Zinc in PDB 1p42: Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form)

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form), PDB code: 1p42 was solved by D.A.Whittington, K.M.Rusche, H.Shin, C.A.Fierke, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 2.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	101.660, 101.660, 125.100, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 21.1

The binding sites of Zinc atom in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form) (pdb code 1p42). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form), PDB code: 1p42:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form)


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 Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:17.1 occ:1.00 O A:HOH602 1.8 17.9 1.0 OD1 A:ASP242 2.0 19.9 1.0 NE2 A:HIS79 2.1 15.4 1.0 NE2 A:HIS238 2.2 18.5 1.0 CG A:ASP242 2.7 17.1 1.0 OD2 A:ASP242 2.8 21.3 1.0 CD2 A:HIS79 3.0 16.8 1.0 CE1 A:HIS238 3.1 18.7 1.0 CE1 A:HIS79 3.1 17.7 1.0 CD2 A:HIS238 3.1 19.1 1.0 ZN A:ZN502 3.4 22.8 1.0 O A:HOH754 3.7 46.4 1.0 CG A:GLU78 4.0 18.3 1.0 O A:HOH732 4.1 44.3 1.0 ND1 A:HIS238 4.2 18.9 1.0 CG A:HIS79 4.2 17.5 1.0 CB A:ASP242 4.2 16.5 1.0 ND1 A:HIS79 4.2 19.6 1.0 CG A:HIS238 4.2 18.3 1.0 OE2 A:GLU78 4.3 18.6 1.0 OG1 A:THR191 4.4 33.1 1.0 CB A:THR191 4.4 26.7 1.0 NE2 A:HIS265 4.5 21.0 1.0 O A:HOH679 4.6 41.9 1.0 CE1 A:HIS265 4.7 21.0 1.0 CD A:GLU78 4.7 17.1 1.0 CA A:ASP242 4.8 17.2 1.0 O A:HIS238 4.8 20.0 1.0 CA A:THR191 4.9 25.3 1.0 O1 A:MYR601 4.9 33.1 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form)


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 Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:22.8 occ:1.00 OE2 A:GLU78 2.0 18.6 1.0 NE2 A:HIS265 2.0 21.0 1.0 O A:HOH602 2.1 17.9 1.0 O1 A:MYR601 2.1 33.1 1.0 CD2 A:HIS265 3.0 22.4 1.0 CE1 A:HIS265 3.0 21.0 1.0 CD A:GLU78 3.0 17.1 1.0 C1 A:MYR601 3.1 40.6 1.0 O2 A:MYR601 3.4 41.4 1.0 ZN A:ZN501 3.4 17.1 1.0 CG A:GLU78 3.5 18.3 1.0 O A:HOH754 3.7 46.4 1.0 OD2 A:ASP242 4.0 21.3 1.0 CA A:SER59 4.0 21.1 1.0 OE1 A:GLU78 4.0 17.9 1.0 ND1 A:HIS265 4.1 22.0 1.0 CG A:HIS265 4.1 22.5 1.0 OD1 A:ASP242 4.1 19.9 1.0 O A:HOH732 4.1 44.3 1.0 CG A:ASP242 4.2 17.1 1.0 C2 A:MYR601 4.4 41.4 1.0 O A:HIS58 4.4 22.2 1.0 NE2 A:HIS79 4.5 15.4 1.0 CB A:GLU78 4.6 16.5 1.0 N A:SER59 4.6 21.5 1.0 C3 A:MYR601 4.7 41.3 1.0 CB A:SER59 4.7 19.7 1.0 C A:HIS58 4.8 22.6 1.0 C A:SER59 4.9 20.4 1.0 N A:THR60 4.9 19.2 1.0 O A:HOH633 5.0 27.2 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form)


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 Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:32.5 occ:1.00 O A:HOH604 1.9 31.0 1.0 O A:HOH603 2.0 21.1 1.0 NE2 A:HIS58 2.2 34.4 1.0 NE2 A:HIS200 2.3 37.5 1.0 CD2 A:HIS58 3.1 30.3 1.0 CE1 A:HIS200 3.2 36.8 1.0 CE1 A:HIS58 3.3 31.5 1.0 CD2 A:HIS200 3.3 34.6 1.0 ND2 A:ASN57 4.2 38.0 1.0 CG A:HIS58 4.3 29.4 1.0 CB A:ASN57 4.3 31.7 1.0 ND1 A:HIS200 4.3 35.7 1.0 ND1 A:HIS58 4.3 29.2 1.0 CG A:HIS200 4.4 35.5 1.0 CG2 A:VAL204 4.5 29.7 1.0 CG1 A:VAL204 4.6 31.4 1.0 CG A:ASN57 4.7 35.2 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:20.8 occ:1.00 OE1 A:GLU126 2.0 23.0 1.0 N A:GLY2 2.2 21.6 1.0 OE2 A:GLU126 2.5 21.7 1.0 CD A:GLU126 2.6 22.0 1.0 CA A:GLY2 3.1 20.6 1.0 C A:GLY2 3.4 22.3 1.0 O A:GLY2 3.5 22.5 1.0 CG A:GLU126 4.1 22.7 1.0 N A:LEU3 4.2 21.9 1.0 CD2 A:LEU3 4.7 21.1 1.0 CB A:GLU126 4.7 22.4 1.0 CA A:GLU126 5.0 24.2 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:18.4 occ:1.00 O B:HOH603 1.9 20.2 1.0 NE2 B:HIS238 2.0 17.3 1.0 NE2 B:HIS79 2.0 15.7 1.0 OD1 B:ASP242 2.1 18.6 1.0 CG B:ASP242 2.9 19.6 1.0 CE1 B:HIS238 2.9 19.5 1.0 OD2 B:ASP242 2.9 20.1 1.0 CD2 B:HIS79 3.0 16.7 1.0 CD2 B:HIS238 3.0 17.6 1.0 CE1 B:HIS79 3.1 17.6 1.0 ZN B:ZN506 3.4 21.1 1.0 O B:HOH670 3.8 41.7 1.0 ND1 B:HIS238 4.0 18.1 1.0 CG B:HIS238 4.1 16.3 1.0 CG B:GLU78 4.1 16.4 1.0 ND1 B:HIS79 4.1 18.1 1.0 O B:HOH734 4.1 34.5 1.0 CG B:HIS79 4.2 16.5 1.0 CB B:THR191 4.2 26.0 1.0 OG1 B:THR191 4.3 31.2 1.0 CB B:ASP242 4.3 16.5 1.0 OE2 B:GLU78 4.4 18.6 1.0 O B:HOH669 4.4 40.9 1.0 NE2 B:HIS265 4.7 23.1 1.0 CA B:THR191 4.7 23.4 1.0 O B:HIS238 4.8 18.3 1.0 CD B:GLU78 4.8 18.5 1.0 CE1 B:HIS265 4.8 20.4 1.0 CA B:ASP242 4.9 17.9 1.0 O1 B:MYR602 4.9 26.7 1.0 CD2 B:PHE241 5.0 21.0 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:21.1 occ:1.00 O B:HOH603 2.0 20.2 1.0 O1 B:MYR602 2.0 26.7 1.0 OE2 B:GLU78 2.0 18.6 1.0 NE2 B:HIS265 2.1 23.1 1.0 C1 B:MYR602 2.9 36.8 1.0 CD B:GLU78 3.0 18.5 1.0 CE1 B:HIS265 3.1 20.4 1.0 CD2 B:HIS265 3.1 20.6 1.0 O2 B:MYR602 3.3 39.0 1.0 ZN B:ZN505 3.4 18.4 1.0 CG B:GLU78 3.5 16.4 1.0 O B:HOH670 3.7 41.7 1.0 O B:HOH734 4.0 34.5 1.0 OD2 B:ASP242 4.0 20.1 1.0 OD1 B:ASP242 4.0 18.6 1.0 OE1 B:GLU78 4.1 19.2 1.0 CA B:SER59 4.1 21.8 1.0 ND1 B:HIS265 4.2 21.3 1.0 CG B:ASP242 4.2 19.6 1.0 CG B:HIS265 4.3 22.2 1.0 C2 B:MYR602 4.3 38.1 1.0 NE2 B:HIS79 4.3 15.7 1.0 O B:HIS58 4.5 21.1 1.0 C3 B:MYR602 4.6 39.6 1.0 CB B:GLU78 4.7 17.3 1.0 N B:SER59 4.7 21.2 1.0 CB B:SER59 4.8 20.2 1.0 C B:HIS58 4.9 23.4 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase (Zinc-Inhibited Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn507 b:33.5 occ:1.00 NE2 B:HIS200 2.0 34.7 1.0 NE2 B:HIS58 2.0 30.5 1.0 O B:HOH605 2.1 33.2 1.0 O B:HOH604 2.3 20.4 1.0 CD2 B:HIS200 3.0 34.6 1.0 CE1 B:HIS58 3.0 29.2 1.0 CD2 B:HIS58 3.0 27.2 1.0 CE1 B:HIS200 3.1 35.4 1.0 ND1 B:HIS58 4.1 27.9 1.0 CG B:HIS200 4.1 35.0 1.0 ND1 B:HIS200 4.1 35.9 1.0 CG B:HIS58 4.2 26.8 1.0 CG2 B:VAL204 4.5 28.8 1.0 ND2 B:ASN57 4.5 37.8 1.0 CB B:ASN57 4.5 33.1 1.0 CG1 B:VAL204 4.6 30.6 1.0

D.A.Whittington, K.M.Rusche, H.Shin, C.A.Fierke, D.W.Christianson. Crystal Structure of Lpxc, A Zinc-Dependent Deacetylase Essential For Endotoxin Biosynthesis Proc.Natl.Acad.Sci.Usa V. 100 8146 2003.
ISSN: ISSN 0027-8424
PubMed: 12819349
DOI: 10.1073/PNAS.1432990100