Zinc in PDB 4oxd: 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: 4oxd 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)	47.80 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	345.954, 42.549, 79.318, 90.00, 93.07, 90.00
R / Rfree (%)	27.3 / 33.4

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

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition (pdb code 4oxd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition, PDB code: 4oxd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 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:36.7 occ:1.00 OXT H:LYS4 1.9 43.2 1.0 O H:LYS4 2.0 43.8 1.0 OD1 A:ASP160 2.0 37.9 1.0 NE2 A:HIS153 2.1 34.3 1.0 ND1 A:HIS207 2.1 33.1 1.0 C H:LYS4 2.3 48.1 1.0 CG A:ASP160 2.7 38.4 1.0 OD2 A:ASP160 2.7 39.4 1.0 CE1 A:HIS153 2.9 33.6 1.0 CE1 A:HIS207 2.9 32.5 1.0 CG A:HIS207 3.1 31.9 1.0 CD2 A:HIS153 3.2 33.6 1.0 CB A:HIS207 3.5 31.5 1.0 CA H:LYS4 3.8 51.3 1.0 NE2 A:HIS207 4.0 32.1 1.0 ND1 A:HIS153 4.0 33.0 1.0 CD2 A:HIS207 4.1 32.0 1.0 CB A:ASP160 4.1 37.9 1.0 CA A:HIS207 4.2 31.3 1.0 NH1 A:ARG120 4.2 42.8 1.0 OD1 H:DSG5 4.2 62.1 1.0 CG A:HIS153 4.3 32.6 1.0 N H:LYS4 4.5 54.2 1.0 N H:DSG5 4.6 57.6 1.0 N A:ASP160 4.7 36.1 1.0 CA A:ASP160 4.8 38.0 1.0 CB H:LYS4 4.8 51.7 1.0 CG H:LYS4 4.9 52.0 1.0 CB H:DSG5 4.9 59.3 1.0 CG H:DSG5 4.9 60.7 1.0 C A:PHE159 5.0 34.0 1.0

Zinc binding site 2 out of 18 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:61.6 occ:1.00 OE2 A:GLU56 2.0 61.6 1.0 OE1 A:GLU56 2.0 62.5 1.0 NE2 A:HIS-2 2.1 66.9 1.0 CD A:GLU56 2.1 61.2 1.0 CE1 A:HIS-2 2.6 67.5 1.0 CD2 A:HIS-2 3.4 67.4 1.0 CG A:GLU56 3.5 59.9 1.0 ND1 A:HIS-2 3.8 67.2 1.0 CG A:HIS-2 4.2 67.1 1.0 CB A:GLU56 4.4 58.6 1.0 CA A:GLU56 4.6 56.9 1.0 O A:GLY230 4.7 35.2 1.0

Zinc binding site 3 out of 18 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:35.0 occ:0.50 OD1 A:ASP62 2.0 34.8 1.0 OD2 A:ASP85 2.0 34.8 1.0 OD1 A:ASP85 2.6 35.5 1.0 CG A:ASP85 2.6 34.4 1.0 CG A:ASP62 2.8 35.0 1.0 OD2 A:ASP62 3.0 35.6 1.0 CB A:ASP85 4.1 34.3 1.0 CB A:ASP62 4.2 35.0 1.0 CB A:SER83 4.2 33.4 1.0 OG A:SER83 4.5 34.0 1.0 CA A:ASP62 4.7 35.2 1.0 N A:TYR86 4.8 34.9 1.0 CA A:ASP85 5.0 34.4 1.0

Zinc binding site 4 out of 18 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 4 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 B:Zn301 b:37.6 occ:1.00 O B:HOH409 1.9 25.5 1.0 OD1 B:ASP160 2.0 38.3 1.0 ND1 B:HIS207 2.1 37.7 1.0 NE2 B:HIS153 2.1 38.9 1.0 OD2 B:ASP160 2.5 39.7 1.0 CG B:ASP160 2.5 38.8 1.0 CE1 B:HIS153 2.7 39.3 1.0 CE1 B:HIS207 2.8 37.8 1.0 CG B:HIS207 3.2 37.8 1.0 CD2 B:HIS153 3.3 39.4 1.0 CB B:HIS207 3.8 38.0 1.0 ND1 B:HIS153 3.9 39.3 1.0 NE2 B:HIS207 4.0 37.4 1.0 CB B:ASP160 4.0 38.8 1.0 CD2 B:HIS207 4.2 37.5 1.0 CG B:HIS153 4.2 39.7 1.0 CA B:HIS207 4.4 38.5 1.0 N B:ASP160 4.5 37.1 1.0 CA B:ASP160 4.6 38.4 1.0 NH1 B:ARG120 4.6 37.1 1.0 C B:PHE159 4.8 35.9 1.0

Zinc binding site 5 out of 18 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 5 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 B:Zn302 b:54.8 occ:1.00 OD1 B:ASP184 2.0 50.9 1.0 ND1 B:HIS181 2.1 47.6 1.0 OD1 A:ASP114 2.5 44.2 1.0 CG B:ASP184 2.5 48.6 1.0 OD2 B:ASP184 2.6 50.4 1.0 ND1 A:HIS115 2.7 45.7 1.0 CE1 B:HIS181 3.0 47.0 1.0 CG B:HIS181 3.0 46.4 1.0 CE1 A:HIS115 3.2 45.9 1.0 CB B:HIS181 3.4 45.5 1.0 CG A:ASP114 3.5 44.1 1.0 CG A:HIS115 3.6 44.7 1.0 CA B:HIS181 3.7 44.5 1.0 OD2 A:ASP114 3.7 44.9 1.0 CB B:ASP184 3.8 46.9 1.0 NE2 B:HIS181 4.1 47.1 1.0 OG A:SER113 4.1 43.1 1.0 CD2 B:HIS181 4.1 46.8 1.0 CB A:HIS115 4.1 43.8 1.0 NE2 A:HIS115 4.2 45.9 1.0 O B:ASP180 4.3 43.1 1.0 O B:HIS181 4.3 45.1 1.0 CD2 A:HIS115 4.4 45.4 1.0 C B:HIS181 4.5 44.1 1.0 N A:HIS115 4.5 42.3 1.0 N B:HIS181 4.7 43.6 1.0 C B:ASP180 4.8 42.5 1.0 O B:HOH401 4.8 30.6 1.0 CB A:ASP114 4.9 43.2 1.0 N A:ASP114 4.9 42.1 1.0 C A:ASP114 5.0 42.3 1.0 CA A:HIS115 5.0 42.9 1.0

Zinc binding site 6 out of 18 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 6 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 B:Zn303 b:60.4 occ:1.00 OE1 B:GLU56 2.0 56.6 1.0 NE2 B:HIS-2 2.1 61.9 1.0 OE2 B:GLU56 2.5 55.7 1.0 CD B:GLU56 2.6 54.8 1.0 O B:HOH410 2.7 25.3 1.0 CE1 B:HIS-2 2.7 62.2 1.0 CD2 B:HIS-2 3.3 62.3 1.0 ND1 B:HIS-2 3.9 62.1 1.0 CG B:GLU56 4.1 53.6 1.0 CG B:HIS-2 4.2 62.1 1.0 O B:MET-1 4.4 55.8 1.0 CA B:GLU56 4.6 53.1 1.0 CB B:GLU56 4.7 53.4 1.0 O B:GLY230 4.8 49.8 1.0 C B:MET-1 4.9 56.6 1.0

Zinc binding site 7 out of 18 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 7 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 B:Zn304 b:57.8 occ:1.00 O B:HOH416 1.7 14.6 1.0 NE2 B:HIS79 2.1 51.9 1.0 CE1 B:HIS79 2.7 51.1 1.0 OE1 B:GLU232 2.9 54.9 1.0 CD2 B:HIS79 3.3 50.3 1.0 ND1 B:HIS79 3.9 50.8 1.0 CD B:GLU232 4.0 53.6 1.0 O B:HOH412 4.1 23.8 1.0 CG B:HIS79 4.2 49.9 1.0 OE2 B:GLU232 4.5 53.9 1.0

Zinc binding site 8 out of 18 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 8 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 B:Zn305 b:44.1 occ:1.00 OD2 E:ASP85 2.0 45.5 1.0 OD1 B:ASP62 2.0 42.8 1.0 OD1 B:ASP85 2.0 43.6 1.0 OD2 E:ASP62 2.0 43.8 1.0 OD1 E:ASP62 2.3 45.4 1.0 OD2 B:ASP85 2.4 43.0 1.0 CG E:ASP62 2.4 44.2 1.0 CG B:ASP85 2.5 43.3 1.0 CG B:ASP62 2.6 43.3 1.0 OD2 B:ASP62 2.6 42.5 1.0 CG E:ASP85 2.8 46.0 1.0 OD1 E:ASP85 3.0 46.5 1.0 CB B:ASP85 3.9 43.2 1.0 CB E:ASP62 3.9 43.7 1.0 O E:HOH410 4.1 39.3 1.0 CB B:ASP62 4.1 43.7 1.0 CB E:ASP85 4.2 46.4 1.0 OG B:SER83 4.5 47.7 1.0 CA B:ASP62 4.7 44.4 1.0 CA E:ASP62 4.8 43.6 1.0 C B:ASP85 4.8 44.2 1.0 N B:TYR86 4.8 43.6 1.0 OG E:SER83 4.8 51.9 1.0 CA B:ASP85 4.9 43.8 1.0 N E:ASP62 5.0 43.6 1.0

Zinc binding site 9 out of 18 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 9 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 B:Zn306 b:39.1 occ:1.00 OD1 B:ASP114 2.0 40.0 1.0 OD2 B:ASP114 2.0 40.1 1.0 ND1 B:HIS115 2.1 35.3 1.0 CG B:ASP114 2.2 39.5 1.0 CE1 B:HIS115 3.0 34.5 1.0 CG B:HIS115 3.1 35.1 1.0 CB B:HIS115 3.5 35.6 1.0 OG B:SER113 3.6 39.2 1.0 N B:HIS115 3.7 36.4 1.0 CB B:ASP114 3.7 38.3 1.0 NE2 B:HIS115 4.1 34.4 1.0 CD2 B:HIS115 4.2 35.0 1.0 CA B:HIS115 4.2 35.5 1.0 N B:ASP114 4.3 38.0 1.0 C B:ASP114 4.3 37.2 1.0 CA B:ASP114 4.3 37.7 1.0 O B:HOH402 4.8 24.8 1.0 CB B:SER113 4.9 38.9 1.0

Zinc binding site 10 out of 18 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 10 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 C:Zn301 b:34.6 occ:1.00 O C:HOH406 1.9 15.1 1.0 OD1 C:ASP160 2.0 36.2 1.0 ND1 C:HIS207 2.1 34.5 1.0 NE2 C:HIS153 2.1 33.7 1.0 CG C:ASP160 2.7 36.6 1.0 OD2 C:ASP160 2.7 36.2 1.0 CE1 C:HIS207 2.8 34.6 1.0 CE1 C:HIS153 2.9 33.6 1.0 CG C:HIS207 3.1 34.6 1.0 CD2 C:HIS153 3.2 33.5 1.0 CB C:HIS207 3.7 35.1 1.0 NE2 C:HIS207 3.9 34.3 1.0 CD2 C:HIS207 4.0 34.4 1.0 ND1 C:HIS153 4.1 33.7 1.0 CB C:ASP160 4.1 37.1 1.0 CG C:HIS153 4.3 33.5 1.0 CA C:HIS207 4.3 35.8 1.0 CA C:ASP160 4.8 37.7 1.0 N C:ASP160 4.8 37.2 1.0 NH1 C:ARG120 4.8 55.4 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