Zinc in PDB 4bpa: Crystal Structure of AMPDH2 From Pseudomonas Aeruginosa in Complex with Nag-Nam-Nag-Nam Tetrasaccharide

The structure of Crystal Structure of AMPDH2 From Pseudomonas Aeruginosa in Complex with Nag-Nam-Nag-Nam Tetrasaccharide, PDB code: 4bpa was solved by C.Artola-Recolons, S.Martinez-Caballero, M.Lee, C.Carrasco-Lopez, D.Hesek, E.Spink, E.Lastochkin, W.Zhang, L.Hellman, B.Boggess, S.Mobashery, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.66 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.230, 93.560, 104.350, 90.00, 90.00, 90.00
R / Rfree (%)	22.251 / 29.015

The binding sites of Zinc atom in the Crystal Structure of AMPDH2 From Pseudomonas Aeruginosa in Complex with Nag-Nam-Nag-Nam Tetrasaccharide (pdb code 4bpa). 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 AMPDH2 From Pseudomonas Aeruginosa in Complex with Nag-Nam-Nag-Nam Tetrasaccharide, PDB code: 4bpa:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of AMPDH2 From Pseudomonas Aeruginosa in Complex with Nag-Nam-Nag-Nam Tetrasaccharide


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 AMPDH2 From Pseudomonas Aeruginosa in Complex with Nag-Nam-Nag-Nam Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1260 b:0.3 occ:1.00 OD2 A:ASP163 2.5 45.8 1.0 ND1 A:HIS42 2.8 40.3 1.0 ND1 A:HIS153 3.0 37.5 1.0 CG A:ASP163 3.3 45.3 1.0 OD1 A:ASP163 3.5 45.3 1.0 CG A:HIS42 3.6 39.6 1.0 CE1 A:HIS153 3.7 37.6 1.0 O A:HOH2013 3.7 14.9 1.0 CE1 A:HIS42 3.7 39.9 1.0 CB A:HIS42 3.7 39.5 1.0 CG A:HIS153 4.1 37.5 1.0 O A:TYR43 4.1 37.3 1.0 CB A:HIS153 4.5 37.6 1.0 OE2 A:GLU106 4.5 37.6 1.0 CB A:ASP163 4.5 45.1 1.0 CA A:HIS42 4.6 39.5 1.0 CD2 A:HIS42 4.7 39.6 1.0 NE2 A:HIS42 4.7 39.5 1.0 OE1 A:GLU106 4.8 37.9 1.0 O A:HIS86 4.8 36.8 1.0 NE2 A:HIS153 4.9 37.5 1.0 N A:TYR43 4.9 39.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of AMPDH2 From Pseudomonas Aeruginosa in Complex with Nag-Nam-Nag-Nam Tetrasaccharide


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 AMPDH2 From Pseudomonas Aeruginosa in Complex with Nag-Nam-Nag-Nam Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1260 b:50.6 occ:1.00 OD2 B:ASP163 2.0 36.5 1.0 ND1 B:HIS42 2.2 36.7 1.0 ND1 B:HIS153 2.3 31.7 1.0 CG B:ASP163 2.9 36.6 1.0 CE1 B:HIS42 3.2 36.7 1.0 OD1 B:ASP163 3.2 36.7 1.0 CG B:HIS42 3.2 36.4 1.0 CE1 B:HIS153 3.2 31.8 1.0 CG B:HIS153 3.3 31.3 1.0 CB B:HIS42 3.5 36.4 1.0 C9 B:AMV1004 3.6 0.8 1.0 CB B:HIS153 3.6 30.9 1.0 C11 B:AMV1004 4.0 0.1 1.0 CA B:HIS42 4.2 36.5 1.0 NZ B:LYS161 4.2 38.9 1.0 NE2 B:HIS42 4.3 36.6 1.0 C10 B:AMV1004 4.3 0.4 1.0 CB B:ASP163 4.3 36.4 1.0 CD2 B:HIS42 4.3 36.3 1.0 NE2 B:HIS153 4.4 31.6 1.0 CD2 B:HIS153 4.4 31.3 1.0 O3 B:AMV1004 4.5 0.1 1.0 CD B:LYS161 4.5 38.8 1.0 O B:TYR43 4.5 38.6 1.0 OXT B:AMV1004 4.7 0.6 1.0 O B:HIS86 4.8 34.5 1.0 O11 B:AMV1004 4.8 0.3 1.0 CE B:LYS161 4.8 39.2 1.0 OE2 B:GLU106 4.8 36.1 1.0 N B:TYR43 4.9 37.3 1.0 O B:LEU41 5.0 36.3 1.0

S.Martinez-Caballero, M.Lee, C.Artola-Recolons, C.Carrasco-Lopez, D.Hesek, E.E.Spink, E.Lastochkin, W.Zhang, L.M.Hellman, B.Boggess, S.Mobashery, J.A.Hermoso. Reaction Products and the X-Ray Structure of AMPDH2, A Virulence Determinant of Pseudomonas Aeruginosa. J.Am.Chem.Soc. V. 135 10318 2013.
ISSN: ISSN 0002-7863
PubMed: 23819763
DOI: 10.1021/JA405464B