Zinc in PDB 4a7k: Bifunctional Aldos-2-Ulose Dehydratase

All present enzymatic activity of Bifunctional Aldos-2-Ulose Dehydratase:
4.2.1.110;

The structure of Bifunctional Aldos-2-Ulose Dehydratase, PDB code: 4a7k was solved by M.Claesson, Y.Lindqvist, S.Madrid, T.Sandalova, R.Fiskesund, S.Yu, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.97 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	132.990, 79.740, 96.880, 90.00, 90.00, 90.00
R / Rfree (%)	17.177 / 21.907

The structure of Bifunctional Aldos-2-Ulose Dehydratase also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Bifunctional Aldos-2-Ulose Dehydratase (pdb code 4a7k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Bifunctional Aldos-2-Ulose Dehydratase, PDB code: 4a7k:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Bifunctional Aldos-2-Ulose Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bifunctional Aldos-2-Ulose Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn950 b:24.0 occ:1.00 O A:HOH2027 2.0 24.6 1.0 NE2 A:HIS337 2.1 22.5 1.0 NE2 A:HIS215 2.1 23.0 1.0 NE2 A:HIS295 2.1 20.7 1.0 CD2 A:HIS337 2.9 21.0 1.0 O A:HOH2193 2.9 12.0 0.5 CE1 A:HIS215 3.0 23.5 1.0 CD2 A:HIS295 3.0 20.7 1.0 CE1 A:HIS295 3.1 22.4 1.0 CD2 A:HIS215 3.1 23.3 1.0 CE1 A:HIS337 3.2 21.3 1.0 OH A:TYR35 3.6 21.2 1.0 O A:HOH2020 3.7 20.4 0.5 CE1 A:PHE294 4.1 24.0 1.0 CG A:HIS337 4.1 22.6 1.0 NH2 A:ARG156 4.1 20.4 1.0 ND1 A:HIS215 4.2 23.7 1.0 CG A:HIS295 4.2 23.7 1.0 ND1 A:HIS337 4.3 22.1 1.0 ND1 A:HIS295 4.3 23.4 1.0 NE2 A:HIS155 4.3 27.7 1.0 CG A:HIS215 4.3 24.0 1.0 CE1 A:TYR35 4.4 20.4 1.0 CZ A:TYR35 4.5 20.8 1.0 CZ A:PHE294 4.7 24.2 1.0 CE1 A:HIS155 4.8 26.7 1.0 CD1 A:PHE294 4.8 23.2 1.0

Zinc binding site 2 out of 3 in the Bifunctional Aldos-2-Ulose Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bifunctional Aldos-2-Ulose Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn951 b:30.2 occ:0.60 O A:GLU349 2.0 24.7 1.0 OD1 A:ASP347 2.0 25.5 1.0 OD1 A:ASP343 2.1 25.9 1.0 OD1 A:ASP345 2.1 25.2 1.0 OE1 A:GLU351 2.1 23.6 1.0 OE2 A:GLU351 2.1 22.1 1.0 CD A:GLU351 2.4 21.5 1.0 CG A:ASP345 3.1 24.8 1.0 CG A:ASP347 3.1 26.8 1.0 C A:GLU349 3.2 25.5 1.0 CG A:ASP343 3.3 24.7 1.0 OD2 A:ASP345 3.5 25.9 1.0 OD2 A:ASP347 3.8 28.1 1.0 N A:GLU349 3.9 27.3 1.0 N A:ASP347 3.9 25.5 1.0 CA A:ASP343 3.9 22.2 1.0 N A:ASP345 4.0 22.0 1.0 CG A:GLU351 4.0 21.8 1.0 CA A:GLU349 4.0 27.6 1.0 OD2 A:ASP343 4.1 24.1 1.0 N A:GLY346 4.1 23.1 1.0 C A:ASP343 4.1 21.7 1.0 CB A:ASP343 4.1 22.6 1.0 N A:GLU351 4.1 20.6 1.0 N A:ILE344 4.2 19.5 1.0 CB A:ASP347 4.2 26.6 1.0 N A:ASP350 4.2 23.5 1.0 CB A:GLU349 4.3 31.0 1.0 CB A:ASP345 4.4 23.1 1.0 C A:ASP350 4.4 21.8 1.0 NZ A:LYS373 4.4 32.9 1.0 CA A:ASP350 4.4 22.6 1.0 CA A:ASP345 4.5 23.2 1.0 C A:ASP345 4.5 22.9 1.0 CA A:ASP347 4.5 26.6 1.0 N A:GLY348 4.5 28.1 1.0 C A:ASP347 4.7 27.1 1.0 O A:ASP343 4.8 19.4 1.0 C A:GLY346 4.9 25.3 1.0 O A:HOH2225 4.9 25.2 1.0 CB A:GLU351 4.9 21.1 1.0 CA A:GLY346 4.9 24.0 1.0 C A:ILE344 5.0 22.9 1.0

Zinc binding site 3 out of 3 in the Bifunctional Aldos-2-Ulose Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bifunctional Aldos-2-Ulose Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn952 b:23.6 occ:1.00 OE2 A:GLU639 2.0 28.8 1.0 NE2 A:HIS632 2.1 18.8 1.0 NE2 A:HIS630 2.1 24.4 1.0 NE2 A:HIS709 2.1 21.0 1.0 O A:HOH2423 2.4 15.8 1.0 CD A:GLU639 2.9 27.2 1.0 CE1 A:HIS632 3.0 19.5 1.0 CD2 A:HIS709 3.0 22.5 1.0 CD2 A:HIS630 3.1 22.3 1.0 CE1 A:HIS630 3.1 24.0 1.0 OE1 A:GLU639 3.2 26.2 1.0 CD2 A:HIS632 3.2 21.4 1.0 CE1 A:HIS709 3.2 22.3 1.0 O A:HOH2437 4.0 26.3 1.0 CG A:GLU639 4.2 27.5 1.0 ND1 A:HIS632 4.2 21.5 1.0 ND1 A:HIS630 4.2 23.7 1.0 CG A:HIS709 4.2 22.6 1.0 CG A:HIS630 4.2 24.1 1.0 CG A:HIS632 4.3 21.3 1.0 ND1 A:HIS709 4.3 24.7 1.0 CE1 A:HIS641 4.5 25.7 1.0 C3 A:GOL1904 4.9 28.5 1.0 NE2 A:HIS641 4.9 27.2 1.0

M.Claesson, Y.Lindqvist, S.Madrid, T.Sandalova, R.Fiskesund, S.Yu, G.Schneider. Crystal Structure of Bifunctional Aldos-2-Ulose Dehydratase/Isomerase From Phanerochaete Chrysosporium with the Reaction Intermediate Ascopyrone M. J.Mol.Biol. V. 417 279 2012.
ISSN: ISSN 0022-2836
PubMed: 22330145
DOI: 10.1016/J.JMB.2012.02.001