Zinc in PDB 4ox5: Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition

The structure of Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition, PDB code: 4ox5 was solved by C.N.Hoyland, C.Aldridge, R.M.Cleverley, K.Sidiq, M.C.Duchene, R.A.Daniel, W.Vollmer, R.J.Lewis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	48.855, 60.414, 138.269, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 25.1

The structure of Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition (pdb code 4ox5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition, PDB code: 4ox5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:39.9 occ:1.00 OD2 A:ASP184 2.1 31.3 1.0 ND1 A:HIS181 2.1 31.4 1.0 CG A:ASP184 3.0 30.7 1.0 CE1 A:HIS181 3.0 31.4 1.0 CG A:HIS181 3.2 29.5 1.0 OD1 A:ASP184 3.2 36.9 1.0 CB A:HIS181 3.6 26.4 1.0 O A:ASP180 3.9 29.8 1.0 CA A:HIS181 3.9 27.4 1.0 O A:HOH417 3.9 42.5 1.0 NE2 A:HIS181 4.2 34.6 1.0 CD2 A:HIS181 4.3 29.3 1.0 CB A:ASP184 4.4 30.2 1.0 C A:ASP180 4.5 29.4 1.0 N A:HIS181 4.6 27.2 1.0 C A:HIS181 4.9 28.6 1.0 O A:HOH460 5.0 60.5 1.0 O A:HIS181 5.0 28.2 1.0

Zinc binding site 2 out of 3 in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:32.4 occ:1.00 OD1 A:ASP160 1.9 30.5 1.0 NE2 A:HIS153 2.1 32.1 1.0 ND1 A:HIS207 2.1 30.6 1.0 CG A:ASP160 2.4 33.3 1.0 OD2 A:ASP160 2.6 35.3 1.0 CE1 A:HIS153 3.0 34.1 1.0 CE1 A:HIS207 3.0 30.1 1.0 CG A:HIS207 3.2 30.5 1.0 CD2 A:HIS153 3.2 33.5 1.0 CB A:HIS207 3.5 30.9 1.0 OE1 A:GLU204 3.9 37.9 1.0 CB A:ASP160 4.0 33.1 1.0 ND1 A:HIS153 4.1 30.3 1.0 NE2 A:HIS207 4.2 28.3 1.0 CG A:HIS153 4.3 31.4 1.0 CD2 A:HIS207 4.3 25.9 1.0 CA A:HIS207 4.3 28.8 1.0 NE1 A:TRP206 4.4 36.3 1.0 CA A:DAL307 4.6 20.0 1.0 N A:DAL307 4.6 20.0 1.0 CD1 A:TRP206 4.6 35.1 1.0 N A:ASP160 4.7 28.4 1.0 CA A:ASP160 4.7 29.7 1.0 NH1 A:ARG120 4.7 62.7 1.0 NH2 A:ARG120 4.8 65.3 1.0 O A:DAL307 4.8 20.0 1.0 C A:DAL307 4.9 20.0 1.0 C A:PHE159 4.9 29.7 1.0

Zinc binding site 3 out of 3 in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:35.2 occ:1.00 O A:HOH408 1.9 31.0 1.0 NE2 A:HIS79 2.1 38.5 1.0 CD2 A:HIS79 3.1 35.7 1.0 CE1 A:HIS79 3.1 35.9 1.0 OE1 A:GLU232 4.0 54.1 1.0 ND1 A:HIS79 4.2 35.6 1.0 CG A:HIS79 4.2 35.6 1.0 O A:HOH404 4.3 41.2 1.0 OH A:TYR80 4.5 34.4 1.0 OE2 A:GLU232 4.5 49.7 1.0 CD A:GLU232 4.5 45.9 1.0 O A:HOH428 4.7 56.0 1.0 CZ A:TYR80 4.8 35.6 1.0

C.N.Hoyland, C.Aldridge, R.M.Cleverley, M.C.Duchene, G.Minasov, O.Onopriyenko, K.Sidiq, P.J.Stogios, W.F.Anderson, R.A.Daniel, A.Savchenko, W.Vollmer, R.J.Lewis. Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition. Structure V. 22 949 2014.
ISSN: ISSN 0969-2126
PubMed: 24909784
DOI: 10.1016/J.STR.2014.04.015