Zinc in PDB 1l6s: 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: 1l6s was solved by E.K.Jaffe, J.Kervinen, J.Martins, 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)	40.00 / 1.70
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	129.000, 129.000, 142.800, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.3

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 1l6s). 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: 1l6s:
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:42.4 occ:1.00 O A:HOH685 2.3 20.7 1.0 SG A:CYS129 2.4 24.9 1.0 SG A:CYS119 2.4 25.3 1.0 SG A:CYS121 2.5 26.9 1.0 CB A:CYS129 3.1 17.1 1.0 CB A:CYS121 3.2 19.1 1.0 CB A:CYS119 3.4 18.8 1.0 O A:HOH514 3.9 23.9 1.0 N A:CYS121 3.9 21.9 1.0 CA A:CYS129 4.0 44.6 1.0 O A:SER164 4.0 25.4 1.0 O A:HOH447 4.1 17.7 1.0 CA A:CYS121 4.2 21.7 1.0 OG A:SER164 4.4 21.8 1.0 O A:HOH687 4.5 32.9 1.0 N A:PHE120 4.5 30.1 1.0 N A:CYS129 4.7 31.5 1.0 C A:SER164 4.7 33.0 1.0 CA A:ALA165 4.7 20.4 1.0 CA A:CYS119 4.8 23.2 1.0 CZ A:ARG215 4.9 33.5 1.0 NH1 A:ARG215 4.9 23.2 1.0 O A:HOH463 5.0 26.6 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:42.0 occ:1.00 SG B:CYS119 2.3 26.2 1.0 SG B:CYS129 2.5 32.9 1.0 SG B:CYS121 2.5 26.8 1.0 O B:HOH686 2.6 38.4 1.0 CB B:CYS121 3.2 28.9 1.0 CB B:CYS129 3.3 30.4 1.0 CB B:CYS119 3.4 20.5 1.0 O B:HOH429 3.8 19.4 1.0 N B:CYS121 3.9 24.3 1.0 O B:HOH431 3.9 18.0 1.0 CA B:CYS129 4.0 50.6 1.0 O B:SER164 4.0 27.3 1.0 CA B:CYS121 4.2 29.9 1.0 O B:HOH512 4.3 25.6 1.0 N B:PHE120 4.5 24.6 1.0 C B:SER164 4.7 28.4 1.0 OG B:SER164 4.7 24.6 1.0 N B:CYS129 4.7 33.9 1.0 CA B:ALA165 4.7 28.6 1.0 CA B:CYS119 4.7 43.0 1.0 O B:HOH511 4.9 27.5 1.0 CZ B:ARG215 4.9 45.1 1.0 N B:ALA165 5.0 20.3 1.0

E.K.Jaffe, J.Kervinen, J.Martins, F.Stauffer, R.Neier, A.Wlodawer, A.Zdanov. Species-Specific Inhibition of Porphobilinogen Synthase By 4-Oxosebacic Acid J.Biol.Chem. V. 277 19792 2002.
ISSN: ISSN 0021-9258
PubMed: 11909869
DOI: 10.1074/JBC.M201486200