Zinc in PDB 2j65: Structure of Lpxc From Aquifex Aeolicus in Complex with Udp

The structure of Structure of Lpxc From Aquifex Aeolicus in Complex with Udp, PDB code: 2j65 was solved by L.Buetow, A.Dawson, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.90 / 2.20
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	101.755, 101.755, 124.243, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 22.5

The structure of Structure of Lpxc From Aquifex Aeolicus in Complex with Udp also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Structure of Lpxc From Aquifex Aeolicus in Complex with Udp (pdb code 2j65). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of Lpxc From Aquifex Aeolicus in Complex with Udp, PDB code: 2j65:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Structure of Lpxc From Aquifex Aeolicus in Complex with Udp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Lpxc From Aquifex Aeolicus in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.9 occ:1.00 O A:HOH2238 2.0 25.4 1.0 NE2 A:HIS226 2.0 12.5 1.0 OD1 A:ASP230 2.0 14.8 1.0 NE2 A:HIS74 2.1 12.2 1.0 CG A:ASP230 2.8 14.8 1.0 OD2 A:ASP230 2.8 16.6 1.0 CD2 A:HIS226 3.0 10.7 1.0 CE1 A:HIS226 3.0 11.8 1.0 CD2 A:HIS74 3.1 11.8 1.0 CE1 A:HIS74 3.1 13.0 1.0 ZN A:ZN302 3.3 26.1 1.0 CG2 A:THR179 3.6 15.4 0.5 OG1 A:THR179 3.7 17.2 0.5 ND1 A:HIS226 4.1 11.7 1.0 CG A:GLU73 4.1 14.5 1.0 CG A:HIS226 4.1 11.7 1.0 ND1 A:HIS74 4.2 13.9 1.0 CG A:HIS74 4.2 12.7 1.0 CB A:ASP230 4.2 13.1 1.0 CB A:THR179 4.3 16.4 0.5 O A:HOH2207 4.3 37.9 1.0 OE2 A:GLU73 4.4 18.2 1.0 O A:HOH2164 4.6 24.5 1.0 NE2 A:HIS253 4.7 13.5 1.0 CE1 A:HIS253 4.8 13.9 1.0 CB A:THR179 4.8 16.3 0.5 CD A:GLU73 4.8 15.7 1.0 O A:HIS226 4.8 11.9 1.0 CA A:THR179 4.8 16.3 0.5 CA A:ASP230 4.8 12.8 1.0 CA A:THR179 4.9 16.3 0.5 O A:HOH2241 4.9 51.0 1.0 O1 A:MYR401 5.0 44.0 1.0

Zinc binding site 2 out of 7 in the Structure of Lpxc From Aquifex Aeolicus in Complex with Udp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Lpxc From Aquifex Aeolicus in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:26.1 occ:1.00 NE2 A:HIS253 2.1 13.5 1.0 O A:HOH2238 2.1 25.4 1.0 O1 A:MYR401 2.2 44.0 1.0 OE2 A:GLU73 2.3 18.2 1.0 CE1 A:HIS253 2.8 13.9 1.0 C1 A:MYR401 3.0 46.0 1.0 CD A:GLU73 3.1 15.7 1.0 CD2 A:HIS253 3.2 13.1 1.0 O2 A:MYR401 3.3 45.8 1.0 ZN A:ZN301 3.3 14.9 1.0 O A:HOH2241 3.3 51.0 1.0 CG A:GLU73 3.5 14.5 1.0 OD2 A:ASP230 3.7 16.6 1.0 OD1 A:ASP230 3.9 14.8 1.0 ND1 A:HIS253 4.0 13.1 1.0 CG A:ASP230 4.0 14.8 1.0 C2 A:MYR401 4.1 45.6 1.0 OE1 A:GLU73 4.1 14.7 1.0 CA A:SER59 4.2 15.5 1.0 CG A:HIS253 4.2 13.3 1.0 NE2 A:HIS74 4.4 12.2 1.0 O A:HIS58 4.5 16.6 1.0 O A:HOH2207 4.5 37.9 1.0 CB A:GLU73 4.7 13.8 1.0 N A:SER59 4.7 16.0 1.0 OG1 A:THR179 4.8 17.2 0.5 C A:HIS58 4.9 17.0 1.0 CB A:SER59 4.9 15.3 1.0

Zinc binding site 3 out of 7 in the Structure of Lpxc From Aquifex Aeolicus in Complex with Udp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Lpxc From Aquifex Aeolicus in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:23.0 occ:1.00 O A:HOH2239 2.0 20.1 1.0 NE2 A:HIS188 2.1 23.4 1.0 NE2 A:HIS58 2.2 20.8 1.0 CL A:CL305 2.2 23.2 1.0 CD2 A:HIS58 3.0 20.4 1.0 CD2 A:HIS188 3.1 22.4 1.0 CE1 A:HIS188 3.1 21.8 1.0 CE1 A:HIS58 3.3 21.4 1.0 CG A:HIS58 4.2 19.8 1.0 ND1 A:HIS188 4.2 22.2 1.0 CG A:HIS188 4.2 22.0 1.0 ND1 A:HIS58 4.3 20.4 1.0 CB A:ASN57 4.5 21.0 1.0 CG2 A:VAL192 4.5 17.4 1.0 ND2 A:ASN57 4.7 27.6 1.0 CG1 A:VAL192 4.7 16.2 1.0 O A:HOH2174 4.8 46.3 1.0 CG A:ASN57 4.9 24.4 1.0

Zinc binding site 4 out of 7 in the Structure of Lpxc From Aquifex Aeolicus in Complex with Udp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Lpxc From Aquifex Aeolicus in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:19.8 occ:1.00 OE1 A:GLU120 2.0 19.6 1.0 N A:GLY2 2.3 13.6 1.0 CD A:GLU120 2.7 20.4 1.0 OE2 A:GLU120 2.7 22.6 1.0 CA A:GLY2 3.0 13.5 1.0 C A:GLY2 3.4 13.7 1.0 O A:GLY2 3.4 13.4 1.0 CG A:GLU120 4.2 19.0 1.0 N A:LEU3 4.2 13.8 1.0 O A:HOH2117 4.7 28.4 1.0 CD2 A:LEU3 4.7 14.2 1.0 CB A:GLU120 4.8 19.3 1.0

Zinc binding site 5 out of 7 in the Structure of Lpxc From Aquifex Aeolicus in Complex with Udp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Lpxc From Aquifex Aeolicus in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:13.1 occ:1.00 OD1 B:ASP230 2.0 13.2 1.0 NE2 B:HIS74 2.0 9.8 1.0 NE2 B:HIS226 2.0 12.0 1.0 O B:HOH2238 2.2 24.3 1.0 CG B:ASP230 2.9 14.6 1.0 CE1 B:HIS226 3.0 12.9 1.0 CE1 B:HIS74 3.0 11.6 1.0 CD2 B:HIS74 3.0 10.3 1.0 CD2 B:HIS226 3.0 12.0 1.0 OD2 B:ASP230 3.1 16.2 1.0 ZN B:ZN302 3.4 25.0 1.0 ND1 B:HIS226 4.1 12.5 1.0 O B:HOH2171 4.1 43.4 1.0 ND1 B:HIS74 4.1 13.7 1.0 CG B:GLU73 4.1 14.1 1.0 CG B:HIS226 4.1 12.0 1.0 CG B:HIS74 4.2 11.8 1.0 OG1 B:THR179 4.2 23.3 1.0 CB B:THR179 4.3 19.9 1.0 CB B:ASP230 4.3 12.4 1.0 OE2 B:GLU73 4.5 17.8 1.0 O B:HOH2170 4.5 29.5 1.0 NE2 B:HIS253 4.7 12.9 1.0 CE1 B:HIS253 4.8 14.1 1.0 CA B:ASP230 4.8 12.7 1.0 CA B:THR179 4.8 19.2 1.0 CD B:GLU73 4.9 15.9 1.0 O B:HIS226 4.9 12.7 1.0 O B:HOH2239 5.0 31.7 1.0

Zinc binding site 6 out of 7 in the Structure of Lpxc From Aquifex Aeolicus in Complex with Udp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Lpxc From Aquifex Aeolicus in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:25.0 occ:1.00 NE2 B:HIS253 2.1 12.9 1.0 OE2 B:GLU73 2.2 17.8 1.0 O B:HOH2239 2.3 31.7 1.0 O B:HOH2238 2.5 24.3 1.0 CE1 B:HIS253 3.0 14.1 1.0 CD2 B:HIS253 3.1 14.4 1.0 CD B:GLU73 3.1 15.9 1.0 ZN B:ZN301 3.4 13.1 1.0 CG B:GLU73 3.5 14.1 1.0 O B:HOH2171 3.7 43.4 1.0 OD2 B:ASP230 3.8 16.2 1.0 OD1 B:ASP230 3.9 13.2 1.0 O B:HOH2024 4.0 42.4 1.0 CG B:ASP230 4.1 14.6 1.0 ND1 B:HIS253 4.2 13.0 1.0 OE1 B:GLU73 4.2 13.7 1.0 CA B:SER59 4.2 16.5 1.0 CG B:HIS253 4.2 14.8 1.0 NE2 B:HIS74 4.4 9.8 1.0 O B:HIS58 4.4 17.0 1.0 N B:SER59 4.8 16.6 1.0 CB B:GLU73 4.8 13.2 1.0 C B:HIS58 4.8 17.4 1.0 CB B:SER59 4.9 16.7 1.0

Zinc binding site 7 out of 7 in the Structure of Lpxc From Aquifex Aeolicus in Complex with Udp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Lpxc From Aquifex Aeolicus in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:23.1 occ:1.00 O B:HOH2240 2.0 19.6 1.0 NE2 B:HIS58 2.1 19.5 1.0 NE2 B:HIS188 2.1 22.9 1.0 CL B:CL304 2.3 26.7 1.0 CE1 B:HIS58 3.0 19.4 1.0 CD2 B:HIS188 3.1 21.7 1.0 CD2 B:HIS58 3.1 17.9 1.0 CE1 B:HIS188 3.1 22.0 1.0 ND1 B:HIS58 4.2 19.7 1.0 ND1 B:HIS188 4.2 22.4 1.0 CG B:HIS58 4.2 19.6 1.0 CG B:HIS188 4.2 21.7 1.0 CG2 B:VAL192 4.5 17.2 1.0 CB B:ASN57 4.6 20.2 1.0 CG1 B:VAL192 4.7 18.0 1.0 O B:HOH2177 4.9 43.5 1.0

L.Buetow, A.Dawson, W.N.Hunter. The Nucleotide-Binding Site of Aquifex Aeolicus Lpxc. Acta Crystallogr.,Sect.F V. 62 1082 2006.
ISSN: ESSN 1744-3091
PubMed: 17077484
DOI: 10.1107/S1744309106041893