Zinc in PDB 4bxd: Crystal Structure of AMPDH3 From Pseudomonas Aeruginosa in Complex with Tetrasaccharide Pentapeptide

The structure of Crystal Structure of AMPDH3 From Pseudomonas Aeruginosa in Complex with Tetrasaccharide Pentapeptide, PDB code: 4bxd was solved by C.Artola-Recolons, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.300 / 3.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.186, 101.186, 162.261, 90.00, 90.00, 90.00
R / Rfree (%)	22.35 / 27.72

The binding sites of Zinc atom in the Crystal Structure of AMPDH3 From Pseudomonas Aeruginosa in Complex with Tetrasaccharide Pentapeptide (pdb code 4bxd). 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 AMPDH3 From Pseudomonas Aeruginosa in Complex with Tetrasaccharide Pentapeptide, PDB code: 4bxd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of AMPDH3 From Pseudomonas Aeruginosa in Complex with Tetrasaccharide Pentapeptide


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 AMPDH3 From Pseudomonas Aeruginosa in Complex with Tetrasaccharide Pentapeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1260 b:35.9 occ:1.00 HD1 A:HIS146 2.2 25.4 1.0 HB3 A:HIS25 2.2 31.6 1.0 HD1 A:HIS25 2.2 31.3 1.0 OD2 A:ASP156 2.4 21.2 1.0 O A:HOH2005 2.4 23.4 1.0 ND1 A:HIS146 2.4 21.1 1.0 ND1 A:HIS25 2.5 26.1 1.0 HB2 A:HIS25 2.5 31.6 1.0 CB A:HIS25 2.6 26.3 1.0 HE1 A:HIS146 2.6 26.0 1.0 CE1 A:HIS146 2.7 21.6 1.0 CG A:HIS25 2.7 25.4 1.0 HA C:ALA1 2.7 65.9 1.0 HE3 A:LYS154 3.3 40.9 1.0 H1 C:ALA1 3.4 70.7 1.0 CG A:HIS146 3.5 20.9 1.0 CA C:ALA1 3.5 54.9 1.0 H2 C:ALA1 3.5 70.7 1.0 CE1 A:HIS25 3.5 25.2 1.0 CG A:ASP156 3.6 22.9 1.0 N C:ALA1 3.7 58.9 1.0 NE2 A:HIS146 3.8 21.8 1.0 CD2 A:HIS25 3.8 24.2 1.0 HB2 A:HIS146 3.8 24.6 1.0 HB1 C:ALA1 3.9 66.1 1.0 CA A:HIS25 4.0 26.3 1.0 HB2 A:ASP156 4.1 27.9 1.0 HE1 A:HIS25 4.1 30.2 1.0 HZ2 A:LYS154 4.1 39.6 1.0 CE A:LYS154 4.1 34.1 1.0 HO3 A:MAG1257 4.1 81.5 1.0 NE2 A:HIS25 4.2 24.0 1.0 CD2 A:HIS146 4.2 21.3 1.0 CB C:ALA1 4.2 55.1 1.0 CB A:HIS146 4.2 20.5 1.0 HA A:HIS25 4.2 31.6 1.0 HE2 A:LYS154 4.3 40.9 1.0 H C:FGA2 4.3 50.7 1.0 HB3 C:ALA1 4.3 66.1 1.0 O A:HIS79 4.4 23.5 1.0 CB A:ASP156 4.4 23.2 1.0 OD1 A:ASP156 4.4 25.5 1.0 HB3 A:HIS146 4.5 24.6 1.0 HE2 A:HIS146 4.5 26.1 1.0 HD2 A:HIS25 4.5 29.1 1.0 O A:TYR26 4.5 28.7 1.0 HG3 A:GLU99 4.6 42.0 1.0 NZ A:LYS154 4.6 33.0 1.0 H A:TYR26 4.6 33.3 1.0 HB3 A:ASP156 4.6 27.9 1.0 OE2 A:GLU99 4.7 39.6 1.0 C C:ALA1 4.7 43.0 1.0 O3 A:MAG1257 4.7 68.0 1.0 CD A:GLU99 4.7 37.6 1.0 HG3 A:LYS154 4.7 44.5 1.0 HZ3 A:LYS154 4.8 39.6 1.0 C A:HIS25 4.8 26.5 1.0 N A:HIS25 4.9 25.3 1.0 HB2 A:HIS79 4.9 29.3 1.0 N C:FGA2 4.9 42.2 1.0 N A:TYR26 4.9 27.8 1.0 OE1 A:GLU99 5.0 39.5 1.0 HB3 A:LYS154 5.0 45.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of AMPDH3 From Pseudomonas Aeruginosa in Complex with Tetrasaccharide Pentapeptide


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 AMPDH3 From Pseudomonas Aeruginosa in Complex with Tetrasaccharide Pentapeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1256 b:36.1 occ:1.00 HD1 B:HIS25 1.1 33.3 1.0 ND1 B:HIS25 2.0 27.8 1.0 HB3 B:HIS25 2.3 34.1 1.0 OD2 B:ASP156 2.4 39.9 1.0 ND1 B:HIS146 2.4 37.2 1.0 O B:HOH2008 2.4 18.3 1.0 CG B:HIS25 2.9 27.6 1.0 HA D:ALA1 3.0 69.5 1.0 CB B:HIS25 3.1 28.4 1.0 CG B:ASP156 3.1 40.2 1.0 CE1 B:HIS25 3.1 27.0 1.0 HZ1 B:LYS154 3.2 49.4 1.0 OD1 B:ASP156 3.2 43.0 1.0 HB2 B:HIS146 3.2 42.7 1.0 CE1 B:HIS146 3.3 33.0 1.0 HE1 B:HIS146 3.3 39.6 1.0 CG B:HIS146 3.4 36.8 1.0 HD3 B:LYS154 3.5 46.1 1.0 HE1 B:HIS25 3.5 32.4 1.0 H2 D:ALA1 3.6 62.1 1.0 H1 D:ALA1 3.6 62.1 1.0 HD2 B:LYS154 3.7 46.1 1.0 CB B:HIS146 3.7 35.6 1.0 HB2 B:HIS25 3.8 34.1 1.0 CA D:ALA1 3.8 58.0 1.0 N D:ALA1 3.9 51.7 1.0 HB3 B:HIS146 3.9 42.7 1.0 HO3 B:MAG1257 3.9 82.3 1.0 HA B:HIS25 4.0 34.4 1.0 CD B:LYS154 4.0 38.4 1.0 CD2 B:HIS25 4.1 26.7 1.0 NZ B:LYS154 4.1 41.2 1.0 O B:HIS79 4.1 27.0 1.0 CA B:HIS25 4.2 28.7 1.0 NE2 B:HIS25 4.2 26.4 1.0 HB1 D:ALA1 4.4 71.9 1.0 H D:FGA2 4.4 49.9 1.0 CB B:ASP156 4.4 38.9 1.0 OE2 B:GLU99 4.4 51.9 1.0 NE2 B:HIS146 4.4 32.3 1.0 HB2 B:ASP156 4.5 46.6 1.0 O3 B:MAG1257 4.5 68.6 1.0 CD2 B:HIS146 4.5 30.9 1.0 CB D:ALA1 4.5 59.9 1.0 HB3 D:ALA1 4.6 71.9 1.0 HZ2 B:LYS154 4.6 49.4 1.0 H B:TYR26 4.6 36.4 1.0 CE B:LYS154 4.6 40.8 1.0 HZ3 B:LYS154 4.6 49.4 1.0 O B:HOH2009 4.6 34.4 1.0 HB2 B:HIS79 4.7 30.9 1.0 HB3 B:LYS154 4.7 45.1 1.0 HB3 B:ASP156 4.8 46.6 1.0 HE3 B:LYS154 4.8 48.9 1.0 O B:LEU24 4.9 28.1 1.0 C D:ALA1 5.0 41.7 1.0 O B:TYR26 5.0 31.4 1.0

M.Lee, C.Artola-Recolons, C.Carrasco-Lopez, S.Martinez-Caballero, D.Hesek, E.Spink, E.Lastochkin, W.Zhang, L.M.Hellman, B.Boggess, J.A.Hermoso, S.Mobashery. Cell-Wall Remodeling By the Zinc-Protease AMPDH3 From Pseudomonas Aeruginosa. J.Am.Chem.Soc. V. 135 12604 2013.
ISSN: ISSN 0002-7863
PubMed: 23931161
DOI: 10.1021/JA407445X