Zinc in PDB 2o3z: X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate

The structure of X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate, PDB code: 2o3z was solved by H.A.Gennadios, D.A.Whittington, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.70 / 2.25
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	101.006, 101.006, 122.674, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 22.7

The structure of X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate (pdb code 2o3z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate, PDB code: 2o3z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:24.7 occ:1.00 NE2 A:HIS238 2.1 20.3 1.0 NE2 A:HIS79 2.1 17.4 1.0 OD1 A:ASP242 2.1 24.6 1.0 OD2 A:ASP242 2.6 23.7 1.0 CG A:ASP242 2.7 22.1 1.0 CE1 A:HIS238 2.9 18.7 1.0 CD2 A:HIS79 3.1 18.1 1.0 CE1 A:HIS79 3.1 19.9 1.0 CD2 A:HIS238 3.1 19.2 1.0 ND1 A:HIS238 4.1 21.2 1.0 CG A:GLU78 4.2 23.8 1.0 OG1 A:THR191 4.2 30.0 1.0 ND1 A:HIS79 4.2 18.2 1.0 CG A:HIS238 4.2 21.2 1.0 CB A:ASP242 4.2 22.4 1.0 CG A:HIS79 4.2 19.1 1.0 OE2 A:GLU78 4.3 25.4 1.0 O A:HOH614 4.5 27.1 1.0 CD A:GLU78 4.8 24.8 1.0 NE2 A:HIS265 4.8 29.6 1.0 CA A:ASP242 4.9 23.2 1.0 CE1 A:HIS265 5.0 28.5 1.0

Zinc binding site 2 out of 5 in the X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:43.6 occ:1.00 CL A:CL601 2.1 47.3 1.0 NE2 A:HIS200 2.2 38.9 1.0 NE2 A:HIS58 2.3 35.5 1.0 O A:HOH602 2.3 27.4 1.0 CD2 A:HIS58 2.9 34.3 1.0 CD2 A:HIS200 3.1 35.6 1.0 CE1 A:HIS200 3.2 37.5 1.0 CE1 A:HIS58 3.4 36.3 1.0 CG A:HIS58 4.2 33.2 1.0 CG A:HIS200 4.3 34.6 1.0 ND1 A:HIS200 4.3 37.8 1.0 ND1 A:HIS58 4.4 34.2 1.0 CG2 A:VAL204 4.5 32.1 1.0 CB A:ASN57 4.5 38.2 1.0

Zinc binding site 3 out of 5 in the X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:25.3 occ:1.00 OD1 B:ASP242 2.0 22.6 1.0 NE2 B:HIS79 2.1 23.2 1.0 NE2 B:HIS238 2.1 18.3 1.0 CG B:ASP242 2.8 25.6 1.0 OD2 B:ASP242 2.8 25.7 1.0 CE1 B:HIS238 3.0 20.2 1.0 CE1 B:HIS79 3.1 23.3 1.0 CD2 B:HIS79 3.1 23.5 1.0 CD2 B:HIS238 3.2 17.8 1.0 OG1 B:THR191 4.0 30.4 1.0 ND1 B:HIS238 4.2 19.0 1.0 CG B:GLU78 4.2 25.9 1.0 ND1 B:HIS79 4.2 24.3 1.0 CG B:HIS79 4.2 25.2 1.0 CB B:ASP242 4.2 23.2 1.0 CG B:HIS238 4.3 19.9 1.0 OE2 B:GLU78 4.3 28.2 1.0 NE2 B:HIS265 4.7 29.0 1.0 O B:HOH541 4.7 37.3 1.0 CD B:GLU78 4.8 28.0 1.0 CA B:ASP242 4.8 22.9 1.0 CE1 B:HIS265 4.9 28.6 1.0 CB B:THR191 4.9 25.4 1.0 CA B:THR191 5.0 25.4 1.0

Zinc binding site 4 out of 5 in the X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:51.0 occ:1.00 O B:HOH508 2.2 28.9 1.0 O B:HOH507 2.2 30.5 1.0 NE2 B:HIS58 2.3 34.2 1.0 NE2 B:HIS200 2.5 42.1 1.0 CD2 B:HIS58 3.0 33.2 1.0 CD2 B:HIS200 3.2 38.7 1.0 CE1 B:HIS58 3.4 34.8 1.0 CE1 B:HIS200 3.5 41.7 1.0 ND2 B:ASN57 4.3 50.4 1.0 CG B:HIS58 4.3 35.6 1.0 ND1 B:HIS58 4.4 34.4 1.0 CG B:HIS200 4.5 39.2 1.0 CG2 B:VAL204 4.5 33.4 1.0 ND1 B:HIS200 4.6 41.1 1.0 CB B:ASN57 4.8 40.8 1.0 CG1 B:VAL204 5.0 30.2 1.0

Zinc binding site 5 out of 5 in the X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of Lpxc Complexed with 3-Heptyloxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:28.8 occ:1.00 OE1 B:GLU95 1.9 28.8 1.0 NE2 B:HIS29 2.0 34.6 1.0 CD B:GLU95 2.8 31.2 1.0 CE1 B:HIS29 2.9 34.0 1.0 CD2 B:HIS29 3.1 33.5 1.0 OE2 B:GLU95 3.2 34.1 1.0 CG2 B:ILE27 3.7 29.3 1.0 CG B:GLU95 4.0 31.8 1.0 ND1 B:HIS29 4.1 33.1 1.0 CB B:ILE27 4.1 29.2 1.0 CG B:HIS29 4.2 32.0 1.0 CG1 B:ILE27 4.5 28.5 1.0 CB B:GLU95 4.6 29.4 1.0 CD1 B:ILE27 4.7 27.2 1.0

H.Shin, H.A.Gennadios, D.A.Whittington, D.W.Christianson. Amphipathic Benzoic Acid Derivatives: Synthesis and Binding in the Hydrophobic Tunnel of the Zinc Deacetylase Lpxc. Bioorg.Med.Chem. V. 15 2617 2007.
ISSN: ISSN 0968-0896
PubMed: 17296300
DOI: 10.1016/J.BMC.2007.01.044