Zinc in PDB 4bol: Crystal Structure of AMPDH2 From Pseudomonas Aeruginosa in Complex with Pentapeptide

The structure of Crystal Structure of AMPDH2 From Pseudomonas Aeruginosa in Complex with Pentapeptide, PDB code: 4bol was solved by C.Artola-Recolons, S.Martinez-Caballero, M.Lee, C.Carrasco-Lopez, D.Hesek, E.E.Spink, E.Lastochkin, W.Zhang, L.M.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)	45.912 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.630, 97.234, 104.169, 90.00, 90.00, 90.00
R / Rfree (%)	14.74 / 17.83

The binding sites of Zinc atom in the Crystal Structure of AMPDH2 From Pseudomonas Aeruginosa in Complex with Pentapeptide (pdb code 4bol). 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 Pentapeptide, PDB code: 4bol:
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 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 AMPDH2 From Pseudomonas Aeruginosa in Complex with Pentapeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1261 b:22.0 occ:1.00 ND1 A:HIS42 2.0 16.5 1.0 O A:HOH2025 2.0 21.2 1.0 OD2 A:ASP163 2.1 22.9 1.0 ND1 A:HIS153 2.1 16.7 1.0 CG A:ASP163 2.9 23.7 1.0 CE1 A:HIS42 2.9 18.6 1.0 HB2 A:HIS153 2.9 23.3 1.0 HE1 A:HIS42 3.0 22.4 1.0 OD1 A:ASP163 3.0 24.0 1.0 HB3 A:HIS42 3.0 24.0 1.0 CG A:HIS153 3.0 18.5 1.0 CG A:HIS42 3.1 17.9 1.0 CE1 A:HIS153 3.1 20.9 1.0 CB A:HIS153 3.3 19.4 1.0 HE1 A:HIS153 3.3 25.0 1.0 HB3 A:HIS153 3.4 23.3 1.0 CB A:HIS42 3.5 20.0 1.0 HA A:HIS42 3.7 19.9 1.0 N03 A:J0J1260 3.8 39.1 1.0 HD2 A:LYS161 3.9 36.1 1.0 NE2 A:HIS42 4.1 17.4 1.0 O A:HOH2150 4.1 36.8 1.0 HN0A A:J0J1260 4.1 46.9 1.0 CD2 A:HIS42 4.2 15.5 1.0 HN03 A:J0J1260 4.2 46.9 1.0 CD2 A:HIS153 4.2 16.6 1.0 CA A:HIS42 4.2 16.5 1.0 NE2 A:HIS153 4.2 19.0 1.0 CB A:ASP163 4.3 20.3 1.0 HB2 A:HIS42 4.4 24.0 1.0 HB3 A:LYS161 4.4 23.2 1.0 HB2 A:ASP163 4.5 24.3 1.0 HG3 A:LYS161 4.5 29.4 1.0 H A:TYR43 4.5 24.2 1.0 HN06 A:J0J1260 4.5 33.5 1.0 HE3 A:LYS161 4.6 50.9 1.0 O A:HIS86 4.6 20.7 1.0 C02 A:J0J1260 4.6 37.0 1.0 CD A:LYS161 4.7 30.1 1.0 HZ3 A:LYS161 4.7 60.8 1.0 HB3 A:ASP163 4.7 24.3 1.0 H01B A:J0J1260 4.7 45.1 1.0 CA A:HIS153 4.8 16.4 1.0 HE2 A:HIS42 4.8 20.9 1.0 H01 A:J0J1260 4.8 45.1 1.0 N06 A:J0J1260 4.8 27.9 1.0 C04 A:J0J1260 4.9 39.2 1.0 O A:TYR43 4.9 24.7 1.0 OE2 A:GLU106 4.9 34.9 1.0 O A:LEU41 4.9 16.9 1.0 HE2 A:HIS153 5.0 22.8 1.0 CG A:LYS161 5.0 24.5 1.0 C01 A:J0J1260 5.0 37.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of AMPDH2 From Pseudomonas Aeruginosa in Complex with 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 AMPDH2 From Pseudomonas Aeruginosa in Complex with Pentapeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1260 b:20.6 occ:1.00 ND1 B:HIS42 2.0 16.4 1.0 OD2 B:ASP163 2.1 19.3 1.0 O B:HOH2021 2.1 15.6 1.0 ND1 B:HIS153 2.1 15.9 1.0 CG B:ASP163 2.9 21.9 1.0 CE1 B:HIS42 3.0 18.6 1.0 OD1 B:ASP163 3.0 19.1 1.0 HB2 B:HIS153 3.0 17.9 1.0 HB3 B:HIS42 3.0 21.3 1.0 CG B:HIS153 3.0 14.2 1.0 CG B:HIS42 3.1 15.1 1.0 HE1 B:HIS42 3.1 22.3 1.0 CE1 B:HIS153 3.1 19.1 1.0 HN0A B:J0J1261 3.2 44.2 1.0 CB B:HIS153 3.3 14.9 1.0 HB3 B:HIS153 3.3 17.9 1.0 HE1 B:HIS153 3.3 22.9 1.0 CB B:HIS42 3.5 17.7 1.0 HD2 B:LYS161 3.6 26.7 1.0 HA B:HIS42 3.7 19.9 1.0 N03 B:J0J1261 3.9 36.8 1.0 NE2 B:HIS42 4.1 18.8 1.0 CA B:HIS42 4.1 16.6 1.0 CD2 B:HIS42 4.2 16.1 1.0 CD2 B:HIS153 4.2 15.6 1.0 NE2 B:HIS153 4.2 17.6 1.0 HN03 B:J0J1261 4.2 44.2 1.0 CB B:ASP163 4.3 17.3 1.0 HB2 B:HIS42 4.3 21.3 1.0 O B:HOH2134 4.3 32.8 1.0 HB3 B:LYS161 4.4 21.9 1.0 HE3 B:LYS161 4.4 44.9 1.0 HB2 B:ASP163 4.4 20.7 1.0 H B:TYR43 4.5 21.4 1.0 CD B:LYS161 4.5 22.3 1.0 HG3 B:LYS161 4.6 25.1 1.0 HZ3 B:LYS161 4.6 42.6 1.0 O B:HIS86 4.7 20.0 1.0 HB3 B:ASP163 4.7 20.7 1.0 OE2 B:GLU106 4.8 33.2 1.0 O B:TYR43 4.8 21.4 1.0 CA B:HIS153 4.8 13.4 1.0 HE2 B:HIS42 4.9 22.6 1.0 CE B:LYS161 4.9 37.4 1.0 O B:LEU41 4.9 17.0 1.0 N B:TYR43 5.0 17.9 1.0 CG B:LYS161 5.0 21.0 1.0 HE2 B:HIS153 5.0 21.1 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