Zinc in PDB 5a23: Sdsa Sulfatase Triclinic Form

The structure of Sdsa Sulfatase Triclinic Form, PDB code: 5a23 was solved by E.De La Mora, E.Flores-Hernandez, J.Jakoncik, V.Stojanoff, N.Sanchez-Puig, A.Moreno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	118.77 / 2.41
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	86.900, 86.800, 129.030, 107.59, 102.96, 95.59
R / Rfree (%)	25.349 / 30.701

The binding sites of Zinc atom in the Sdsa Sulfatase Triclinic Form (pdb code 5a23). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Sdsa Sulfatase Triclinic Form, PDB code: 5a23:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Sdsa Sulfatase Triclinic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sdsa Sulfatase Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:39.5 occ:1.00 OD2 A:ASP173 1.8 28.2 1.0 NE2 A:HIS174 2.1 15.8 1.0 NE2 A:HIS344 2.3 23.6 1.0 OE1 A:GLU299 2.8 13.6 1.0 OE2 A:GLU299 2.9 13.6 1.0 CE1 A:HIS174 2.9 17.0 1.0 CG A:ASP173 2.9 28.1 1.0 ZN A:ZN1002 3.1 44.8 1.0 CD2 A:HIS344 3.1 22.3 1.0 CD A:GLU299 3.2 14.5 1.0 CD2 A:HIS174 3.2 16.1 1.0 CE1 A:HIS344 3.4 22.3 1.0 OD1 A:ASP173 3.4 30.3 1.0 OE2 A:GLU280 3.8 29.7 1.0 ND1 A:HIS174 4.1 16.6 1.0 NE2 A:HIS169 4.1 19.2 1.0 CE1 A:HIS169 4.1 19.2 1.0 CG A:HIS174 4.2 16.9 1.0 CB A:ASP173 4.3 27.4 1.0 CG A:HIS344 4.3 22.6 1.0 ND1 A:HIS344 4.4 22.6 1.0 CD1 A:ILE239 4.6 42.3 1.0 CG A:GLU299 4.6 14.6 1.0 CG2 A:VAL343 4.6 16.6 1.0 CB A:ALA123 4.7 21.6 1.0 CD A:GLU280 4.7 31.9 1.0 OE1 A:GLU280 4.9 36.1 1.0 CD2 A:LEU122 5.0 25.5 1.0

Zinc binding site 2 out of 8 in the Sdsa Sulfatase Triclinic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sdsa Sulfatase Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:44.8 occ:1.00 OE2 A:GLU280 1.1 29.7 1.0 NE2 A:HIS169 2.1 19.2 1.0 ND1 A:HIS171 2.4 28.1 1.0 CD A:GLU280 2.4 31.9 1.0 OE1 A:GLU299 2.9 13.6 1.0 OE1 A:GLU280 3.0 36.1 1.0 ZN A:ZN1001 3.1 39.5 1.0 CD2 A:HIS169 3.1 20.0 1.0 CE1 A:HIS169 3.1 19.2 1.0 CG A:HIS171 3.2 29.4 1.0 CB A:HIS171 3.3 28.7 1.0 CD A:GLU299 3.4 14.5 1.0 CE1 A:HIS171 3.4 28.6 1.0 NE2 A:HIS174 3.4 15.8 1.0 OE2 A:GLU299 3.5 13.6 1.0 CG A:GLU280 3.6 27.2 1.0 CD2 A:HIS174 3.8 16.1 1.0 OD1 A:ASP173 3.9 30.3 1.0 OD2 A:ASP173 4.0 28.2 1.0 ND1 A:HIS169 4.2 19.4 1.0 CG A:HIS169 4.2 20.3 1.0 CD2 A:HIS171 4.3 29.4 1.0 CG A:ASP173 4.4 28.1 1.0 NE2 A:HIS171 4.4 31.6 1.0 CG A:GLU299 4.4 14.6 1.0 CE1 A:HIS174 4.5 17.0 1.0 CA A:HIS171 4.7 28.5 1.0 CB A:GLU299 4.8 15.4 1.0 CG A:HIS174 4.9 16.9 1.0

Zinc binding site 3 out of 8 in the Sdsa Sulfatase Triclinic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sdsa Sulfatase Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:57.5 occ:1.00 OE2 B:GLU299 1.4 24.9 1.0 OD2 B:ASP173 2.2 49.9 1.0 NE2 B:HIS344 2.2 42.2 1.0 NE2 B:HIS174 2.4 44.1 1.0 CD B:GLU299 2.6 28.8 1.0 CG B:ASP173 3.0 54.1 1.0 CE1 B:HIS344 3.1 37.8 1.0 CB B:ASP173 3.1 51.3 1.0 CD2 B:HIS344 3.2 38.7 1.0 OE1 B:GLU299 3.2 26.5 1.0 CE1 B:HIS174 3.3 45.8 1.0 ZN B:ZN1002 3.4 52.3 1.0 CD2 B:HIS174 3.4 43.4 1.0 CG B:GLU299 3.9 28.3 1.0 OD1 B:ASP173 4.2 62.8 1.0 ND1 B:HIS344 4.2 38.5 1.0 CG B:HIS344 4.3 38.4 1.0 NE2 B:HIS169 4.3 29.2 1.0 ND1 B:HIS174 4.4 44.1 1.0 CB B:ALA123 4.4 37.5 1.0 CG B:HIS174 4.5 43.1 1.0 CD1 B:ILE239 4.5 43.4 1.0 CE1 B:HIS169 4.6 32.3 1.0 CA B:ASP173 4.6 44.4 1.0 CD2 B:LEU122 5.0 49.5 1.0 ND1 B:HIS171 5.0 43.5 1.0 C B:ASP173 5.0 42.9 1.0

Zinc binding site 4 out of 8 in the Sdsa Sulfatase Triclinic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sdsa Sulfatase Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:52.3 occ:1.00 ND1 B:HIS171 2.0 43.5 1.0 NE2 B:HIS169 2.3 29.2 1.0 CE1 B:HIS171 2.8 41.8 1.0 OE2 B:GLU299 2.9 24.9 1.0 OE1 B:GLU280 2.9 36.2 1.0 CD B:GLU299 3.0 28.8 1.0 CD2 B:HIS169 3.1 29.4 1.0 CG B:HIS171 3.1 41.0 1.0 OE2 B:GLU280 3.2 46.8 1.0 OE1 B:GLU299 3.4 26.5 1.0 ZN B:ZN1001 3.4 57.5 1.0 CD B:GLU280 3.4 40.2 1.0 CE1 B:HIS169 3.5 32.3 1.0 CB B:HIS171 3.5 42.7 1.0 CG B:GLU299 3.6 28.3 1.0 NE2 B:HIS174 3.8 44.1 1.0 NE2 B:HIS171 4.0 41.0 1.0 CD2 B:HIS174 4.1 43.4 1.0 CD2 B:HIS171 4.1 40.3 1.0 CG B:HIS169 4.3 32.7 1.0 CB B:GLU299 4.3 29.0 1.0 ND1 B:HIS169 4.5 33.1 1.0 OD2 B:ASP173 4.7 49.9 1.0 CE1 B:HIS174 4.9 45.8 1.0 CG B:GLU280 4.9 39.5 1.0 CA B:HIS171 5.0 40.4 1.0

Zinc binding site 5 out of 8 in the Sdsa Sulfatase Triclinic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sdsa Sulfatase Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:52.7 occ:1.00 OE2 C:GLU299 1.3 33.9 1.0 OD2 C:ASP173 2.1 33.6 1.0 NE2 C:HIS174 2.2 27.9 1.0 NE2 C:HIS344 2.4 35.3 1.0 CD C:GLU299 2.6 30.2 1.0 CE1 C:HIS174 2.9 28.8 1.0 CG C:ASP173 3.0 31.7 1.0 CD2 C:HIS344 3.2 34.4 1.0 OE1 C:GLU299 3.2 28.1 1.0 OD1 C:ASP173 3.3 31.1 1.0 CE1 C:HIS344 3.3 34.3 1.0 ZN C:ZN1002 3.3 50.7 1.0 CD2 C:HIS174 3.4 26.7 1.0 CG C:GLU299 3.7 28.4 1.0 CD1 C:ILE239 4.0 40.1 1.0 NE2 C:HIS169 4.1 25.8 1.0 OE2 C:GLU280 4.1 46.0 1.0 ND1 C:HIS174 4.1 28.2 1.0 CG C:HIS344 4.3 36.5 1.0 ND1 C:HIS344 4.3 36.7 1.0 CE1 C:HIS169 4.3 28.8 1.0 CG C:HIS174 4.4 26.9 1.0 CB C:ASP173 4.4 30.3 1.0 CB C:ALA123 4.8 34.6 1.0

Zinc binding site 6 out of 8 in the Sdsa Sulfatase Triclinic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sdsa Sulfatase Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1002 b:50.7 occ:1.00 OE2 C:GLU280 1.7 46.0 1.0 NE2 C:HIS169 2.2 25.8 1.0 CD2 C:HIS171 2.3 32.8 1.0 CD C:GLU280 2.7 46.1 1.0 CD2 C:HIS169 2.9 28.5 1.0 OE2 C:GLU299 3.0 33.9 1.0 CG C:HIS171 3.0 33.1 1.0 CD C:GLU299 3.1 30.2 1.0 OE1 C:GLU280 3.2 47.1 1.0 CB C:HIS171 3.3 32.1 1.0 ZN C:ZN1001 3.3 52.7 1.0 CE1 C:HIS169 3.3 28.8 1.0 NE2 C:HIS171 3.4 35.6 1.0 OE1 C:GLU299 3.5 28.1 1.0 NE2 C:HIS174 3.6 27.9 1.0 CG C:GLU299 3.9 28.4 1.0 CD2 C:HIS174 3.9 26.7 1.0 CG C:GLU280 4.0 44.0 1.0 OD1 C:ASP173 4.1 31.1 1.0 CG C:HIS169 4.1 30.1 1.0 ND1 C:HIS171 4.2 32.9 1.0 ND1 C:HIS169 4.3 28.9 1.0 CE1 C:HIS171 4.4 34.5 1.0 CB C:GLU299 4.4 28.6 1.0 OD2 C:ASP173 4.6 33.6 1.0 CA C:HIS171 4.7 33.2 1.0 CE1 C:HIS174 4.7 28.8 1.0 CG C:ASP173 4.8 31.7 1.0 N C:HIS171 4.9 34.9 1.0

Zinc binding site 7 out of 8 in the Sdsa Sulfatase Triclinic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Sdsa Sulfatase Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:28.0 occ:0.76 OE2 D:GLU299 1.2 27.7 1.0 OD2 D:ASP173 1.8 42.5 1.0 NE2 D:HIS174 2.0 19.9 1.0 NE2 D:HIS344 2.2 26.9 1.0 CD D:GLU299 2.4 26.5 1.0 CE1 D:HIS174 2.7 22.6 1.0 CG D:ASP173 3.0 39.1 1.0 CD2 D:HIS344 3.1 28.5 1.0 CE1 D:HIS344 3.1 28.8 1.0 CD2 D:HIS174 3.1 20.6 1.0 OE1 D:GLU299 3.2 25.6 1.0 ZN D:ZN1002 3.2 48.2 0.8 OD1 D:ASP173 3.5 47.9 1.0 CG D:GLU299 3.6 26.6 1.0 OE2 D:GLU280 3.9 49.0 1.0 ND1 D:HIS174 3.9 22.9 1.0 CG D:HIS174 4.1 22.3 1.0 CB D:ASP173 4.2 35.1 1.0 ND1 D:HIS344 4.2 30.6 1.0 NE2 D:HIS169 4.2 20.9 1.0 CG D:HIS344 4.2 29.4 1.0 CE1 D:HIS169 4.4 21.5 1.0 CD1 D:ILE239 4.7 48.7 1.0 CB D:ALA123 4.7 24.1 1.0 O D:ASP173 4.8 37.2 1.0 CD2 D:LEU122 4.8 29.1 1.0 CD D:GLU280 4.9 49.6 1.0 CB D:GLU299 5.0 26.2 1.0 CG2 D:VAL343 5.0 20.0 1.0

Zinc binding site 8 out of 8 in the Sdsa Sulfatase Triclinic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Sdsa Sulfatase Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1002 b:48.2 occ:0.82 OE2 D:GLU280 1.4 49.0 1.0 ND1 D:HIS171 2.2 30.1 1.0 CD D:GLU280 2.3 49.6 1.0 NE2 D:HIS169 2.4 20.9 1.0 OE1 D:GLU280 2.6 59.2 1.0 OE2 D:GLU299 2.8 27.7 1.0 CD D:GLU299 3.0 26.5 1.0 CG D:HIS171 3.1 29.4 1.0 ZN D:ZN1001 3.2 28.0 0.8 CB D:HIS171 3.2 30.5 1.0 CD2 D:HIS169 3.2 20.7 1.0 CE1 D:HIS171 3.3 29.4 1.0 NE2 D:HIS174 3.4 19.9 1.0 CE1 D:HIS169 3.4 21.5 1.0 OE1 D:GLU299 3.5 25.6 1.0 CG D:GLU299 3.6 26.6 1.0 CG D:GLU280 3.7 43.5 1.0 CD2 D:HIS174 3.7 20.6 1.0 OD1 D:ASP173 4.1 47.9 1.0 OD2 D:ASP173 4.1 42.5 1.0 CB D:GLU299 4.2 26.2 1.0 CD2 D:HIS171 4.3 27.2 1.0 NE2 D:HIS171 4.3 29.8 1.0 CG D:HIS169 4.4 21.3 1.0 CE1 D:HIS174 4.4 22.6 1.0 ND1 D:HIS169 4.5 22.0 1.0 CG D:ASP173 4.6 39.1 1.0 CA D:HIS171 4.7 29.9 1.0 CB D:GLU280 4.8 39.4 1.0 CG D:HIS174 4.9 22.3 1.0

E.De La Mora, E.Flores-Hernandez, J.Jakoncic, V.Stojanoff, D.Siliqi, N.Sanchez-Puig, A.Moreno. Sdsa Polymorph Isolation and Improvement of Their Crystal Quality Using Nonconventional Crystallization Techniques J.Appl.Crystallogr. V. 48 1551 2015.
ISSN: ISSN 0021-8898
DOI: 10.1107/S1600576715016556