Zinc in PDB 3hk8: Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate

The structure of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate, PDB code: 3hk8 was solved by A.A.Fedorov, E.V.Fedorov, T.T.Nguyen, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.93 / 2.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	149.305, 149.305, 254.018, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 22.6

The structure of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate (pdb code 3hk8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate, PDB code: 3hk8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate


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 Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn430 b:34.2 occ:1.00 OD1 A:ASP355 2.0 31.4 1.0 NE2 A:HIS28 2.0 27.9 1.0 O2 A:HDL428 2.1 37.7 1.0 NE2 A:HIS26 2.2 33.1 1.0 O1A A:HDL428 2.2 34.2 1.0 CG A:ASP355 2.9 32.4 1.0 C1 A:HDL428 3.0 37.6 1.0 CE1 A:HIS28 3.0 29.4 1.0 C2 A:HDL428 3.0 39.5 1.0 CE1 A:HIS26 3.0 31.8 1.0 CD2 A:HIS28 3.1 31.1 1.0 OD2 A:ASP355 3.1 34.0 1.0 CD2 A:HIS26 3.2 31.4 1.0 O3 A:HDL428 3.3 41.8 1.0 C3 A:HDL428 3.8 40.6 1.0 N6 A:HDL428 4.0 46.2 1.0 ND1 A:HIS28 4.1 31.0 1.0 ND1 A:HIS26 4.1 33.5 1.0 NH2 A:ARG170 4.2 36.6 1.0 CG A:HIS28 4.2 32.2 1.0 O1B A:HDL428 4.2 38.8 1.0 CG A:HIS26 4.2 31.7 1.0 NE1 A:TRP325 4.2 32.0 1.0 CB A:ASP355 4.3 31.0 1.0 CE A:MET258 4.6 29.9 1.0 C5 A:HDL428 4.6 44.5 1.0 SD A:MET258 4.6 28.3 1.0 O6 A:HDL428 4.6 49.6 1.0 CA A:ASP355 4.7 28.8 1.0 C4 A:HDL428 4.8 42.5 1.0 CD1 A:TRP325 4.9 32.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate


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 Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn431 b:34.5 occ:0.33 O A:HOH594 2.2 34.9 1.0 O A:HOH593 2.3 25.1 1.0 OE2 A:GLU332 3.8 30.1 1.0 O A:HOH450 4.1 24.4 1.0 OE2 A:GLU336 4.4 33.4 1.0 CB A:GLU336 4.9 29.4 1.0 CD A:GLU332 5.0 34.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate


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 Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn430 b:35.7 occ:1.00 OD1 B:ASP355 2.0 34.2 1.0 NE2 B:HIS28 2.0 36.4 1.0 O2 B:HDL428 2.1 36.9 1.0 NE2 B:HIS26 2.2 35.9 1.0 O1A B:HDL428 2.3 37.8 1.0 CG B:ASP355 2.9 35.3 1.0 CD2 B:HIS28 3.0 34.5 1.0 CE1 B:HIS28 3.0 35.6 1.0 CE1 B:HIS26 3.0 35.5 1.0 C2 B:HDL428 3.1 39.2 1.0 C1 B:HDL428 3.1 37.9 1.0 OD2 B:ASP355 3.1 34.4 1.0 CD2 B:HIS26 3.2 35.5 1.0 O3 B:HDL428 3.4 41.8 1.0 C3 B:HDL428 3.8 40.2 1.0 N6 B:HDL428 3.9 41.5 1.0 ND1 B:HIS28 4.1 34.8 1.0 CG B:HIS28 4.1 36.5 1.0 ND1 B:HIS26 4.2 37.1 1.0 NH2 B:ARG170 4.2 35.7 1.0 NE1 B:TRP325 4.2 33.1 1.0 CB B:ASP355 4.3 35.5 1.0 CG B:HIS26 4.3 36.1 1.0 O1B B:HDL428 4.3 42.1 1.0 C5 B:HDL428 4.5 42.8 1.0 O6 B:HDL428 4.5 50.6 1.0 SD B:MET258 4.6 32.1 1.0 CA B:ASP355 4.7 37.6 1.0 C4 B:HDL428 4.7 40.5 1.0 CD1 B:TRP325 4.9 32.9 1.0 CE B:MET258 5.0 38.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate


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 Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn431 b:33.2 occ:0.33 O B:HOH522 2.2 31.3 1.0 O B:HOH523 2.2 32.0 1.0 OE2 B:GLU332 3.7 39.3 1.0 O B:HOH462 4.0 29.5 1.0 OE2 B:GLU336 4.3 37.7 1.0 CB B:GLU336 4.9 34.0 1.0 CD B:GLU332 4.9 41.7 1.0

T.T.Nguyen, A.A.Fedorov, L.Williams, E.V.Fedorov, Y.Li, C.Xu, S.C.Almo, F.M.Raushel. The Mechanism of the Reaction Catalyzed By Uronate Isomerase Illustrates How An Isomerase May Have Evolved From A Hydrolase Within the Amidohydrolase Superfamily. Biochemistry V. 48 8879 2009.
ISSN: ISSN 0006-2960
PubMed: 19678710
DOI: 10.1021/BI901046X