Zinc in PDB 2ier: Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate, PDB code: 2ier was solved by H.A.Gennadios, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	101.206, 101.206, 122.240, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 24.1

The binding sites of Zinc atom in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate (pdb code 2ier). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate, PDB code: 2ier:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate


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 Uridine 5'- Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:26.7 occ:1.00 NE2 A:HIS238 2.1 20.5 1.0 NE2 A:HIS79 2.2 14.5 1.0 OD1 A:ASP242 2.2 22.1 1.0 O A:HOH802 2.5 22.4 1.0 OD2 A:ASP242 2.8 21.8 1.0 CG A:ASP242 2.8 19.9 1.0 CE1 A:HIS238 3.0 19.1 1.0 ZN A:ZN606 3.1 26.1 0.5 CE1 A:HIS79 3.1 14.8 1.0 CD2 A:HIS79 3.2 14.3 1.0 CD2 A:HIS238 3.2 18.1 1.0 CG2 A:THR191 3.9 15.2 1.0 ND1 A:HIS238 4.1 19.2 1.0 O A:HOH835 4.1 35.1 1.0 CG A:GLU78 4.2 21.5 1.0 CG A:HIS238 4.2 19.0 1.0 ND1 A:HIS79 4.3 15.8 1.0 CB A:ASP242 4.3 17.6 1.0 CG A:HIS79 4.3 15.8 1.0 NE2 A:HIS265 4.5 18.0 1.0 OE2 A:GLU78 4.5 21.9 1.0 CB A:THR191 4.5 16.8 1.0 O A:HOH830 4.5 30.6 1.0 CE1 A:HIS265 4.6 18.3 1.0 CD A:GLU78 4.9 22.0 1.0 CA A:ASP242 4.9 14.8 1.0 CA A:THR191 4.9 15.6 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate


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 Uridine 5'- Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:21.5 occ:0.50 NE2 A:HIS58 2.1 25.5 1.0 NE2 A:HIS200 2.4 34.4 1.0 CD2 A:HIS58 3.0 25.2 1.0 CE1 A:HIS58 3.1 26.0 1.0 CE1 A:HIS200 3.4 33.4 1.0 CD2 A:HIS200 3.4 34.2 1.0 CG A:HIS58 4.2 25.3 1.0 ND1 A:HIS58 4.2 25.9 1.0 CB A:ASN57 4.5 30.7 1.0 ND1 A:HIS200 4.5 33.1 1.0 CG A:HIS200 4.5 31.8 1.0 CG2 A:VAL204 4.6 22.8 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate


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 Uridine 5'- Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:27.4 occ:1.00 NE2 B:HIS29 2.0 31.0 1.0 OE1 A:GLU126 2.1 24.5 1.0 OE1 B:GLU95 2.3 27.0 1.0 N A:GLY2 2.3 19.7 1.0 OE2 A:GLU126 2.5 26.7 1.0 CE1 B:HIS29 2.6 27.1 1.0 CD A:GLU126 2.7 24.7 1.0 OE2 B:GLU95 2.7 22.9 1.0 CD B:GLU95 2.7 24.0 1.0 CA A:GLY2 3.0 19.2 1.0 C A:GLY2 3.3 20.0 1.0 CD2 B:HIS29 3.3 31.0 1.0 O A:GLY2 3.4 19.2 1.0 CG2 B:ILE27 3.5 24.1 1.0 ND1 B:HIS29 3.9 26.6 1.0 CB B:ILE27 3.9 24.2 1.0 CG B:GLU95 4.1 24.2 1.0 N A:LEU3 4.1 21.1 1.0 CG A:GLU126 4.2 24.6 1.0 CG B:HIS29 4.2 28.7 1.0 CG1 B:ILE27 4.4 23.5 1.0 CB B:GLU95 4.5 22.2 1.0 CD B:LYS10 4.8 42.3 1.0 CB A:GLU126 4.9 23.6 1.0 O A:HOH833 4.9 26.1 1.0 CD2 A:LEU3 4.9 22.4 1.0 CD1 B:ILE27 5.0 23.2 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate


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 Uridine 5'- Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:26.1 occ:0.50 O A:HOH830 2.1 30.6 1.0 O A:HOH802 2.3 22.4 1.0 NE2 A:HIS265 2.4 18.0 1.0 OE2 A:GLU78 2.5 21.9 1.0 ZN A:ZN601 3.1 26.7 1.0 CE1 A:HIS265 3.3 18.3 1.0 CD2 A:HIS265 3.4 14.3 1.0 CD A:GLU78 3.5 22.0 1.0 O A:HOH835 3.8 35.1 1.0 O A:HIS58 3.8 19.3 1.0 CG A:GLU78 3.9 21.5 1.0 OD2 A:ASP242 3.9 21.8 1.0 OD1 A:ASP242 3.9 22.1 1.0 CA A:SER59 3.9 19.0 1.0 CG A:ASP242 4.2 19.9 1.0 C A:HIS58 4.2 20.6 1.0 N A:SER59 4.3 19.8 1.0 NE2 A:HIS79 4.4 14.5 1.0 ND1 A:HIS265 4.5 17.4 1.0 CG A:HIS265 4.5 16.4 1.0 CB A:SER59 4.6 19.0 1.0 OE1 A:GLU78 4.6 23.4 1.0 O2B A:UDP801 4.8 44.0 1.0 NE2 A:HIS238 4.9 20.5 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate


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 Uridine 5'- Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn608 b:29.1 occ:0.40 O2B A:UDP801 2.3 44.0 1.0 CF A:PLM701 2.3 10.8 0.6 ND1 A:HIS58 2.5 25.9 1.0 CE A:PLM701 2.8 10.6 0.6 O5' A:UDP801 3.1 45.8 1.0 CG A:PLM701 3.1 12.2 0.6 CE1 A:HIS58 3.4 26.0 1.0 PB A:UDP801 3.5 45.4 1.0 O3A A:UDP801 3.5 46.0 1.0 CG A:HIS58 3.5 25.3 1.0 CA A:HIS58 3.6 21.9 1.0 C5' A:UDP801 3.7 44.7 1.0 CB A:HIS58 3.8 22.9 1.0 PA A:UDP801 4.0 44.9 1.0 CD A:PLM701 4.2 11.5 0.6 O1B A:UDP801 4.2 47.2 1.0 O A:HOH830 4.2 30.6 1.0 N A:HIS58 4.3 22.8 1.0 NE2 A:HIS58 4.6 25.5 1.0 CD2 A:HIS58 4.6 25.2 1.0 O3B A:UDP801 4.7 44.2 1.0 C A:HIS58 4.7 20.6 1.0 O2A A:UDP801 4.8 46.9 1.0 O A:HIS58 4.9 19.3 1.0 C4' A:UDP801 4.9 43.0 1.0 OE1 A:GLU197 5.0 47.5 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate


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 Complexed with Uridine 5'- Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:27.6 occ:1.00 O B:HOH808 1.9 20.9 1.0 OD1 B:ASP242 2.1 16.9 1.0 NE2 B:HIS79 2.1 13.2 1.0 NE2 B:HIS238 2.1 21.1 1.0 CG B:ASP242 2.8 15.9 1.0 OD2 B:ASP242 2.8 14.3 1.0 CE1 B:HIS238 3.0 18.6 1.0 CD2 B:HIS79 3.1 13.2 1.0 CE1 B:HIS79 3.1 12.3 1.0 CD2 B:HIS238 3.2 18.3 1.0 ZN B:ZN607 3.4 36.8 0.4 CG2 B:THR191 4.0 16.7 1.0 CG B:GLU78 4.1 21.1 1.0 ND1 B:HIS238 4.1 19.1 1.0 CB B:ASP242 4.2 14.8 1.0 CG B:HIS238 4.2 18.8 1.0 ND1 B:HIS79 4.2 14.1 1.0 CG B:HIS79 4.2 15.5 1.0 OE2 B:GLU78 4.4 20.9 1.0 NE2 B:HIS265 4.4 20.1 1.0 CB B:THR191 4.6 15.9 1.0 CE1 B:HIS265 4.6 19.2 1.0 CD B:GLU78 4.8 21.9 1.0 CA B:ASP242 4.8 14.6 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate


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 Complexed with Uridine 5'- Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:39.1 occ:0.50 NE2 B:HIS200 2.4 35.2 1.0 NE2 B:HIS58 2.4 24.6 1.0 CE1 B:HIS200 3.3 35.4 1.0 CD2 B:HIS58 3.3 24.8 1.0 CE1 B:HIS58 3.3 24.4 1.0 CD2 B:HIS200 3.4 35.4 1.0 ND1 B:HIS58 4.4 24.6 1.0 CG B:HIS58 4.4 24.4 1.0 ND1 B:HIS200 4.4 34.8 1.0 CG B:HIS200 4.6 33.9 1.0 CB B:ASN57 4.6 30.6 1.0 CG2 B:VAL204 4.7 20.1 1.0 CG1 B:VAL204 5.0 19.3 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn607 b:36.8 occ:0.40 O B:HOH808 1.8 20.9 1.0 OE2 B:GLU78 2.0 20.9 1.0 NE2 B:HIS265 2.4 20.1 1.0 CD B:GLU78 3.1 21.9 1.0 CE1 B:HIS265 3.3 19.2 1.0 CD2 B:HIS265 3.3 17.3 1.0 ZN B:ZN602 3.4 27.6 1.0 CG B:GLU78 3.6 21.1 1.0 CA B:SER59 3.6 20.7 1.0 O B:HIS58 3.7 21.6 1.0 N B:SER59 4.1 20.1 1.0 C B:HIS58 4.1 21.4 1.0 OD1 B:ASP242 4.1 16.9 1.0 CB B:SER59 4.2 20.8 1.0 OE1 B:GLU78 4.2 23.3 1.0 OD2 B:ASP242 4.3 14.3 1.0 ND1 B:HIS265 4.4 16.8 1.0 CG B:ASP242 4.4 15.9 1.0 CG B:HIS265 4.4 17.3 1.0 NE2 B:HIS79 4.4 13.2 1.0 O2B B:UDP802 4.5 50.9 1.0 C B:SER59 4.6 20.4 1.0 CB B:GLU78 4.8 18.1 1.0 N B:THR60 4.8 19.8 1.0 CG2 B:THR76 4.9 15.6 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Uridine 5'- Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn609 b:27.4 occ:0.50 O2B B:UDP802 2.4 50.9 1.0 CG B:PLM702 2.5 14.8 0.7 ND1 B:HIS58 2.5 24.6 1.0 CF B:PLM702 2.7 14.6 0.7 O3A B:UDP802 2.7 52.1 1.0 O5' B:UDP802 3.1 53.3 1.0 PB B:UDP802 3.2 51.3 1.0 CA B:HIS58 3.4 21.8 1.0 CG B:HIS58 3.5 24.4 1.0 CE1 B:HIS58 3.5 24.4 1.0 PA B:UDP802 3.6 50.4 1.0 CB B:HIS58 3.7 22.3 1.0 C5' B:UDP802 3.8 51.6 1.0 N B:HIS58 4.0 23.2 1.0 O1B B:UDP802 4.0 51.7 1.0 CE B:PLM702 4.1 14.3 0.7 O3B B:UDP802 4.4 48.5 1.0 C B:HIS58 4.4 21.4 1.0 O2A B:UDP802 4.5 52.8 1.0 O1A B:UDP802 4.6 51.6 1.0 NE2 B:HIS58 4.6 24.6 1.0 CD2 B:HIS58 4.6 24.8 1.0 O B:HIS58 4.7 21.6 1.0

H.A.Gennadios, D.W.Christianson. Binding of Uridine 5-Diphosphate in the Basic Patch of the Zinc Metalloenzyme Deacetylase Lpxc and Implications For Substrate Binding Biochemistry V. 45 15216 2006.
ISSN: ISSN 0006-2960
PubMed: 17176043
DOI: 10.1021/BI0619021