Zinc in PDB 6nwz: Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase

The structure of Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase, PDB code: 6nwz was solved by N.C.Bamford, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.87 / 2.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.970, 77.970, 640.310, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 24.2

The structure of Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase (pdb code 6nwz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase, PDB code: 6nwz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase


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 AGD3 A Novel Carbohydrate Deacetylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn910 b:85.2 occ:1.00 OD2 A:ASP652 1.9 88.6 1.0 NE2 A:HIS656 2.4 37.8 1.0 O A:HOH1108 2.9 45.4 1.0 CG A:ASP652 3.1 66.3 1.0 CD2 A:HIS656 3.2 33.3 1.0 CE1 A:HIS656 3.5 33.7 1.0 OD1 A:ASP652 3.5 74.0 1.0 O A:HOH1096 3.6 44.4 1.0 CE3 A:TRP614 3.9 34.9 1.0 O A:ALA615 4.1 47.4 1.0 CD2 A:TRP614 4.3 40.5 1.0 CB A:ASP652 4.3 39.9 1.0 CG A:HIS656 4.4 30.4 1.0 CB A:TRP614 4.5 27.3 1.0 CZ3 A:TRP614 4.5 29.4 1.0 ND1 A:HIS656 4.5 37.2 1.0 CG A:TRP614 4.5 41.3 1.0 O A:ASP652 4.7 38.8 1.0 C A:ASP652 4.9 34.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase


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 AGD3 A Novel Carbohydrate Deacetylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn911 b:0.1 occ:1.00 O A:LEU806 2.1 0.8 1.0 OE1 A:GLU332 2.4 90.1 1.0 C A:LEU806 2.9 0.8 1.0 OXT A:LEU806 3.0 0.2 1.0 CD A:GLU332 3.0 66.2 1.0 OE2 A:GLU332 3.1 83.0 1.0 CG A:GLU332 4.3 38.3 1.0 NH2 A:ARG237 4.3 36.4 1.0 CA A:LEU806 4.3 74.2 1.0 NH2 A:ARG361 4.6 36.6 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase


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 AGD3 A Novel Carbohydrate Deacetylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn912 b:0.1 occ:0.50 OD1 A:ASN415 4.3 44.2 1.0 CD A:PRO416 4.3 20.7 1.0 CB A:ASP708 4.5 46.6 1.0 NZ A:LYS281 4.6 33.5 1.0 CE A:LYS281 4.6 20.8 1.0 CG A:PRO416 4.9 26.2 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase


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 AGD3 A Novel Carbohydrate Deacetylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn913 b:55.0 occ:1.00 OD1 A:ASP378 2.0 51.2 1.0 NE2 A:HIS510 2.2 37.2 1.0 NE2 A:HIS514 2.4 40.0 1.0 CD2 A:HIS514 3.0 35.3 1.0 CG A:ASP378 3.0 43.8 1.0 CD2 A:HIS510 3.1 35.7 1.0 CE1 A:HIS510 3.3 37.3 1.0 OD2 A:ASP378 3.4 64.7 1.0 ZN A:ZN914 3.5 74.3 1.0 CE1 A:HIS514 3.6 45.0 1.0 N A:ALA556 4.0 44.0 1.0 CB A:ASP377 4.0 33.2 1.0 CG A:HIS514 4.3 44.3 1.0 CG A:HIS510 4.3 38.8 1.0 ND1 A:HIS510 4.3 39.2 1.0 CB A:ASP378 4.4 45.2 1.0 N A:ASP378 4.4 27.0 1.0 CD2 A:HIS668 4.4 46.4 1.0 NE2 A:HIS668 4.5 52.2 1.0 OD2 A:ASP377 4.5 45.6 1.0 ND1 A:HIS514 4.5 44.3 1.0 CA A:ASP378 4.6 40.5 1.0 CA A:PRO555 4.6 43.4 1.0 CG A:ASP377 4.7 46.2 1.0 CA A:ALA556 4.7 38.9 1.0 C A:PRO555 4.8 41.8 1.0 C A:ASP377 4.9 39.1 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn914 b:74.3 occ:1.00 NE2 A:HIS668 2.3 52.2 1.0 OD2 A:ASP377 2.4 45.6 1.0 CE1 A:HIS668 3.1 47.9 1.0 CD2 A:HIS668 3.3 46.4 1.0 CG A:ASP377 3.4 46.2 1.0 ZN A:ZN913 3.5 55.0 1.0 CB A:ASP377 3.6 33.2 1.0 NH1 A:ARG613 4.1 47.6 1.0 ND1 A:HIS668 4.2 49.5 1.0 NE2 A:HIS510 4.3 37.2 1.0 CG A:HIS668 4.4 50.5 1.0 CE1 A:HIS510 4.4 37.3 1.0 CG A:MET666 4.5 44.6 1.0 CA A:ALA556 4.5 38.9 1.0 N A:ALA556 4.5 44.0 1.0 OD1 A:ASP377 4.6 52.6 1.0 SD A:MET666 4.6 44.4 1.0 OD1 A:ASP378 4.6 51.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of AGD3 A Novel Carbohydrate Deacetylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn915 b:0.6 occ:1.00 OE1 A:GLU516 2.8 79.7 1.0 OD2 A:ASP457 2.8 0.4 1.0 OD1 A:ASP457 2.8 0.0 1.0 CG A:ASP457 3.0 92.5 1.0 CD A:GLU516 3.4 76.7 1.0 OE2 A:GLU516 3.5 86.2 1.0 CB A:ASP457 4.3 75.3 1.0 CG A:GLU516 4.6 68.0 1.0

N.C.Bamford, F.Le Mauff, J.Van Loon, H.Ostapska, B.D.Snarr, E.Kitova, J.Klassen, D.C.Sheppard, P.L.Howell. Structural and Functional Characterization of AGD3: the Founding Member of A New Carbohydrate Esterase Family To Be Published.