Zinc in PDB 8q57: Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions

The structure of Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions, PDB code: 8q57 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)	61.01 / 1.70
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.734, 87.525, 104.312, 90, 107.73, 90
R / Rfree (%)	18.5 / 20.5

The structure of Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions (pdb code 8q57). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions, PDB code: 8q57:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions


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 Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:33.7 occ:0.50 ND1 A:HIS208 1.9 32.6 1.0 ZN A:ZN304 1.9 42.9 0.3 NE2 A:HIS180 2.0 31.5 0.5 NE2 A:HIS83 2.1 29.8 1.0 CE1 A:HIS180 2.1 47.0 0.5 NE2 A:HIS180 2.5 49.9 0.5 O A:HOH492 2.7 32.5 1.0 CE1 A:HIS180 2.8 35.9 0.5 CG A:HIS208 2.9 27.2 1.0 CE1 A:HIS83 2.9 32.1 1.0 CE1 A:HIS208 2.9 34.7 1.0 CD2 A:HIS180 3.2 36.2 0.5 CB A:HIS208 3.2 25.4 1.0 CD2 A:HIS83 3.3 28.1 1.0 ND1 A:HIS180 3.4 51.8 0.5 CD2 A:HIS180 3.9 51.0 0.5 NE2 A:HIS208 4.0 26.7 1.0 CD2 A:HIS208 4.0 29.7 1.0 ND1 A:HIS180 4.0 37.0 0.5 ND1 A:HIS83 4.1 30.3 1.0 CG A:HIS180 4.2 33.7 0.5 CG A:HIS180 4.3 45.8 0.5 CG A:HIS83 4.3 26.3 1.0 CA A:HIS208 4.3 26.0 1.0 O A:HOH415 4.4 39.3 1.0 ND2 A:ASN230 4.7 25.6 1.0 OE1 A:GLU134 4.7 33.2 1.0 OD1 A:ASP82 4.9 25.6 1.0 N A:GLY209 4.9 31.6 1.0 CG2 A:ILE138 5.0 38.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions


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 Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:42.9 occ:0.30 ZN A:ZN303 1.9 33.7 0.5 NE2 A:HIS180 2.6 49.9 0.5 CE1 A:HIS180 2.6 35.9 0.5 NE2 A:HIS83 2.7 29.8 1.0 NE2 A:HIS180 2.8 31.5 0.5 ND1 A:HIS208 2.9 32.6 1.0 CE1 A:HIS180 3.1 47.0 0.5 CD2 A:HIS83 3.1 28.1 1.0 OE1 A:GLU134 3.4 33.2 1.0 CE1 A:HIS208 3.6 34.7 1.0 CG A:HIS208 3.7 27.2 1.0 CE1 A:HIS83 3.8 32.1 1.0 CD2 A:HIS180 3.9 51.0 0.5 ND1 A:HIS180 3.9 37.0 0.5 CB A:HIS208 4.1 25.4 1.0 CD2 A:HIS180 4.2 36.2 0.5 CB A:ILE138 4.2 37.7 1.0 OE2 A:GLU134 4.2 34.0 1.0 CD A:GLU134 4.2 36.2 1.0 O A:ILE138 4.3 41.5 1.0 OD2 A:ASP104 4.3 29.5 1.0 CG A:HIS83 4.4 26.3 1.0 ND1 A:HIS180 4.4 51.8 0.5 CG2 A:ILE138 4.5 38.4 1.0 CD1 A:ILE138 4.5 37.9 1.0 O A:HOH492 4.5 32.5 1.0 NE2 A:HIS208 4.6 26.7 1.0 O A:HOH480 4.7 35.1 1.0 CD2 A:HIS208 4.7 29.7 1.0 CG A:HIS180 4.7 33.7 0.5 ND1 A:HIS83 4.7 30.3 1.0 CG A:HIS180 4.8 45.8 0.5 CG1 A:ILE138 4.9 40.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:35.5 occ:0.50 ZN B:ZN304 1.9 49.4 0.4 CE1 B:HIS180 1.9 77.3 0.5 NE2 B:HIS180 1.9 32.5 0.5 ND1 B:HIS208 1.9 30.7 1.0 NE2 B:HIS83 2.1 29.0 1.0 NE2 B:HIS180 2.5 80.9 0.5 CE1 B:HIS180 2.6 37.1 0.5 O B:HOH471 2.7 35.8 1.0 CE1 B:HIS83 2.9 32.4 1.0 CG B:HIS208 2.9 27.5 1.0 CE1 B:HIS208 2.9 28.6 1.0 CD2 B:HIS180 3.1 38.0 0.5 ND1 B:HIS180 3.2 74.8 0.5 CB B:HIS208 3.2 27.4 1.0 CD2 B:HIS83 3.3 29.6 1.0 CD2 B:HIS180 3.8 76.6 0.5 ND1 B:HIS180 3.8 39.4 0.5 NE2 B:HIS208 4.0 27.6 1.0 CD2 B:HIS208 4.0 30.0 1.0 CG B:HIS180 4.1 36.8 0.5 ND1 B:HIS83 4.1 29.2 1.0 CG B:HIS180 4.1 65.9 0.5 CG B:HIS83 4.3 24.9 1.0 CA B:HIS208 4.4 27.9 1.0 O B:HOH457 4.7 45.7 1.0 ND2 B:ASN230 4.7 28.1 1.0 OE1 B:GLU134 4.7 32.0 1.0 OD1 B:ASP82 4.9 24.0 1.0 CG2 B:ILE138 5.0 53.9 1.0 N B:GLY209 5.0 32.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:49.4 occ:0.40 ZN B:ZN303 1.9 35.5 0.5 NE2 B:HIS180 2.5 80.9 0.5 CE1 B:HIS180 2.6 37.1 0.5 NE2 B:HIS83 2.8 29.0 1.0 NE2 B:HIS180 2.8 32.5 0.5 ND1 B:HIS208 2.9 30.7 1.0 CE1 B:HIS180 2.9 77.3 0.5 CD2 B:HIS83 3.3 29.6 1.0 OE1 B:GLU134 3.4 32.0 1.0 CE1 B:HIS208 3.6 28.6 1.0 CG B:HIS208 3.6 27.5 1.0 CD2 B:HIS180 3.8 76.6 0.5 ND1 B:HIS180 3.9 39.4 0.5 CE1 B:HIS83 4.0 32.4 1.0 CB B:HIS208 4.0 27.4 1.0 CB B:ILE138 4.0 54.7 1.0 OE2 B:GLU134 4.1 37.8 1.0 CD B:GLU134 4.2 34.1 1.0 CD2 B:HIS180 4.2 38.0 0.5 O B:ILE138 4.2 54.9 1.0 ND1 B:HIS180 4.2 74.8 0.5 CG2 B:ILE138 4.4 53.9 1.0 OD2 B:ASP104 4.5 33.9 1.0 CD1 B:ILE138 4.5 40.9 1.0 NE2 B:HIS208 4.5 27.6 1.0 O B:HOH471 4.5 35.8 1.0 CG B:HIS83 4.6 24.9 1.0 CD2 B:HIS208 4.6 30.0 1.0 CG B:HIS180 4.7 36.8 0.5 CG B:HIS180 4.7 65.9 0.5 O B:HOH473 4.7 37.6 1.0 CG1 B:ILE138 4.8 50.1 1.0 ND1 B:HIS83 4.9 29.2 1.0 C B:ILE138 4.9 58.1 1.0 CA B:ILE138 5.0 54.9 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