Zinc in PDB 3hk5: Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate

The structure of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate, PDB code: 3hk5 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)	24.94 / 2.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	149.347, 149.347, 254.158, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 23.8

The structure of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Arabinarate 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-Arabinarate (pdb code 3hk5). 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-Arabinarate, PDB code: 3hk5:
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-Arabinarate


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-Arabinarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn430 b:31.2 occ:1.00 OD1 A:ASP355 2.0 30.2 1.0 NE2 A:HIS28 2.0 25.9 1.0 O2 A:RAT428 2.1 28.1 1.0 NE2 A:HIS26 2.2 28.9 1.0 O1B A:RAT428 2.3 27.0 1.0 CG A:ASP355 2.9 30.6 1.0 CE1 A:HIS28 2.9 26.6 1.0 CE1 A:HIS26 3.0 28.7 1.0 C1 A:RAT428 3.0 30.7 1.0 C2 A:RAT428 3.0 32.8 1.0 CD2 A:HIS28 3.1 28.2 1.0 OD2 A:ASP355 3.2 32.5 1.0 CD2 A:HIS26 3.2 27.9 1.0 O3 A:RAT428 3.3 36.9 1.0 C3 A:RAT428 3.8 34.0 1.0 ND1 A:HIS28 4.1 27.3 1.0 O5B A:RAT428 4.1 38.4 1.0 ND1 A:HIS26 4.1 31.4 1.0 CG A:HIS28 4.2 29.4 1.0 NH2 A:ARG170 4.2 32.4 1.0 NE1 A:TRP325 4.2 27.0 1.0 CE A:MET258 4.3 28.9 1.0 O1A A:RAT428 4.3 33.2 1.0 CG A:HIS26 4.3 29.1 1.0 CB A:ASP355 4.3 27.9 1.0 C5 A:RAT428 4.5 36.9 1.0 SD A:MET258 4.7 28.0 1.0 CA A:ASP355 4.7 26.4 1.0 C4 A:RAT428 4.8 34.8 1.0 CD1 A:TRP325 5.0 29.1 1.0

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


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-Arabinarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn431 b:25.9 occ:0.33 O A:HOH596 2.2 35.2 1.0 O A:HOH595 2.3 23.8 1.0 OE2 A:GLU332 3.8 27.3 1.0 O A:HOH450 4.1 20.2 1.0 OE2 A:GLU336 4.3 27.6 1.0 CD A:GLU332 4.9 32.0 1.0 CB A:GLU336 4.9 28.2 1.0

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


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-Arabinarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn430 b:36.8 occ:1.00 OD1 B:ASP355 2.0 30.6 1.0 NE2 B:HIS28 2.0 39.0 1.0 O2 B:RAT428 2.2 33.2 1.0 NE2 B:HIS26 2.2 39.3 1.0 O1B B:RAT428 2.2 34.5 1.0 CG B:ASP355 2.9 32.5 1.0 CE1 B:HIS28 3.0 38.1 1.0 C1 B:RAT428 3.0 34.4 1.0 CE1 B:HIS26 3.0 39.6 1.0 C2 B:RAT428 3.0 36.5 1.0 CD2 B:HIS28 3.1 38.0 1.0 OD2 B:ASP355 3.2 33.3 1.0 CD2 B:HIS26 3.2 38.3 1.0 O3 B:RAT428 3.3 39.5 1.0 C3 B:RAT428 3.8 37.1 1.0 O5B B:RAT428 4.1 33.9 1.0 ND1 B:HIS28 4.1 37.0 1.0 CG B:HIS28 4.2 37.6 1.0 ND1 B:HIS26 4.2 39.0 1.0 NE1 B:TRP325 4.2 34.1 1.0 NH2 B:ARG170 4.2 35.1 1.0 O1A B:RAT428 4.2 36.6 1.0 CB B:ASP355 4.3 32.8 1.0 CE B:MET258 4.3 30.1 1.0 CG B:HIS26 4.3 38.3 1.0 C5 B:RAT428 4.5 36.8 1.0 CA B:ASP355 4.7 34.5 1.0 SD B:MET258 4.7 30.2 1.0 C4 B:RAT428 4.7 37.2 1.0 CD1 B:TRP325 4.9 34.9 1.0

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


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-Arabinarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn431 b:25.9 occ:0.33 O B:HOH526 2.2 23.3 1.0 O B:HOH527 2.2 30.7 1.0 OE2 B:GLU332 3.7 37.1 1.0 O B:HOH463 4.0 31.9 1.0 OE2 B:GLU336 4.3 35.9 1.0 CD B:GLU332 4.9 39.3 1.0 CB B:GLU336 4.9 33.7 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