Zinc in PDB 1b4e: X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid

All present enzymatic activity of X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid:
4.2.1.24;

The structure of X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid, PDB code: 1b4e was solved by P.T.Erskine, J.B.Cooper, G.Lewis, P.Spencer, S.P.Wood, P.M.Shoolingin-Jordan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.00
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	126.700, 126.700, 141.600, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid (pdb code 1b4e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid, PDB code: 1b4e:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:17.8 occ:0.50 OE2 A:GLU40 1.7 22.4 1.0 NE2 A:HIS84 2.2 25.7 1.0 CE1 A:HIS84 2.4 24.2 1.0 CD A:GLU40 2.5 18.1 1.0 OE1 A:GLU40 2.5 23.9 1.0 CD2 A:HIS84 3.5 20.7 1.0 ND1 A:HIS84 3.7 29.7 1.0 CG A:GLU40 3.9 12.7 1.0 CG A:HIS84 4.3 20.5 1.0 O A:HOH829 4.5 47.6 1.0 O A:HIS83 4.8 25.5 1.0

Zinc binding site 2 out of 3 in the X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:15.0 occ:1.00 O A:HOH869 1.7 4.5 1.0 SG A:CYS120 2.1 12.4 1.0 SG A:CYS130 2.1 11.8 1.0 SG A:CYS122 2.3 18.3 1.0 CB A:CYS122 3.1 19.0 1.0 CB A:CYS120 3.2 2.0 1.0 CB A:CYS130 3.3 17.6 1.0 O A:HOH674 3.7 18.0 1.0 N A:CYS122 3.8 22.1 1.0 CA A:CYS130 3.8 14.5 1.0 O A:HOH810 3.9 29.2 1.0 O A:SER165 4.1 14.9 1.0 O A:HOH680 4.1 19.1 1.0 CA A:CYS122 4.1 11.4 1.0 OG A:SER165 4.3 19.3 1.0 N A:PHE121 4.4 18.8 1.0 O A:HOH664 4.4 22.5 1.0 CA A:ALA166 4.5 8.8 1.0 NH1 A:ARG216 4.5 28.4 1.0 C A:SER165 4.5 14.9 1.0 CA A:CYS120 4.6 13.5 1.0 N A:CYS130 4.6 28.2 1.0 N A:ALA166 4.8 13.7 1.0 O A:HOH811 4.8 33.6 1.0 C A:CYS130 4.9 27.2 1.0 C A:CYS120 4.9 18.0 1.0 C A:PHE121 5.0 27.9 1.0

Zinc binding site 3 out of 3 in the X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of 5-Aminolevulinic Acid Dehydratase Complexed with the Inhibitor Levulinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:17.5 occ:1.00 O A:HOH871 1.9 11.6 1.0 O A:HOH870 2.0 13.0 1.0 O A:HOH698 2.0 12.2 1.0 O A:HOH697 2.1 13.3 1.0 OE1 A:GLU232 2.2 18.9 1.0 O A:HOH699 2.2 13.9 1.0 CD A:GLU232 3.3 35.9 1.0 OE2 A:GLU232 3.7 14.8 1.0 O A:HOH700 3.8 13.3 1.0 OD1 A:ASP236 3.9 16.9 1.0 O A:HOH696 3.9 17.7 1.0 O A:SER193 4.1 11.1 1.0 O A:GLU232 4.1 9.8 1.0 O A:MET168 4.2 13.8 1.0 OD2 A:ASP236 4.3 8.2 1.0 NE2 A:GLN171 4.3 13.4 1.0 CG A:ASP236 4.4 10.0 1.0 O A:HOH702 4.4 14.8 1.0 OD1 A:ASP169 4.4 16.1 1.0 CG A:GLU232 4.5 10.1 1.0 CB A:GLU232 4.7 11.5 1.0 CA A:ASP169 4.8 2.9 1.0 CA A:GLU232 4.8 3.2 1.0 C A:GLU232 4.8 25.1 1.0 C A:MET168 4.8 4.3 1.0

P.T.Erskine, E.Norton, J.B.Cooper, R.Lambert, A.Coker, G.Lewis, P.Spencer, M.Sarwar, S.P.Wood, M.J.Warren, P.M.Shoolingin-Jordan. X-Ray Structure of 5-Aminolevulinic Acid Dehydratase From Escherichia Coli Complexed with the Inhibitor Levulinic Acid at 2.0 A Resolution. Biochemistry V. 38 4266 1999.
ISSN: ISSN 0006-2960
PubMed: 10194344
DOI: 10.1021/BI982137W