Chlorine in PDB 3hk9: Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Glucuronate

The structure of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Glucuronate, PDB code: 3hk9 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)	24.95 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	274.091, 156.880, 185.206, 90.00, 115.78, 90.00
R / Rfree (%)	22.7 / 25.8

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

Zinc

(Zn)

12 atoms

The binding sites of Chlorine atom in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Glucuronate (pdb code 3hk9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Glucuronate, PDB code: 3hk9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Glucuronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl432 b:23.0 occ:1.00 NZ C:LYS278 3.0 15.0 1.0 NZ A:LYS278 3.1 20.8 1.0 NZ B:LYS278 3.3 19.1 1.0 CG B:GLU304 3.5 22.2 1.0 CG C:GLU304 3.5 20.7 1.0 CG A:GLU304 3.6 20.3 1.0 CB C:GLU304 3.6 20.3 1.0 CD A:LYS278 3.7 19.0 1.0 CD C:LYS278 3.7 17.3 1.0 CB B:GLU304 3.7 19.9 1.0 CD B:LYS278 3.7 19.5 1.0 CB A:GLU304 3.8 19.6 1.0 CE C:LYS278 3.8 19.4 1.0 CE A:LYS278 3.9 20.1 1.0 CE B:LYS278 3.9 20.6 1.0 O B:HOH774 4.8 24.7 1.0 CD B:GLU304 4.9 23.1 1.0 CA C:GLU304 4.9 20.7 1.0 O B:HOH440 4.9 20.8 1.0 CD C:GLU304 4.9 21.4 1.0 O C:HOH448 4.9 21.7 1.0 O B:HOH1302 5.0 30.3 1.0 O C:GLU304 5.0 20.6 1.0 CA B:GLU304 5.0 20.7 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Glucuronate within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl431 b:20.7 occ:1.00 NZ F:LYS278 3.0 14.5 1.0 NZ D:LYS278 3.1 15.8 1.0 NZ E:LYS278 3.2 17.6 1.0 CG F:GLU304 3.5 18.8 1.0 CG E:GLU304 3.5 19.6 1.0 CG D:GLU304 3.6 19.3 1.0 CB F:GLU304 3.6 20.3 1.0 CD F:LYS278 3.6 17.9 1.0 CB E:GLU304 3.7 18.4 1.0 CB D:GLU304 3.7 16.5 1.0 CD D:LYS278 3.7 14.5 1.0 CD E:LYS278 3.7 21.0 1.0 CE F:LYS278 3.8 18.1 1.0 CE E:LYS278 3.9 20.4 1.0 CE D:LYS278 3.9 16.1 1.0 O E:HOH433 4.8 15.6 1.0 CD E:GLU304 4.9 21.6 1.0 CA F:GLU304 4.9 19.8 1.0 O F:HOH435 4.9 19.1 1.0 CD F:GLU304 4.9 20.6 1.0 O F:HOH1679 4.9 37.7 1.0 O F:GLU304 4.9 19.5 1.0 O E:HOH982 5.0 29.0 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Glucuronate within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl431 b:21.9 occ:1.00 NZ G:LYS278 3.2 19.9 1.0 NZ H:LYS278 3.2 17.8 1.0 NZ I:LYS278 3.3 18.7 1.0 CG H:GLU304 3.5 22.0 1.0 CG G:GLU304 3.6 20.3 1.0 CG I:GLU304 3.6 23.1 1.0 CB G:GLU304 3.7 18.1 1.0 CB I:GLU304 3.7 21.8 1.0 CB H:GLU304 3.7 21.4 1.0 CD I:LYS278 3.8 19.9 1.0 CD G:LYS278 3.8 20.5 1.0 CD H:LYS278 3.8 18.6 1.0 CE G:LYS278 3.9 21.1 1.0 CE H:LYS278 4.0 16.4 1.0 CE I:LYS278 4.0 21.8 1.0 O H:HOH448 4.7 23.1 1.0 O I:HOH457 4.8 23.3 1.0 O I:HOH441 4.9 17.1 1.0 CD H:GLU304 4.9 23.5 1.0 O I:HOH1381 4.9 33.7 1.0 CA G:GLU304 5.0 19.6 1.0 O I:GLU304 5.0 21.0 1.0 CA H:GLU304 5.0 21.1 1.0 CD I:GLU304 5.0 22.8 1.0 CD G:GLU304 5.0 20.5 1.0 O G:GLU304 5.0 19.0 1.0 CA I:GLU304 5.0 21.0 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Glucuronate within 5.0Å range: probe atom residue distance (Å) B Occ K:Cl431 b:21.5 occ:1.00 NZ K:LYS278 3.1 19.6 1.0 NZ J:LYS278 3.1 18.9 1.0 NZ L:LYS278 3.3 18.1 1.0 CG K:GLU304 3.5 19.3 1.0 CG L:GLU304 3.5 21.9 1.0 CG J:GLU304 3.6 19.3 1.0 CB J:GLU304 3.7 17.9 1.0 CB K:GLU304 3.7 18.3 1.0 CB L:GLU304 3.7 20.0 1.0 CD J:LYS278 3.7 18.9 1.0 CD K:LYS278 3.8 18.8 1.0 CD L:LYS278 3.8 16.2 1.0 CE J:LYS278 3.8 19.6 1.0 CE K:LYS278 3.9 17.3 1.0 CE L:LYS278 4.0 19.7 1.0 O L:HOH443 4.7 15.6 1.0 O L:HOH447 4.8 23.3 1.0 O L:HOH993 4.9 27.5 1.0 O K:HOH1179 4.9 27.0 1.0 O J:HOH434 4.9 17.9 1.0 CD L:GLU304 4.9 21.7 1.0 CD K:GLU304 4.9 19.9 1.0 CA K:GLU304 5.0 19.7 1.0 O J:GLU304 5.0 19.1 1.0 CA J:GLU304 5.0 18.7 1.0 CA L:GLU304 5.0 18.6 1.0 CD J:GLU304 5.0 20.3 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