.4 27.9 1.0 SG A:CYS119 2.4 27.5 1.0 SG A:CYS121 2.4 33.2 1.0 CB A:CYS121 3.2 24.8 1.0 CB A:CYS129 3.2 32.2 1.0 CB A:CYS119 3.4 22.9 1.0 O A:HOH514 3.8 30.2 1.0 N A:CYS121 3.9 29.7 1.0 CA A:CYS129 3.9 37.9 1.0 O A:SER164 4.0 29.8 1.0 O A:HOH447 4.1 17.2 1.0 CA A:CYS121 4.2 28.0 1.0 OG A:SER164 4.5 25.3 1.0 N A:PHE120 4.5 31.0 1.0 N A:CYS129 4.6 37.6 1.0 C A:SER164 4.6 25.7 1.0 CA A:ALA165 4.7 21.2 1.0 O A:HOH687 4.7 43.2 1.0 CA A:CYS119 4.7 27.5 1.0 CZ A:ARG215 4.9 26.3 1.0 NH1 A:ARG215 4.9 25.8 1.0 O A:HOH463 4.9 28.1 1.0 N A:ALA165 5.0 27.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:36.1 occ:1.00 O B:HOH686 2.1 54.6 1.0 SG B:CYS119 2.4 29.8 1.0 SG B:CYS129 2.4 40.5 1.0 SG B:CYS121 2.5 32.3 1.0 CB B:CYS121 3.2 27.6 1.0 CB B:CYS119 3.4 23.4 1.0 CB B:CYS129 3.4 42.1 1.0 O B:HOH429 3.7 17.3 1.0 N B:CYS121 3.8 30.5 1.0 CA B:CYS129 4.0 44.7 1.0 O B:SER164 4.0 30.0 1.0 O B:HOH431 4.0 19.2 1.0 CA B:CYS121 4.2 35.1 1.0 OG B:SER164 4.2 31.8 1.0 O B:HOH512 4.3 31.7 1.0 N B:PHE120 4.5 31.1 1.0 C B:SER164 4.6 27.5 1.0 N B:CYS129 4.7 44.8 1.0 CA B:CYS119 4.7 29.3 1.0 CA B:ALA165 4.7 28.5 1.0 O B:HOH511 4.7 25.2 1.0 C8 B:DSB350 4.9 34.3 1.0 CZ B:ARG215 4.9 41.9 1.0 N B:ALA165 5.0 24.5 1.0

J.Kervinen, E.K.Jaffe, F.Stauffer, R.Neier, A.Wlodawer, A.Zdanov. Mechanistic Basis For Suicide Inactivation of Porphobilinogen Synthase By 4,7-Dioxosebacic Acid, An Inhibitor That Shows Dramatic Species Selectivity. Biochemistry V. 40 8227 2001.
ISSN: ISSN 0006-2960
PubMed: 11444968
DOI: 10.1021/BI010656K