Zinc in PDB 2y2d: Crystal Structure of Ampd Holoenzyme

All present enzymatic activity of Crystal Structure of Ampd Holoenzyme:
3.5.1.28;

The structure of Crystal Structure of Ampd Holoenzyme, PDB code: 2y2d 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)	9.997 / 2.00
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	67.691, 67.691, 92.805, 90.00, 90.00, 120.00
R / Rfree (%)	20.55 / 27.83

The binding sites of Zinc atom in the Crystal Structure of Ampd Holoenzyme (pdb code 2y2d). 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 Holoenzyme, PDB code: 2y2d:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Ampd Holoenzyme


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 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1180 b:25.3 occ:1.00 ND1 A:HIS34 2.0 26.4 1.0 ND1 A:HIS154 2.1 26.8 1.0 OD1 A:ASP164 2.1 25.3 1.0 OD2 A:ASP164 2.1 21.1 1.0 O A:HOH2273 2.3 23.1 1.0 CG A:ASP164 2.4 23.9 1.0 CE1 A:HIS34 2.8 24.6 1.0 CG A:HIS154 2.9 22.6 1.0 CE1 A:HIS154 3.1 28.0 1.0 CG A:HIS34 3.1 25.0 1.0 CB A:HIS154 3.2 21.6 1.0 O A:HOH2102 3.4 18.8 1.0 CB A:HIS34 3.6 19.3 1.0 CB A:ASP164 3.8 22.0 1.0 CA A:HIS34 3.8 19.7 1.0 NE2 A:HIS34 3.9 23.2 1.0 CD2 A:HIS154 4.0 19.9 1.0 CE A:LYS162 4.0 23.0 1.0 CD2 A:HIS34 4.0 24.4 1.0 NE2 A:HIS154 4.1 22.4 1.0 O A:HOH2186 4.2 18.6 1.0 N A:ASN35 4.2 16.6 1.0 O A:ASN35 4.6 29.8 1.0 C A:HIS34 4.6 14.9 1.0 O A:HOH2187 4.6 29.5 1.0 CA A:HIS154 4.7 20.1 1.0 O A:ASP164 4.8 21.8 1.0 OE2 A:GLU116 4.8 21.4 1.0 CG A:LYS162 4.8 28.5 1.0 O A:VAL33 4.9 14.8 1.0 CD A:LYS162 4.9 23.4 1.0 CA A:ASP164 4.9 22.7 1.0 NZ A:LYS162 5.0 21.9 1.0 C A:ASP164 5.0 20.2 1.0 N A:HIS34 5.0 23.5 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Ampd Holoenzyme


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 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1180 b:12.4 occ:1.00 ND1 B:HIS154 2.0 13.7 1.0 OD2 B:ASP164 2.0 11.7 1.0 ND1 B:HIS34 2.1 11.7 1.0 O B:HOH2314 2.2 10.3 1.0 OD1 B:ASP164 2.3 15.2 1.0 CG B:ASP164 2.5 15.7 1.0 CG B:HIS154 2.9 16.1 1.0 CE1 B:HIS34 2.9 13.5 1.0 CE1 B:HIS154 2.9 16.4 1.0 CG B:HIS34 3.2 11.3 1.0 CB B:HIS154 3.3 11.3 1.0 CB B:HIS34 3.6 10.1 1.0 NE2 B:HIS154 4.0 20.2 1.0 CD2 B:HIS154 4.0 15.7 1.0 CB B:ASP164 4.1 11.8 1.0 NE2 B:HIS34 4.1 11.6 1.0 CA B:HIS34 4.2 12.9 1.0 CD2 B:HIS34 4.2 12.8 1.0 O B:HOH2176 4.4 15.6 1.0 N B:ASN35 4.6 8.9 1.0 O B:ASN35 4.7 9.2 1.0 OE2 B:GLU116 4.7 22.6 1.0 CA B:HIS154 4.8 11.6 1.0 CB B:LYS162 4.9 19.6 1.0 C B:HIS34 5.0 12.5 1.0 CE B:LYS162 5.0 23.6 1.0 CG B:LYS162 5.0 15.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Ampd Holoenzyme


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 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1180 b:13.2 occ:1.00 ND1 C:HIS34 2.0 9.8 1.0 OD2 C:ASP164 2.0 10.5 1.0 ND1 C:HIS154 2.0 10.4 1.0 O C:HOH2276 2.2 12.7 1.0 OD1 C:ASP164 2.2 11.7 1.0 CG C:ASP164 2.4 9.8 1.0 CG C:HIS154 2.9 12.2 1.0 CE1 C:HIS34 2.9 12.6 1.0 CG C:HIS34 3.0 9.1 1.0 CE1 C:HIS154 3.1 11.0 1.0 CB C:HIS154 3.1 11.2 1.0 O C:HOH2202 3.4 15.9 1.0 CB C:HIS34 3.4 12.0 1.0 CB C:ASP164 3.9 14.2 1.0 CD2 C:HIS154 4.0 9.0 1.0 NE2 C:HIS34 4.0 12.4 1.0 NE2 C:HIS154 4.1 14.0 1.0 CA C:HIS34 4.1 10.4 1.0 CD2 C:HIS34 4.1 9.7 1.0 O C:HOH2258 4.5 25.3 1.0 O C:ASN35 4.6 10.7 1.0 CA C:HIS154 4.7 10.1 1.0 O C:HIS96 4.7 9.1 1.0 N C:ASN35 4.7 7.3 1.0 NZ C:LYS162 4.7 11.1 1.0 OE2 C:GLU116 4.9 14.7 1.0 CG C:LYS162 4.9 15.7 1.0 O C:ASP164 4.9 10.5 1.0 CE C:LYS162 4.9 10.2 1.0 CA C:ASP164 5.0 11.2 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