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

The structure of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Fructuronate, PDB code: 3hka 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)	24.85 / 1.90
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.596, 132.596, 195.638, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.1

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

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Fructuronate (pdb code 3hka). 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-Fructuronate, PDB code: 3hka:
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-Fructuronate


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-Fructuronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn430 b:26.2 occ:1.00 O2 A:FIX428 2.0 28.9 1.0 OD1 A:ASP355 2.1 26.7 1.0 O1A A:FIX428 2.1 24.5 1.0 NE2 A:HIS26 2.1 19.9 1.0 NE2 A:HIS28 2.1 25.4 1.0 C1 A:FIX428 2.8 26.4 1.0 C2 A:FIX428 2.8 30.3 1.0 CD2 A:HIS28 3.0 25.3 1.0 CE1 A:HIS26 3.0 21.9 1.0 CG A:ASP355 3.0 26.9 1.0 CD2 A:HIS26 3.2 20.1 1.0 CE1 A:HIS28 3.2 27.3 1.0 OD2 A:ASP355 3.3 25.6 1.0 C3 A:FIX428 3.6 32.6 1.0 O5 A:FIX428 3.6 39.9 1.0 O1B A:FIX428 4.1 26.1 1.0 NE1 A:TRP325 4.1 18.4 1.0 ND1 A:HIS26 4.1 22.7 1.0 CG A:HIS28 4.2 26.7 1.0 C5 A:FIX428 4.2 37.7 1.0 ND1 A:HIS28 4.2 26.7 1.0 CG A:HIS26 4.3 19.6 1.0 CE A:MET258 4.3 26.7 1.0 CB A:ASP355 4.4 25.8 1.0 C4 A:FIX428 4.5 34.6 1.0 O3 A:FIX428 4.7 34.1 1.0 CA A:ASP355 4.8 24.1 1.0 NH1 A:ARG170 4.8 23.1 1.0 CD1 A:TRP325 4.9 17.8 1.0 SD A:MET258 4.9 26.8 1.0

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


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-Fructuronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn431 b:31.7 occ:1.00 O2 B:FIX428 2.1 35.2 1.0 NE2 B:HIS28 2.2 27.3 1.0 NE2 B:HIS26 2.2 22.9 1.0 OD1 B:ASP355 2.2 28.3 1.0 O1A B:FIX428 2.3 31.1 1.0 C2 B:FIX428 3.0 34.9 1.0 C1 B:FIX428 3.0 34.8 1.0 CD2 B:HIS28 3.0 24.7 1.0 CG B:ASP355 3.1 28.8 1.0 CE1 B:HIS26 3.1 23.7 1.0 CD2 B:HIS26 3.2 25.2 1.0 CE1 B:HIS28 3.2 26.7 1.0 OD2 B:ASP355 3.3 32.7 1.0 O5 B:FIX428 3.6 42.3 1.0 C3 B:FIX428 3.6 37.3 1.0 NE1 B:TRP325 4.2 23.1 1.0 CG B:HIS28 4.2 26.9 1.0 C5 B:FIX428 4.2 38.9 1.0 ND1 B:HIS26 4.2 22.8 1.0 ND1 B:HIS28 4.2 26.2 1.0 O1B B:FIX428 4.2 34.4 1.0 CG B:HIS26 4.3 23.0 1.0 CE B:MET258 4.3 28.6 1.0 CB B:ASP355 4.4 27.3 1.0 C4 B:FIX428 4.5 37.0 1.0 NH1 B:ARG170 4.7 26.9 1.0 O3 B:FIX428 4.8 40.4 1.0 CA B:ASP355 4.8 26.3 1.0 SD B:MET258 4.8 29.8 1.0 CD1 B:TRP325 4.9 21.5 1.0

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


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-Fructuronate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn429 b:23.1 occ:1.00 O2 C:FIX428 2.0 24.1 1.0 OD2 C:ASP355 2.2 24.4 1.0 NE2 C:HIS26 2.2 14.6 1.0 NE2 C:HIS28 2.2 21.0 1.0 O1A C:FIX428 2.2 20.1 1.0 C2 C:FIX428 2.9 26.0 1.0 C1 C:FIX428 2.9 25.1 1.0 CE1 C:HIS26 3.0 17.6 1.0 CG C:ASP355 3.0 24.8 1.0 CD2 C:HIS28 3.1 20.7 1.0 CE1 C:HIS28 3.2 20.6 1.0 OD1 C:ASP355 3.3 28.9 1.0 CD2 C:HIS26 3.3 15.4 1.0 C3 C:FIX428 3.6 30.1 1.0 O5 C:FIX428 3.6 39.5 1.0 NE1 C:TRP325 4.1 19.1 1.0 ND1 C:HIS26 4.2 16.4 1.0 O1B C:FIX428 4.2 24.3 1.0 CE C:MET258 4.2 18.6 1.0 C5 C:FIX428 4.2 35.5 1.0 CG C:HIS28 4.2 20.1 1.0 ND1 C:HIS28 4.3 21.3 1.0 CG C:HIS26 4.3 16.6 1.0 CB C:ASP355 4.4 23.6 1.0 C4 C:FIX428 4.5 32.5 1.0 O3 C:FIX428 4.7 28.7 1.0 NH1 C:ARG170 4.7 17.8 1.0 CA C:ASP355 4.8 19.5 1.0 CD1 C:TRP325 4.9 19.0 1.0 SD C:MET258 5.0 21.9 1.0

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


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-Fructuronate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn430 b:18.4 occ:0.33 O C:HOH581 2.0 17.1 1.0 O B:HOH583 2.1 24.2 1.0 O B:HOH582 2.1 22.2 1.0 O A:HOH579 2.1 21.2 1.0 O A:HOH468 2.2 19.8 1.0 O C:HOH600 2.2 20.8 1.0 OE2 C:GLU332 3.8 19.6 1.0 OE2 B:GLU332 3.8 23.8 1.0 OE2 A:GLU332 3.9 23.1 1.0 O B:HOH493 4.0 22.0 1.0 O A:HOH492 4.1 21.5 1.0 O C:HOH447 4.1 18.2 1.0 OE2 C:GLU336 4.4 17.1 1.0 OE2 A:GLU336 4.4 20.3 1.0 OE2 B:GLU336 4.5 21.8 1.0 CD C:GLU332 4.9 21.1 1.0 CD B:GLU332 4.9 23.6 1.0 CB C:GLU336 5.0 17.5 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