Zinc in PDB 1l6y: Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid

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

The structure of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid, PDB code: 1l6y 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 / 1.90
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 (%)	20.6 / 26.3

The structure of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic 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-Oxosebacic Acid (pdb code 1l6y). 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-Oxosebacic Acid, PDB code: 1l6y:
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-Oxosebacic 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-Oxosebacic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:51.8 occ:1.00 SG A:CYS119 2.3 36.9 1.0 SG A:CYS129 2.4 43.6 1.0 O A:HOH685 2.6 40.6 1.0 SG A:CYS121 2.7 44.2 1.0 CB A:CYS121 3.2 38.7 1.0 CB A:CYS129 3.2 75.1 1.0 CB A:CYS119 3.4 13.6 1.0 O A:SER164 3.8 41.2 1.0 O A:HOH514 3.9 44.2 1.0 CA A:CYS129 3.9 37.5 1.0 N A:CYS121 4.0 30.2 1.0 O A:HOH447 4.1 29.4 1.0 CA A:CYS121 4.2 43.7 1.0 C A:SER164 4.4 49.6 1.0 N A:PHE120 4.5 40.0 1.0 C7 A:4OX350 4.6 26.9 1.0 CA A:ALA165 4.6 28.6 1.0 N A:CYS129 4.6 35.6 1.0 C8 A:4OX350 4.7 22.0 1.0 CA A:CYS119 4.8 70.5 1.0 N A:ALA165 4.9 24.8 1.0 OG A:SER164 4.9 41.0 1.0 CB A:SER164 4.9 21.8 1.0 C6 A:4OX350 5.0 34.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic 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-Oxosebacic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:69.6 occ:1.00 SG B:CYS129 2.3 35.5 1.0 O B:HOH686 2.3 42.8 1.0 SG B:CYS119 2.6 43.7 1.0 SG B:CYS121 2.8 41.5 1.0 CB B:CYS121 3.2 34.6 1.0 CB B:CYS129 3.4 54.5 1.0 CB B:CYS119 3.6 29.0 1.0 O B:SER164 3.8 31.2 1.0 N B:CYS121 4.0 37.0 1.0 O B:HOH431 4.1 44.1 1.0 O B:HOH429 4.2 38.8 1.0 CA B:CYS129 4.2 59.6 1.0 CA B:CYS121 4.2 30.0 1.0 C8 B:4OX350 4.4 27.5 1.0 C B:SER164 4.4 29.2 1.0 OG B:SER164 4.4 82.7 1.0 C7 B:4OX350 4.4 56.0 1.0 NH1 B:ARG215 4.5 38.8 1.0 CA B:ALA165 4.6 25.4 1.0 N B:PHE120 4.8 35.0 1.0 O B:HOH512 4.8 25.9 1.0 N B:ALA165 4.8 49.1 1.0 N B:CYS129 4.9 76.8 1.0 C6 B:4OX350 4.9 45.1 1.0 CA B:CYS119 5.0 24.4 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