Zinc in PDB 1gvf: Structure of Tagatose-1,6-Bisphosphate Aldolase

All present enzymatic activity of Structure of Tagatose-1,6-Bisphosphate Aldolase:
4.1.2.40;

The structure of Structure of Tagatose-1,6-Bisphosphate Aldolase, PDB code: 1gvf was solved by D.R.Hall, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.45
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	72.650, 100.460, 206.660, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 17.3

The structure of Structure of Tagatose-1,6-Bisphosphate Aldolase also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Structure of Tagatose-1,6-Bisphosphate Aldolase (pdb code 1gvf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Tagatose-1,6-Bisphosphate Aldolase, PDB code: 1gvf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Tagatose-1,6-Bisphosphate Aldolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Tagatose-1,6-Bisphosphate Aldolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn288 b:12.6 occ:1.00 O2 A:PGH287 2.0 18.2 1.0 NE2 A:HIS180 2.0 13.9 1.0 ND1 A:HIS208 2.0 12.2 1.0 NE2 A:HIS83 2.1 13.9 1.0 O1 A:PGH287 2.4 14.7 1.0 C1 A:PGH287 2.8 14.5 1.0 N2 A:PGH287 2.9 17.5 1.0 CE1 A:HIS208 2.9 11.9 1.0 CE1 A:HIS180 3.0 20.0 1.0 CD2 A:HIS180 3.1 13.4 1.0 CE1 A:HIS83 3.1 12.9 1.0 CG A:HIS208 3.1 11.3 1.0 CD2 A:HIS83 3.1 13.3 1.0 CB A:HIS208 3.5 12.3 1.0 ND2 A:ASN230 4.0 15.6 1.0 ND1 A:HIS180 4.1 20.0 1.0 NE2 A:HIS208 4.1 11.9 1.0 ND1 A:HIS83 4.2 13.1 1.0 OD2 A:ASP82 4.2 17.1 1.0 CG A:HIS180 4.2 14.1 1.0 CD2 A:HIS208 4.2 12.3 1.0 CG A:HIS83 4.2 12.1 1.0 OD1 A:ASP82 4.3 14.8 1.0 CD1 A:LEU138 4.3 20.9 1.0 C2 A:PGH287 4.4 16.6 1.0 CA A:HIS208 4.4 11.9 1.0 O A:HOH2348 4.6 26.7 1.0 CG A:ASP82 4.6 14.4 1.0 N A:GLY209 4.6 11.9 1.0 O A:HOH2174 4.7 49.6 1.0 O1P A:PGH287 4.8 15.7 1.0

Zinc binding site 2 out of 2 in the Structure of Tagatose-1,6-Bisphosphate Aldolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Tagatose-1,6-Bisphosphate Aldolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn288 b:12.9 occ:1.00 NE2 B:HIS180 2.0 13.2 1.0 NE2 B:HIS83 2.1 13.3 1.0 ND1 B:HIS208 2.1 13.5 1.0 O2 B:PGH287 2.1 20.2 1.0 O1 B:PGH287 2.3 15.2 1.0 N2 B:PGH287 2.9 16.6 1.0 C1 B:PGH287 2.9 14.1 1.0 CE1 B:HIS208 2.9 12.0 1.0 CE1 B:HIS180 2.9 15.5 1.0 CE1 B:HIS83 3.0 13.8 1.0 CD2 B:HIS180 3.1 14.5 1.0 CD2 B:HIS83 3.1 14.8 1.0 CG B:HIS208 3.1 13.7 1.0 CB B:HIS208 3.5 13.1 1.0 CD1 B:LEU138 4.0 17.8 1.0 ND2 B:ASN230 4.1 13.9 1.0 ND1 B:HIS180 4.1 17.9 1.0 NE2 B:HIS208 4.1 11.4 1.0 ND1 B:HIS83 4.2 14.4 1.0 CG B:HIS180 4.2 13.8 1.0 OD2 B:ASP82 4.2 16.7 1.0 OD1 B:ASP82 4.2 16.3 1.0 CD2 B:HIS208 4.2 13.2 1.0 CG B:HIS83 4.3 13.2 1.0 CA B:HIS208 4.5 11.9 1.0 C2 B:PGH287 4.5 15.0 1.0 N B:GLY209 4.6 12.5 1.0 O B:HOH2297 4.6 27.7 1.0 CG B:ASP82 4.6 14.1 1.0 O1P B:PGH287 4.8 15.2 1.0

D.R.Hall, C.S.Bond, G.A.Leonard, C.I.Watt, A.Berry, W.N.Hunter. Structure of Tagatose-1,6-Bisphosphate Aldolase; Insight Into Chiral Discrimination, Mechanism and Specificity of Class II Aldolases J.Biol.Chem. V. 277 22018 2002.
ISSN: ISSN 0021-9258
PubMed: 11940603
DOI: 10.1074/JBC.M202464200