Zinc in PDB 2wyi: Structure of the Streptococcus Pyogenes Family GH38 Alpha- Mannosidase Complexed with Swainsonine

All present enzymatic activity of Structure of the Streptococcus Pyogenes Family GH38 Alpha- Mannosidase Complexed with Swainsonine:
3.2.1.24;

The structure of Structure of the Streptococcus Pyogenes Family GH38 Alpha- Mannosidase Complexed with Swainsonine, PDB code: 2wyi was solved by M.D.L.Suits, Y.Zhu, E.J.Taylor, D.L.Zechel, H.J.Gilbert, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	132.45 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.680, 178.680, 198.237, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.3

The binding sites of Zinc atom in the Structure of the Streptococcus Pyogenes Family GH38 Alpha- Mannosidase Complexed with Swainsonine (pdb code 2wyi). 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 the Streptococcus Pyogenes Family GH38 Alpha- Mannosidase Complexed with Swainsonine, PDB code: 2wyi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Streptococcus Pyogenes Family GH38 Alpha- Mannosidase Complexed with Swainsonine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Streptococcus Pyogenes Family GH38 Alpha- Mannosidase Complexed with Swainsonine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1906 b:69.0 occ:1.00 O13 A:SWA1907 2.4 51.2 1.0 O11 A:SWA1907 2.4 50.6 1.0 NE2 A:HIS13 2.4 23.8 1.0 OD1 A:ASP15 2.4 30.9 1.0 OD2 A:ASP125 2.4 35.2 1.0 NE2 A:HIS351 2.6 34.7 1.0 CD2 A:HIS13 3.1 23.3 1.0 CE1 A:HIS351 3.1 34.6 1.0 CG A:ASP15 3.2 28.8 1.0 CG A:ASP125 3.3 33.1 1.0 OD2 A:ASP15 3.3 31.9 1.0 C8 A:SWA1907 3.4 50.6 1.0 C7 A:SWA1907 3.4 50.0 1.0 CE1 A:HIS13 3.5 24.3 1.0 CB A:ASP125 3.5 30.5 1.0 CD2 A:HIS351 3.8 31.5 1.0 C9 A:SWA1907 4.1 50.1 1.0 N4 A:SWA1907 4.2 49.7 1.0 OD2 A:ASP352 4.3 26.4 1.0 CG A:HIS13 4.3 25.0 1.0 C3 A:SWA1907 4.3 49.4 1.0 ND1 A:HIS351 4.4 34.2 1.0 OH A:TYR192 4.4 32.1 1.0 ND1 A:HIS13 4.5 25.0 1.0 OD1 A:ASP125 4.5 35.3 1.0 CB A:ASP15 4.6 26.1 1.0 O A:HOH2030 4.6 34.6 1.0 CG A:HIS351 4.7 30.1 1.0 C1 A:SWA1907 4.9 47.8 1.0 O A:HOH2064 4.9 31.2 1.0 CA A:ASP125 5.0 30.1 1.0

Zinc binding site 2 out of 2 in the Structure of the Streptococcus Pyogenes Family GH38 Alpha- Mannosidase Complexed with Swainsonine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Streptococcus Pyogenes Family GH38 Alpha- Mannosidase Complexed with Swainsonine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1908 b:70.8 occ:1.00 O11 B:SWA1909 2.4 50.4 1.0 O13 B:SWA1909 2.4 51.5 1.0 OD1 B:ASP15 2.5 29.4 1.0 NE2 B:HIS351 2.5 34.6 1.0 NE2 B:HIS13 2.5 24.6 1.0 OD1 B:ASP125 3.0 34.4 1.0 CD2 B:HIS13 3.1 23.7 1.0 OD2 B:ASP15 3.2 31.6 1.0 CG B:ASP15 3.2 28.2 1.0 C8 B:SWA1909 3.3 50.7 1.0 CE1 B:HIS351 3.3 34.3 1.0 C7 B:SWA1909 3.3 50.3 1.0 CD2 B:HIS351 3.6 31.9 1.0 CE1 B:HIS13 3.7 23.6 1.0 C9 B:SWA1909 3.7 50.1 1.0 CB B:ASP125 3.7 30.4 1.0 CG B:ASP125 3.8 33.6 1.0 OD2 B:ASP352 4.0 28.4 1.0 CG B:HIS13 4.3 24.2 1.0 C3 B:SWA1909 4.4 49.6 1.0 ND1 B:HIS351 4.5 34.0 1.0 OH B:TYR192 4.5 31.1 1.0 ND1 B:HIS13 4.6 24.8 1.0 N4 B:SWA1909 4.6 49.8 1.0 CB B:ASP15 4.6 25.8 1.0 CG B:HIS351 4.7 30.4 1.0 C1 B:SWA1909 4.8 48.2 1.0 O B:HOH2051 4.9 15.7 1.0 CG B:ASP352 4.9 27.1 1.0 OD2 B:ASP125 5.0 36.6 1.0

M.D.L.Suits, Y.Zhu, E.J.Taylor, D.L.Zechel, H.J.Gilbert, G.J.Davies. Structure and Kinetic Investigation of Streptococcus Pyogenes Family GH38 Alpha-Mannosidase Plos One V. 5 E9006 2010.
ISSN: ESSN 1932-6203
PubMed: 20140249
DOI: 10.1371/JOURNAL.PONE.0009006