Zinc in PDB 2go4: Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514, PDB code: 2go4 was solved by H.A.Gennadios, D.A.Whittington, X.Li, 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)	50.00 / 2.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	100.729, 100.729, 121.299, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 24.1

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514 (pdb code 2go4). 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 Complexed with Tu-514, PDB code: 2go4:
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 Complexed with Tu-514


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 Complexed with Tu-514 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:41.6 occ:1.00 OXH A:TUX901 2.0 54.3 1.0 NE2 A:HIS238 2.0 38.7 1.0 NE2 A:HIS79 2.1 43.3 1.0 OD1 A:ASP242 2.2 45.7 1.0 OYH A:TUX901 2.2 55.5 1.0 NXH A:TUX901 2.8 54.0 1.0 OD2 A:ASP242 2.8 45.5 1.0 CG A:ASP242 2.8 46.1 1.0 CYH A:TUX901 2.8 56.9 1.0 CE1 A:HIS238 2.9 38.5 1.0 CE1 A:HIS79 3.0 41.9 1.0 CD2 A:HIS238 3.1 38.8 1.0 CD2 A:HIS79 3.1 44.7 1.0 OG1 A:THR191 3.8 55.8 1.0 ND1 A:HIS238 4.0 39.0 1.0 ND1 A:HIS79 4.1 45.0 1.0 CG A:HIS238 4.1 40.0 1.0 CG A:HIS79 4.2 43.4 1.0 CB A:ASP242 4.3 46.1 1.0 CZH A:TUX901 4.3 60.5 1.0 OE2 A:GLU78 4.4 52.0 1.0 CG A:GLU78 4.5 51.7 1.0 CB A:THR191 4.7 52.2 1.0 CG2 A:THR191 4.8 54.0 1.0 CA A:THR191 4.8 51.3 1.0 NE2 A:HIS265 4.9 51.1 1.0 O A:HIS238 4.9 39.5 1.0 CA A:ASP242 5.0 43.3 1.0 CD A:GLU78 5.0 53.9 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514


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 Complexed with Tu-514 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:51.7 occ:0.80 CL A:CL401 2.0 55.1 1.0 NE2 A:HIS58 2.2 56.2 1.0 O A:HOH925 2.3 36.8 1.0 NE2 A:HIS200 2.3 63.0 1.0 CD2 A:HIS58 3.0 55.0 1.0 CE1 A:HIS200 3.0 62.8 1.0 CE1 A:HIS58 3.3 56.9 1.0 CD2 A:HIS200 3.5 62.3 1.0 CG A:HIS58 4.2 55.2 1.0 ND1 A:HIS200 4.2 63.1 1.0 ND1 A:HIS58 4.3 56.1 1.0 CG2 A:VAL204 4.4 59.0 1.0 CG A:HIS200 4.5 62.2 1.0 CB A:ASN57 4.6 60.9 1.0 CG1 A:VAL204 4.7 58.7 1.0 OD1 A:ASN57 5.0 66.7 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514


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 Complexed with Tu-514 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:52.5 occ:1.00 N A:GLY2 2.1 61.5 1.0 OE1 A:GLU126 2.1 73.4 1.0 OE2 A:GLU126 2.4 72.3 1.0 CD A:GLU126 2.5 73.4 1.0 CA A:GLY2 3.2 59.4 1.0 C A:GLY2 3.5 59.9 1.0 O A:GLY2 3.5 58.0 1.0 CG A:GLU126 4.0 73.5 1.0 N A:LEU3 4.4 61.5 1.0 CB A:GLU126 4.8 72.5 1.0 CD2 A:LEU3 5.0 64.5 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514


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 Complexed with Tu-514 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:48.2 occ:1.00 OXH B:TUX902 1.9 56.0 1.0 OD1 B:ASP242 2.0 46.5 1.0 OYH B:TUX902 2.1 56.8 1.0 NE2 B:HIS79 2.1 41.7 1.0 NE2 B:HIS238 2.1 41.3 1.0 NXH B:TUX902 2.7 57.1 1.0 CG B:ASP242 2.7 46.7 1.0 OD2 B:ASP242 2.7 49.5 1.0 CYH B:TUX902 2.7 60.2 1.0 CE1 B:HIS238 3.0 43.3 1.0 CE1 B:HIS79 3.1 44.0 1.0 CD2 B:HIS79 3.1 43.5 1.0 CD2 B:HIS238 3.1 43.1 1.0 OG1 B:THR191 4.0 54.0 1.0 ND1 B:HIS238 4.1 43.5 1.0 CB B:ASP242 4.1 44.8 1.0 ND1 B:HIS79 4.2 45.0 1.0 CZH B:TUX902 4.2 63.0 1.0 CG B:HIS79 4.2 44.7 1.0 CG B:HIS238 4.2 43.6 1.0 OE2 B:GLU78 4.3 55.8 1.0 CG B:GLU78 4.3 51.8 1.0 NE2 B:HIS265 4.7 52.2 1.0 CA B:ASP242 4.8 44.9 1.0 CE1 B:HIS265 4.8 53.7 1.0 CD B:GLU78 4.9 54.2 1.0 O B:HIS238 4.9 43.0 1.0 CB B:THR191 4.9 51.9 1.0 C2G B:TUX902 4.9 66.5 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514


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 Complexed with Tu-514 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:64.0 occ:0.80 NE2 B:HIS58 2.2 58.9 1.0 NE2 B:HIS200 2.2 63.9 1.0 CE1 B:HIS200 3.0 63.0 1.0 CE1 B:HIS58 3.1 58.0 1.0 CD2 B:HIS58 3.2 57.6 1.0 CD2 B:HIS200 3.4 62.9 1.0 ND1 B:HIS58 4.2 56.5 1.0 ND1 B:HIS200 4.2 62.4 1.0 CG B:HIS58 4.3 56.0 1.0 CG B:HIS200 4.4 61.7 1.0 CB B:ASN57 4.8 61.9 1.0 CG2 B:VAL204 4.9 57.8 1.0

H.A.Gennadios, D.A.Whittington, X.Li, C.A.Fierke, D.W.Christianson. Mechanistic Inferences From the Binding of Ligands to Lpxc, A Metal-Dependent Deacetylase Biochemistry V. 45 7940 2006.
ISSN: ISSN 0006-2960
PubMed: 16800620
DOI: 10.1021/BI060823M