Zinc in PDB 2y28: Crystal Structure of Se-Met Ampd Derivative

All present enzymatic activity of Crystal Structure of Se-Met Ampd Derivative:
3.5.1.28;

The structure of Crystal Structure of Se-Met Ampd Derivative, PDB code: 2y28 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)	58.624 / 1.80
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	67.693, 67.693, 92.681, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 23.18

The binding sites of Zinc atom in the Crystal Structure of Se-Met Ampd Derivative (pdb code 2y28). 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 Se-Met Ampd Derivative, PDB code: 2y28:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Se-Met Ampd Derivative


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 Se-Met Ampd Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1181 b:10.3 occ:1.00 OD2 A:ASP164 2.0 10.2 1.0 ND1 A:HIS154 2.0 10.1 1.0 ND1 A:HIS34 2.1 8.6 1.0 O A:HOH2220 2.1 7.3 1.0 OD1 A:ASP164 2.5 11.0 1.0 CG A:ASP164 2.6 10.4 1.0 CG A:HIS154 2.9 9.6 1.0 CE1 A:HIS34 3.1 7.8 1.0 CE1 A:HIS154 3.1 11.0 1.0 CG A:HIS34 3.2 9.4 1.0 CB A:HIS154 3.2 8.8 1.0 CB A:HIS34 3.5 9.3 1.0 O A:HOH2164 3.9 19.1 1.0 CD2 A:HIS154 4.1 11.6 1.0 CB A:ASP164 4.1 10.9 1.0 CE A:LYS162 4.1 19.2 1.0 CA A:HIS34 4.1 9.2 1.0 NE2 A:HIS154 4.1 10.4 1.0 NE2 A:HIS34 4.2 7.1 1.0 O A:HOH2205 4.3 27.4 1.0 CD2 A:HIS34 4.3 8.2 1.0 O A:HIS96 4.5 11.3 1.0 N A:ASN35 4.7 10.4 1.0 CA A:HIS154 4.7 8.0 1.0 O A:ASN35 4.9 11.8 1.0 OE2 A:GLU116 4.9 13.4 1.0 O A:HOH2139 4.9 22.6 1.0 NZ A:LYS162 4.9 25.0 1.0 C A:HIS34 5.0 10.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Se-Met Ampd Derivative


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 Se-Met Ampd Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1181 b:8.8 occ:1.00 OD2 B:ASP164 1.9 9.4 1.0 ND1 B:HIS154 2.0 8.7 1.0 ND1 B:HIS34 2.0 8.4 1.0 O B:HOH2257 2.2 5.9 1.0 CG B:ASP164 2.8 9.9 1.0 CG B:HIS154 2.9 8.6 1.0 CE1 B:HIS34 3.0 8.6 1.0 OD1 B:ASP164 3.0 9.8 1.0 CE1 B:HIS154 3.0 8.3 1.0 CG B:HIS34 3.1 7.7 1.0 CB B:HIS154 3.2 7.7 1.0 CB B:HIS34 3.5 9.1 1.0 O B:HOH2070 4.0 18.6 1.0 CD2 B:HIS154 4.1 9.7 1.0 NE2 B:HIS154 4.1 11.1 1.0 NE2 B:HIS34 4.1 8.4 1.0 CA B:HIS34 4.1 8.5 1.0 CD2 B:HIS34 4.2 8.3 1.0 CB B:ASP164 4.2 8.5 1.0 CE B:LYS162 4.4 14.2 1.0 O B:HOH2236 4.4 23.2 1.0 O B:HIS96 4.5 8.1 1.0 O B:ASN35 4.6 9.0 1.0 N B:ASN35 4.7 7.4 1.0 CA B:HIS154 4.7 7.9 1.0 OE1 B:GLU116 4.9 12.7 1.0 O B:HOH2069 5.0 22.4 1.0 OE2 B:GLU116 5.0 14.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Se-Met Ampd Derivative


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 Se-Met Ampd Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1181 b:18.5 occ:1.00 ND1 C:HIS34 2.0 18.9 1.0 OD2 C:ASP164 2.0 18.8 1.0 ND1 C:HIS154 2.1 18.8 1.0 O C:HOH2212 2.2 13.1 1.0 CE1 C:HIS34 2.9 21.4 1.0 CG C:ASP164 2.9 21.3 1.0 CG C:HIS154 3.0 20.3 1.0 OD1 C:ASP164 3.1 20.6 1.0 CE1 C:HIS154 3.1 20.1 1.0 CG C:HIS34 3.1 18.6 1.0 CB C:HIS154 3.3 18.3 1.0 CB C:HIS34 3.6 16.6 1.0 O C:HOH2059 3.8 25.2 1.0 CE C:LYS162 3.9 28.9 1.0 NE2 C:HIS34 4.1 18.7 1.0 CA C:HIS34 4.1 18.1 1.0 O C:HOH2148 4.1 23.4 1.0 CD2 C:HIS154 4.1 20.3 1.0 NE2 C:HIS154 4.2 22.2 1.0 CD2 C:HIS34 4.2 19.1 1.0 CB C:ASP164 4.3 19.8 1.0 O C:HIS96 4.5 20.1 1.0 NZ C:LYS162 4.7 32.6 1.0 N C:ASN35 4.7 18.1 1.0 CA C:HIS154 4.8 17.8 1.0 O C:ASN35 4.8 19.2 1.0 OE2 C:GLU116 4.8 21.5 1.0 C C:HIS34 5.0 17.9 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