Zinc in PDB 5mhb: Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase

All present enzymatic activity of Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase:
4.2.1.24;

The structure of Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase, PDB code: 5mhb was solved by E.Norton, P.T.Erskine, P.M.Shoolingin-Jordan, J.B.Cooper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.57 / 2.10
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.619, 128.619, 142.815, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 21.3

The binding sites of Zinc atom in the Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase (pdb code 5mhb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase, PDB code: 5mhb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:42.5 occ:0.50 OE2 A:GLU40 1.7 43.6 1.0 CD A:GLU40 2.5 42.1 1.0 NE2 A:HIS84 2.5 51.6 1.0 CE1 A:HIS84 2.5 52.5 1.0 OE1 A:GLU40 2.5 43.7 1.0 ND1 A:HIS84 3.8 51.4 1.0 CD2 A:HIS84 3.9 50.8 1.0 CG A:GLU40 3.9 41.2 1.0 CG A:HIS84 4.5 48.6 1.0 O A:HIS83 4.9 43.5 1.0

Zinc binding site 2 out of 3 in the Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:31.8 occ:1.00 SG A:CYS120 2.2 30.7 1.0 N1 A:PBG401 2.3 33.5 1.0 SG A:CYS130 2.3 31.1 1.0 SG A:CYS122 2.4 35.2 1.0 CB A:CYS122 3.0 33.8 1.0 CHA A:PBG401 3.0 37.5 1.0 CB A:CYS130 3.3 35.0 1.0 CB A:CYS120 3.5 29.6 1.0 O A:HOH522 3.7 53.0 1.0 N A:CYS122 3.8 36.3 1.0 CA A:CYS130 3.8 35.0 1.0 CA A:CYS122 4.0 35.8 1.0 O A:HOH574 4.1 23.4 1.0 O A:SER165 4.1 29.2 1.0 C1A A:PBG401 4.4 36.9 1.0 O A:HOH671 4.4 35.6 1.0 OG A:SER165 4.5 32.0 1.0 N A:CYS130 4.5 36.9 1.0 N A:PHE121 4.6 33.5 1.0 CA A:ALA166 4.7 27.7 1.0 C A:SER165 4.7 28.7 1.0 NH1 A:ARG216 4.8 39.9 1.0 CA A:CYS120 4.8 29.8 1.0 CZ A:ARG216 4.9 41.8 1.0 N A:ALA166 4.9 28.7 1.0 C A:PHE121 5.0 37.8 1.0

Zinc binding site 3 out of 3 in the Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Product-Complex of E.Coli 5-Amino Laevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:33.9 occ:1.00 O A:HOH560 2.1 30.2 1.0 OE1 A:GLU232 2.2 32.0 1.0 O A:HOH516 2.2 24.7 1.0 O A:HOH584 2.2 24.3 1.0 O A:HOH535 2.3 19.1 1.0 O A:HOH740 2.4 24.3 1.0 CD A:GLU232 3.2 29.0 1.0 OE2 A:GLU232 3.4 26.9 1.0 O A:HOH679 3.8 28.2 1.0 O A:HOH561 3.9 25.9 1.0 OD1 A:ASP236 4.0 20.1 1.0 O A:HOH590 4.0 34.2 1.0 O A:SER193 4.1 24.2 1.0 O A:GLU232 4.2 25.2 1.0 OD2 A:ASP236 4.3 20.0 1.0 O A:MET168 4.3 22.1 1.0 O A:HOH548 4.4 21.2 1.0 O A:HOH601 4.5 26.2 1.0 CG A:GLU232 4.5 28.8 1.0 CG A:ASP236 4.5 19.9 1.0 OD1 A:ASP169 4.6 30.9 1.0 NE2 A:GLN171 4.6 33.0 1.0 CB A:GLU232 4.7 26.1 1.0 CA A:GLU232 4.8 24.1 1.0 C A:GLU232 4.9 24.2 1.0 CA A:ASP169 4.9 27.2 1.0 C A:MET168 4.9 26.0 1.0

N.Mills-Davies, D.Butler, E.Norton, D.Thompson, M.Sarwar, J.Guo, R.Gill, N.Azim, A.Coker, S.P.Wood, P.T.Erskine, L.Coates, J.B.Cooper, N.Rashid, M.Akhtar, P.M.Shoolingin-Jordan. Structural Studies of Substrate and Product Complexes of 5-Aminolaevulinic Acid Dehydratase From Humans, Escherichia Coli and the Hyperthermophile Pyrobaculum Calidifontis. Acta Crystallogr D Struct V. 73 9 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28045381
DOI: 10.1107/S2059798316019525