Zinc in PDB 4nt9: Crystal Structure of An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia

The structure of Crystal Structure of An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia, PDB code: 4nt9 was solved by Y.H.Yang, J.Zhang, Y.L.Jiang, C.Z.Zhou, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.47 / 1.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.110, 68.080, 80.350, 90.00, 108.41, 90.00
R / Rfree (%)	17.7 / 21.2

The binding sites of Zinc atom in the Crystal Structure of An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia (pdb code 4nt9). 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 An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia, PDB code: 4nt9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia


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 An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:16.2 occ:1.00 O B:HOH406 2.0 13.4 1.0 ND1 B:HIS207 2.0 13.0 1.0 OD1 B:ASP160 2.1 14.5 1.0 NE2 B:HIS153 2.1 13.4 1.0 O B:HOH416 2.1 14.5 1.0 OE1 B:GLU204 2.2 17.4 1.0 CE1 B:HIS207 2.9 12.9 1.0 CE1 B:HIS153 3.1 12.6 1.0 CG B:ASP160 3.1 15.5 1.0 CD2 B:HIS153 3.1 12.5 1.0 CG B:HIS207 3.1 11.8 1.0 CD B:GLU204 3.2 14.6 1.0 OD2 B:ASP160 3.4 15.9 1.0 OE2 B:GLU204 3.5 18.2 1.0 CB B:HIS207 3.6 11.6 1.0 NE2 B:HIS207 4.1 13.7 1.0 O1 B:GOL303 4.2 24.1 1.0 NE1 B:TRP206 4.2 17.2 1.0 CD2 B:HIS207 4.2 13.1 1.0 ND1 B:HIS153 4.2 13.1 1.0 OXT B:ACT302 4.2 18.6 1.0 CG B:HIS153 4.3 12.5 1.0 NH1 B:ARG120 4.3 21.0 1.0 CB B:ASP160 4.5 16.9 1.0 CD1 B:TRP206 4.6 15.7 1.0 CG B:GLU204 4.6 16.4 1.0 CA B:HIS207 4.7 10.8 1.0 C B:ACT302 4.8 20.8 1.0 NH2 B:ARG120 4.9 18.9 1.0 CE2 B:TYR191 4.9 13.3 1.0 CA B:ASP160 5.0 13.4 1.0 CH3 B:ACT302 5.0 23.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia


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 An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:18.6 occ:1.00 ND1 A:HIS207 2.0 14.5 1.0 OD1 A:ASP160 2.1 17.4 1.0 NE2 A:HIS153 2.1 15.3 1.0 O A:HOH413 2.1 18.1 1.0 O A:HOH434 2.2 17.8 1.0 OE1 A:GLU204 2.3 18.1 1.0 CE1 A:HIS207 2.9 13.5 1.0 CG A:ASP160 3.0 16.5 1.0 CD2 A:HIS153 3.1 15.9 1.0 CE1 A:HIS153 3.1 15.7 1.0 CG A:HIS207 3.2 13.6 1.0 OD2 A:ASP160 3.2 17.7 1.0 CD A:GLU204 3.3 16.9 1.0 OE2 A:GLU204 3.6 18.0 1.0 CB A:HIS207 3.6 13.6 1.0 NE2 A:HIS207 4.0 13.2 1.0 CD2 A:HIS207 4.2 13.5 1.0 ND1 A:HIS153 4.2 16.9 1.0 NE1 A:TRP206 4.2 19.6 1.0 CG A:HIS153 4.2 15.3 1.0 O A:ACT302 4.3 22.2 1.0 O A:HOH476 4.4 26.1 1.0 NH1 A:ARG120 4.4 26.9 1.0 CB A:ASP160 4.5 17.1 1.0 CD1 A:TRP206 4.6 16.2 1.0 CA A:HIS207 4.7 13.6 1.0 CG A:GLU204 4.7 15.1 1.0 NH2 A:ARG120 4.9 23.8 1.0 CE2 A:TYR191 4.9 15.0 1.0 CA A:ASP160 5.0 16.5 1.0 C A:ACT302 5.0 25.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia


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 An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:18.6 occ:1.00 ND1 C:HIS207 2.0 15.2 1.0 OD1 C:ASP160 2.1 15.8 1.0 O C:HOH413 2.1 18.8 1.0 NE2 C:HIS153 2.1 17.3 1.0 O C:HOH430 2.2 18.6 1.0 OE1 C:GLU204 2.3 20.1 1.0 CE1 C:HIS207 2.9 16.2 1.0 CG C:ASP160 3.1 17.5 1.0 CG C:HIS207 3.1 13.1 1.0 CE1 C:HIS153 3.1 16.7 1.0 CD2 C:HIS153 3.2 16.2 1.0 CD C:GLU204 3.2 17.7 1.0 OD2 C:ASP160 3.3 17.4 1.0 OE2 C:GLU204 3.4 17.1 1.0 CB C:HIS207 3.5 12.3 1.0 NE2 C:HIS207 4.0 15.8 1.0 CD2 C:HIS207 4.2 15.8 1.0 NE1 C:TRP206 4.2 17.5 1.0 ND1 C:HIS153 4.2 19.1 1.0 O C:HOH431 4.3 21.0 1.0 CG C:HIS153 4.3 17.9 1.0 O C:ACT302 4.3 21.5 1.0 NH1 C:ARG120 4.4 22.1 1.0 CB C:ASP160 4.5 16.7 1.0 CA C:HIS207 4.6 13.4 1.0 CD1 C:TRP206 4.6 17.7 1.0 CG C:GLU204 4.6 17.1 1.0 NH2 C:ARG120 4.8 21.8 1.0 CE2 C:TYR191 4.9 15.4 1.0 C C:ACT302 4.9 22.1 1.0

Y.H.Yang, J.Zhang, Y.L.Jiang, C.Z.Zhou, Y.Chen. Crystal Structure of An L,D-Carboxypeptidase Dacb From Streptococcus Pneumonia To Be Published.