Zinc in PDB 1yh8: Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate, PDB code: 1yh8 was solved by M.Hernick, H.A.Gennadios, D.A.Whittington, K.M.Rusche, D.W.Christianson, C.A.Fierke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	101.610, 101.610, 124.180, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 23.9

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate (pdb code 1yh8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate, PDB code: 1yh8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate


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 Complexed with Palmitate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:21.3 occ:1.00 NE2 A:HIS79 2.0 18.5 1.0 NE2 A:HIS238 2.0 18.0 1.0 OD1 A:ASP242 2.1 21.4 1.0 O2 A:PAM801 2.3 31.7 1.0 O1 A:PAM801 2.4 32.6 1.0 C1 A:PAM801 2.7 33.6 1.0 OD2 A:ASP242 2.7 23.0 1.0 CG A:ASP242 2.7 21.9 1.0 CE1 A:HIS238 2.9 18.6 1.0 CD2 A:HIS79 3.0 18.6 1.0 CE1 A:HIS79 3.0 18.1 1.0 CD2 A:HIS238 3.0 19.0 1.0 OG1 A:THR191 4.0 26.2 1.0 ND1 A:HIS238 4.0 18.8 1.0 CG A:HIS238 4.1 20.1 1.0 ND1 A:HIS79 4.1 19.8 1.0 CG A:HIS79 4.1 18.5 1.0 CB A:ASP242 4.2 20.5 1.0 C2 A:PAM801 4.2 32.9 1.0 CG A:GLU78 4.4 23.6 1.0 OE2 A:GLU78 4.7 26.0 1.0 O A:HOH825 4.7 21.1 1.0 O A:HOH810 4.8 26.5 1.0 CA A:ASP242 4.8 18.7 1.0 NE2 A:HIS265 4.8 23.3 1.0 O A:HIS238 4.9 20.3 1.0 CB A:THR191 5.0 25.1 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate


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 Complexed with Palmitate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:44.0 occ:1.00 NE2 A:HIS200 2.1 32.2 1.0 NE2 A:HIS58 2.2 25.1 1.0 CE1 A:HIS200 3.0 31.2 1.0 CD2 A:HIS200 3.1 29.4 1.0 CD2 A:HIS58 3.1 24.8 1.0 CE1 A:HIS58 3.3 25.4 1.0 ND1 A:HIS200 4.1 29.6 1.0 CG A:HIS200 4.2 28.9 1.0 CG A:HIS58 4.3 25.2 1.0 ND1 A:HIS58 4.4 22.6 1.0 CB A:ASN57 4.6 30.9 1.0 CG2 A:VAL204 4.8 23.4 1.0 CG1 A:VAL204 4.9 22.6 1.0 OD1 A:ASN57 5.0 38.2 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate


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 Complexed with Palmitate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:28.4 occ:1.00 NE2 A:HIS29 2.1 36.5 1.0 OE1 A:GLU95 2.5 37.2 1.0 OE2 A:GLU95 2.7 32.9 1.0 CE1 A:HIS29 2.7 32.5 1.0 CD A:GLU95 2.9 33.5 1.0 CD2 A:HIS29 3.4 35.9 1.0 CG2 A:ILE27 3.6 26.6 1.0 ND1 A:HIS29 4.0 33.0 1.0 CD1 A:ILE27 4.0 29.7 1.0 CB A:ILE27 4.2 27.2 1.0 CG A:GLU95 4.3 31.1 1.0 CG A:HIS29 4.3 34.7 1.0 CB A:GLU95 4.7 27.7 1.0 CG1 A:ILE27 4.7 27.3 1.0 CD A:LYS10 4.8 41.1 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate


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 Complexed with Palmitate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:19.1 occ:1.00 NE2 B:HIS238 2.0 20.3 1.0 O2 B:PAM802 2.0 24.9 1.0 NE2 B:HIS79 2.1 17.8 1.0 OD1 B:ASP242 2.2 20.7 1.0 O1 B:PAM802 2.3 26.7 1.0 C1 B:PAM802 2.5 26.2 1.0 OD2 B:ASP242 2.7 22.6 1.0 CG B:ASP242 2.8 19.4 1.0 CE1 B:HIS238 2.9 20.1 1.0 CD2 B:HIS238 3.0 20.0 1.0 CE1 B:HIS79 3.1 16.4 1.0 CD2 B:HIS79 3.1 18.2 1.0 OG1 B:THR191 4.0 26.6 1.0 ND1 B:HIS238 4.0 21.2 1.0 C2 B:PAM802 4.0 26.9 1.0 CG B:HIS238 4.1 20.8 1.0 ND1 B:HIS79 4.2 15.8 1.0 CG B:HIS79 4.2 17.6 1.0 CB B:ASP242 4.3 18.1 1.0 O B:HOH820 4.3 25.7 1.0 CG B:GLU78 4.5 21.4 1.0 OE2 B:GLU78 4.8 22.6 1.0 C3 B:PAM802 4.8 29.0 1.0 CB B:THR191 4.9 25.6 1.0 NE2 B:HIS265 4.9 22.7 1.0 O B:HIS238 4.9 19.5 1.0 CA B:ASP242 4.9 16.6 1.0 CG2 B:THR191 4.9 26.2 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate


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 Complexed with Palmitate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn507 b:38.4 occ:1.00 O B:HOH863 1.8 13.5 1.0 CL B:CL603 2.0 38.3 1.0 NE2 B:HIS200 2.1 33.3 1.0 NE2 B:HIS58 2.3 26.8 1.0 CE1 B:HIS200 3.0 31.7 1.0 CD2 B:HIS58 3.1 25.1 1.0 CD2 B:HIS200 3.2 31.1 1.0 CE1 B:HIS58 3.4 26.5 1.0 ND1 B:HIS200 4.1 30.9 1.0 CG B:HIS200 4.3 30.5 1.0 CG B:HIS58 4.3 25.2 1.0 ND1 B:HIS58 4.4 24.8 1.0 CG2 B:VAL204 4.5 24.1 1.0 CB B:ASN57 4.5 31.2 1.0 CG1 B:VAL204 4.7 23.6 1.0 OD1 B:ASN57 4.9 34.0 1.0

M.Hernick, H.A.Gennadios, D.A.Whittington, K.M.Rusche, D.W.Christianson, C.A.Fierke. Udp-3-O-((R)-3-Hydroxymyristoyl)-N- Acetylglucosamine Deacetylase Functions Through A General Acid-Base Catalyst Pair Mechanism J.Biol.Chem. V. 280 16969 2005.
ISSN: ISSN 0021-9258
PubMed: 15705580
DOI: 10.1074/JBC.M413560200