Zinc in PDB 2y2b: Crystal Structure of Ampd in Complex with Reaction Products

All present enzymatic activity of Crystal Structure of Ampd in Complex with Reaction Products:
3.5.1.28;

The structure of Crystal Structure of Ampd in Complex with Reaction Products, PDB code: 2y2b was solved by C.Carrasco-Lopez, A.Rojas-Altuve, W.Zhang, D.Hesek, M.Lee, S.Barbe, I.Andre, N.Silva-Martin, M.Martinez-Ripoll, S.Mobashery, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	67.774, 67.774, 92.836, 90.00, 90.00, 120.00
R / Rfree (%)	16.96 / 22.35

The binding sites of Zinc atom in the Crystal Structure of Ampd in Complex with Reaction Products (pdb code 2y2b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Ampd in Complex with Reaction Products, PDB code: 2y2b:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Ampd in Complex with Reaction Products


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 Ampd in Complex with Reaction Products within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1180 b:7.0 occ:1.00 OD2 A:ASP164 2.0 7.1 1.0 ND1 A:HIS34 2.0 8.1 1.0 ND1 A:HIS154 2.0 8.4 1.0 OXT A:AH01000 2.3 9.9 1.0 OD1 A:ASP164 2.5 9.8 1.0 CG A:ASP164 2.6 8.5 1.0 C A:AH01000 2.6 25.3 1.0 O A:AH01000 2.7 22.5 1.0 CE1 A:HIS34 2.9 6.8 1.0 CG A:HIS154 3.0 6.5 1.0 CE1 A:HIS154 3.1 8.3 1.0 CG A:HIS34 3.1 7.4 1.0 CB A:HIS154 3.2 6.7 1.0 CB A:HIS34 3.5 6.6 1.0 N1 A:MHI1001 3.7 22.1 1.0 CA A:AH01000 4.0 33.2 1.0 NE2 A:HIS34 4.1 10.2 1.0 CB A:ASP164 4.1 7.0 1.0 CE A:LYS162 4.1 13.6 1.0 CA A:HIS34 4.1 5.9 1.0 CD2 A:HIS154 4.1 5.6 1.0 NE2 A:HIS154 4.1 5.8 1.0 CD2 A:HIS34 4.2 8.7 1.0 O A:HIS96 4.6 6.7 1.0 O A:ASN35 4.7 5.5 1.0 CB A:AH01000 4.7 26.4 1.0 N A:ASN35 4.7 5.7 1.0 CA A:HIS154 4.8 6.3 1.0 NZ A:LYS162 4.8 28.9 1.0 O3 A:AH01000 4.9 47.5 1.0 OE2 A:GLU116 4.9 15.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Ampd in Complex with Reaction Products


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 Ampd in Complex with Reaction Products within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1180 b:9.8 occ:1.00 OD2 B:ASP164 2.0 6.8 1.0 ND1 B:HIS154 2.0 10.8 1.0 ND1 B:HIS34 2.1 11.8 1.0 O B:HOH2187 2.2 6.2 1.0 OD1 B:ASP164 2.5 12.8 1.0 CG B:ASP164 2.6 10.8 1.0 CG B:HIS154 3.0 7.4 1.0 CE1 B:HIS34 3.0 8.6 1.0 CE1 B:HIS154 3.1 11.0 1.0 CG B:HIS34 3.1 9.8 1.0 CB B:HIS154 3.2 4.8 1.0 CB B:HIS34 3.5 8.7 1.0 O B:HOH2127 3.5 21.3 1.0 CE B:LYS162 4.0 22.1 1.0 CA B:HIS34 4.1 7.2 1.0 CD2 B:HIS154 4.1 11.6 1.0 CB B:ASP164 4.1 9.6 1.0 NE2 B:HIS154 4.1 12.7 1.0 NE2 B:HIS34 4.1 7.7 1.0 CD2 B:HIS34 4.2 10.6 1.0 O B:HOH2171 4.5 24.3 1.0 O B:HIS96 4.5 9.9 1.0 N B:ASN35 4.7 7.3 1.0 O B:ASN35 4.7 9.0 1.0 CA B:HIS154 4.7 6.4 1.0 NZ B:LYS162 4.8 22.0 1.0 OE2 B:GLU116 4.8 16.1 1.0 C B:HIS34 5.0 7.1 1.0 O B:ASP164 5.0 6.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Ampd in Complex with Reaction Products


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 Ampd in Complex with Reaction Products within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1180 b:14.1 occ:1.00 OD2 C:ASP164 2.0 12.5 1.0 ND1 C:HIS154 2.0 14.2 1.0 ND1 C:HIS34 2.1 16.0 1.0 O C:HOH2164 2.2 5.3 1.0 OD1 C:ASP164 2.4 15.0 1.0 CG C:ASP164 2.6 15.4 1.0 CE1 C:HIS34 2.9 15.1 1.0 CG C:HIS154 3.0 14.8 1.0 CE1 C:HIS154 3.0 14.5 1.0 CG C:HIS34 3.1 13.1 1.0 CB C:HIS154 3.2 13.0 1.0 O C:HOH2148 3.4 28.3 1.0 CB C:HIS34 3.6 16.2 1.0 CE C:LYS162 4.0 26.1 1.0 CB C:ASP164 4.1 15.0 1.0 CD2 C:HIS154 4.1 18.1 1.0 NE2 C:HIS154 4.1 15.3 1.0 NE2 C:HIS34 4.1 15.2 1.0 CA C:HIS34 4.2 14.1 1.0 CD2 C:HIS34 4.2 13.7 1.0 O C:HOH2109 4.4 24.2 1.0 O C:HIS96 4.6 16.5 1.0 NZ C:LYS162 4.6 31.6 1.0 CA C:HIS154 4.8 14.8 1.0 N C:ASN35 4.8 13.8 1.0 O C:HOH2041 4.8 24.6 1.0 O C:ASN35 4.9 16.9 1.0 CG C:LYS162 4.9 17.2 1.0

C.Carrasco-Lopez, A.Rojas-Altuve, W.Zhang, D.Hesek, M.Lee, S.Barbe, I.Andre, P.Ferrer, N.Silva-Martin, G.R.Castro, M.Martinez-Ripoll, S.Mobashery, J.A.Hermoso. Crystal Structures of Bacterial Peptidoglycan Amidase Ampd and An Unprecedented Activation Mechanism. J.Biol.Chem. V. 286 31714 2011.
ISSN: ISSN 0021-9258
PubMed: 21775432
DOI: 10.1074/JBC.M111.264366