Zinc in PDB 8q59: Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp)

The structure of Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp), PDB code: 8q59 was solved by M.Sharma, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.637, 87.739, 91.008, 90, 110.66, 90
R / Rfree (%)	18.7 / 21.2

The structure of Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp) (pdb code 8q59). 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 Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp), PDB code: 8q59:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp)


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 Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:35.0 occ:1.00 ND1 A:HIS208 2.0 31.3 1.0 NE2 A:HIS180 2.0 35.9 1.0 NE2 A:HIS83 2.2 31.7 1.0 O A:HOH465 2.3 34.1 1.0 O1 A:JP9303 2.4 38.9 0.9 CE1 A:HIS83 2.9 39.6 1.0 CE1 A:HIS180 3.0 41.8 1.0 CE1 A:HIS208 3.0 30.8 1.0 CG A:HIS208 3.0 28.9 1.0 CD2 A:HIS180 3.0 32.9 1.0 O7 A:JP9303 3.1 69.6 0.9 CD2 A:HIS83 3.3 32.9 1.0 CB A:HIS208 3.4 28.4 1.0 C1 A:JP9303 3.5 42.0 0.9 O6 A:JP9303 3.8 34.0 0.9 C3 A:JP9303 4.1 46.8 0.9 ND1 A:HIS180 4.1 39.9 1.0 NE2 A:HIS208 4.1 30.5 1.0 ND1 A:HIS83 4.1 38.0 1.0 CD2 A:HIS208 4.1 29.7 1.0 CG A:HIS180 4.1 35.3 1.0 C4 A:JP9303 4.2 55.3 0.9 CG A:HIS83 4.3 28.7 1.0 CA A:HIS208 4.5 27.7 1.0 ND2 A:ASN230 4.7 28.6 1.0 C2 A:JP9303 4.7 50.7 0.9 OE1 A:GLU134 4.8 39.0 1.0 OD1 A:ASP82 4.8 25.1 1.0 N A:GLY209 4.9 32.7 1.0 O A:HOH508 5.0 58.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp)


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 Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:36.7 occ:1.00 O B:HOH416 1.9 33.4 1.0 ND1 B:HIS208 1.9 33.1 1.0 NE2 B:HIS180 2.1 38.8 1.0 NE2 B:HIS83 2.2 31.6 1.0 O1 B:JP9303 2.4 29.4 0.8 CE1 B:HIS208 2.9 38.8 1.0 CE1 B:HIS83 2.9 38.9 1.0 CG B:HIS208 3.0 32.7 1.0 CD2 B:HIS180 3.0 34.7 1.0 CE1 B:HIS180 3.0 39.0 1.0 O7 B:JP9303 3.1 70.9 0.8 CD2 B:HIS83 3.3 33.7 1.0 CB B:HIS208 3.3 31.8 1.0 C1 B:JP9303 3.6 35.4 0.8 O6 B:JP9303 3.9 43.7 0.8 NE2 B:HIS208 4.0 34.3 1.0 CD2 B:HIS208 4.1 34.8 1.0 ND1 B:HIS180 4.1 41.7 1.0 ND1 B:HIS83 4.2 43.2 1.0 CG B:HIS180 4.2 38.0 1.0 C3 B:JP9303 4.2 44.9 0.8 C4 B:JP9303 4.3 49.8 0.8 CG B:HIS83 4.3 33.1 1.0 CA B:HIS208 4.4 34.5 1.0 ND2 B:ASN230 4.6 31.8 1.0 C2 B:JP9303 4.7 49.0 0.8 OE1 B:GLU134 4.8 42.2 1.0 OD1 B:ASP82 4.8 28.5 1.0 O B:HOH451 4.8 47.3 1.0 N B:GLY209 4.9 41.9 1.0

M.Sharma, A.Kaur, N.M.Soler, J.P.Lingford, R.Epa, E.D.Goddard-Borger, G.J.Davies, S.J.Williams. Defining the Molecular Architecture, Metal Dependence, and Distribution of Metal-Dependent Class II Sulfofructose-1-Phosphate Aldolases. J.Biol.Chem. 05338 2023.
ISSN: ESSN 1083-351X
PubMed: 37838169
DOI: 10.1016/J.JBC.2023.105338