Zinc 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:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc 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 Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Uronate Isomerase From Bacillus Halodurans Complexed with Zinc and D-Glucuronate, PDB code: 3hk9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 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 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-Glucuronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn431 b:27.5 occ:1.00 O5 A:REL428 1.9 29.4 1.0 NE2 A:HIS28 2.2 26.6 1.0 NE2 A:HIS26 2.2 23.4 1.0 OD1 A:ASP355 2.2 28.2 1.0 O6B A:REL428 2.3 29.8 1.0 C5 A:REL428 2.9 31.6 1.0 C6 A:REL428 2.9 31.5 1.0 CG A:ASP355 3.0 29.4 1.0 CE1 A:HIS26 3.1 24.1 1.0 CD2 A:HIS28 3.1 26.2 1.0 CE1 A:HIS28 3.1 28.1 1.0 OD2 A:ASP355 3.2 29.4 1.0 CD2 A:HIS26 3.2 22.0 1.0 C4 A:REL428 3.5 32.6 1.0 C2 A:REL428 3.8 31.7 1.0 NE1 A:TRP325 4.0 21.5 1.0 O6A A:REL428 4.2 30.0 1.0 ND1 A:HIS28 4.2 25.7 1.0 ND1 A:HIS26 4.2 21.6 1.0 CE A:MET258 4.2 28.0 1.0 CG A:HIS28 4.2 26.4 1.0 C3 A:REL428 4.3 32.2 1.0 CG A:HIS26 4.3 22.9 1.0 CB A:ASP355 4.4 27.9 1.0 O2 A:REL428 4.5 32.9 1.0 O4 A:REL428 4.7 31.8 1.0 C1 A:REL428 4.7 32.4 1.0 O1 A:REL428 4.8 29.0 1.0 CD1 A:TRP325 4.8 21.8 1.0 CA A:ASP355 4.8 26.2 1.0 NH1 A:ARG170 5.0 23.7 1.0

Zinc binding site 2 out of 12 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 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-Glucuronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn429 b:36.5 occ:1.00 O5 B:REL428 2.0 29.4 1.0 NE2 B:HIS26 2.2 26.5 1.0 NE2 B:HIS28 2.3 31.7 1.0 OD1 B:ASP355 2.3 29.5 1.0 O6B B:REL428 2.6 30.2 1.0 C5 B:REL428 2.9 32.6 1.0 CE1 B:HIS26 3.0 24.8 1.0 CG B:ASP355 3.0 27.8 1.0 CD2 B:HIS28 3.1 30.6 1.0 C6 B:REL428 3.1 31.8 1.0 OD2 B:ASP355 3.2 30.2 1.0 CD2 B:HIS26 3.2 25.9 1.0 CE1 B:HIS28 3.3 33.6 1.0 C4 B:REL428 3.5 32.6 1.0 C2 B:REL428 3.9 34.2 1.0 ND1 B:HIS26 4.1 26.6 1.0 NE1 B:TRP325 4.2 22.5 1.0 CG B:HIS26 4.2 27.1 1.0 CG B:HIS28 4.3 30.6 1.0 C3 B:REL428 4.3 33.5 1.0 ND1 B:HIS28 4.3 30.1 1.0 O6A B:REL428 4.3 31.6 1.0 CE B:MET258 4.4 23.9 1.0 CB B:ASP355 4.4 25.8 1.0 O4 B:REL428 4.7 31.9 1.0 O2 B:REL428 4.7 35.0 1.0 C1 B:REL428 4.8 34.6 1.0 CA B:ASP355 4.8 25.0 1.0 CD1 B:TRP325 4.9 20.2 1.0 O1 B:REL428 4.9 34.4 1.0 NH1 B:ARG170 4.9 33.1 1.0

Zinc binding site 3 out of 12 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 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-Glucuronate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn430 b:26.7 occ:1.00 OD1 C:ASP355 2.1 22.5 1.0 NE2 C:HIS28 2.1 25.5 1.0 O5 C:REL428 2.2 30.1 1.0 NE2 C:HIS26 2.2 24.1 1.0 O6B C:REL428 2.4 26.4 1.0 CD2 C:HIS28 2.9 23.7 1.0 CE1 C:HIS26 3.0 25.5 1.0 CG C:ASP355 3.0 24.7 1.0 C5 C:REL428 3.0 30.7 1.0 C6 C:REL428 3.1 29.6 1.0 CE1 C:HIS28 3.2 24.9 1.0 OD2 C:ASP355 3.2 22.9 1.0 CD2 C:HIS26 3.3 25.2 1.0 C4 C:REL428 3.6 30.7 1.0 C2 C:REL428 3.8 29.6 1.0 CG C:HIS28 4.1 26.0 1.0 ND1 C:HIS26 4.1 25.5 1.0 ND1 C:HIS28 4.2 23.1 1.0 NE1 C:TRP325 4.2 19.6 1.0 C3 C:REL428 4.3 29.7 1.0 CG C:HIS26 4.3 25.4 1.0 O6A C:REL428 4.4 28.1 1.0 CB C:ASP355 4.4 22.1 1.0 O2 C:REL428 4.4 26.6 1.0 CE C:MET258 4.5 29.1 1.0 C1 C:REL428 4.6 29.5 1.0 O1 C:REL428 4.7 28.5 1.0 O4 C:REL428 4.8 29.1 1.0 CA C:ASP355 4.8 21.1 1.0 NH1 C:ARG170 4.9 24.9 1.0 CD1 C:TRP325 4.9 19.8 1.0

Zinc binding site 4 out of 12 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 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-Glucuronate within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn431 b:21.7 occ:1.00 O5 D:REL428 2.1 27.0 1.0 OD1 D:ASP355 2.1 21.9 1.0 NE2 D:HIS26 2.2 21.0 1.0 NE2 D:HIS28 2.2 23.5 1.0 O6B D:REL428 2.4 25.5 1.0 C5 D:REL428 2.9 27.6 1.0 CE1 D:HIS26 3.0 22.0 1.0 CG D:ASP355 3.0 24.6 1.0 C6 D:REL428 3.0 27.7 1.0 CD2 D:HIS28 3.1 21.1 1.0 CE1 D:HIS28 3.2 24.1 1.0 CD2 D:HIS26 3.2 20.5 1.0 OD2 D:ASP355 3.3 23.4 1.0 C4 D:REL428 3.5 28.2 1.0 C2 D:REL428 3.7 27.2 1.0 NE1 D:TRP325 4.1 17.6 1.0 ND1 D:HIS26 4.1 18.3 1.0 C3 D:REL428 4.3 27.5 1.0 CE D:MET258 4.3 26.4 1.0 ND1 D:HIS28 4.3 20.8 1.0 CG D:HIS26 4.3 21.1 1.0 CG D:HIS28 4.3 22.0 1.0 O6A D:REL428 4.3 26.6 1.0 O2 D:REL428 4.3 27.3 1.0 CB D:ASP355 4.4 23.1 1.0 O1 D:REL428 4.6 28.3 1.0 C1 D:REL428 4.7 29.0 1.0 O4 D:REL428 4.7 26.8 1.0 CA D:ASP355 4.8 22.8 1.0 CD1 D:TRP325 4.9 18.3 1.0 NH1 D:ARG170 5.0 23.3 1.0

Zinc binding site 5 out of 12 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 Zinc with other atoms in the Zn binding site number 5 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 E:Zn429 b:27.1 occ:1.00 O5 E:REL428 2.0 27.1 1.0 NE2 E:HIS26 2.1 21.9 1.0 NE2 E:HIS28 2.2 28.2 1.0 OD1 E:ASP355 2.2 27.0 1.0 O6B E:REL428 2.5 27.9 1.0 C5 E:REL428 2.9 30.9 1.0 CE1 E:HIS26 3.0 22.1 1.0 CD2 E:HIS28 3.0 27.1 1.0 C6 E:REL428 3.0 30.2 1.0 CG E:ASP355 3.1 25.5 1.0 CD2 E:HIS26 3.2 25.4 1.0 CE1 E:HIS28 3.2 30.0 1.0 OD2 E:ASP355 3.2 26.6 1.0 C4 E:REL428 3.5 31.2 1.0 C2 E:REL428 3.9 32.6 1.0 ND1 E:HIS26 4.1 23.1 1.0 NE1 E:TRP325 4.2 23.6 1.0 CG E:HIS28 4.2 27.2 1.0 O6A E:REL428 4.2 30.0 1.0 CG E:HIS26 4.3 25.3 1.0 ND1 E:HIS28 4.3 27.8 1.0 C3 E:REL428 4.3 31.9 1.0 CB E:ASP355 4.4 24.6 1.0 CE E:MET258 4.5 26.9 1.0 O1 E:REL428 4.5 34.2 1.0 C1 E:REL428 4.6 34.2 1.0 O4 E:REL428 4.7 31.1 1.0 O2 E:REL428 4.7 30.4 1.0 NH1 E:ARG170 4.8 29.5 1.0 CA E:ASP355 4.8 24.0 1.0 CD1 E:TRP325 4.9 21.7 1.0

Zinc binding site 6 out of 12 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 Zinc with other atoms in the Zn binding site number 6 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:Zn430 b:30.1 occ:1.00 OD1 F:ASP355 2.0 19.6 1.0 O5 F:REL428 2.0 26.9 1.0 NE2 F:HIS28 2.1 24.2 1.0 NE2 F:HIS26 2.1 25.8 1.0 O6B F:REL428 2.4 25.0 1.0 CG F:ASP355 2.9 25.2 1.0 CD2 F:HIS28 2.9 24.3 1.0 C5 F:REL428 2.9 28.7 1.0 CE1 F:HIS26 3.0 28.6 1.0 C6 F:REL428 3.0 28.5 1.0 OD2 F:ASP355 3.1 23.9 1.0 CE1 F:HIS28 3.2 25.0 1.0 CD2 F:HIS26 3.2 27.4 1.0 C4 F:REL428 3.6 29.6 1.0 C2 F:REL428 3.8 31.1 1.0 NE1 F:TRP325 4.1 19.2 1.0 CG F:HIS28 4.1 26.4 1.0 ND1 F:HIS26 4.1 29.5 1.0 ND1 F:HIS28 4.2 22.7 1.0 O6A F:REL428 4.2 28.0 1.0 CG F:HIS26 4.3 28.0 1.0 CB F:ASP355 4.3 22.6 1.0 CE F:MET258 4.3 30.2 1.0 C3 F:REL428 4.3 30.1 1.0 O2 F:REL428 4.4 30.9 1.0 CA F:ASP355 4.7 22.9 1.0 O4 F:REL428 4.8 28.1 1.0 C1 F:REL428 4.8 31.8 1.0 O1 F:REL428 4.8 31.2 1.0 CD1 F:TRP325 4.8 19.1 1.0 NH1 F:ARG170 4.9 26.7 1.0

Zinc binding site 7 out of 12 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 Zinc with other atoms in the Zn binding site number 7 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 G:Zn430 b:27.0 occ:1.00 O5 G:REL428 2.0 25.7 1.0 OD1 G:ASP355 2.1 27.0 1.0 NE2 G:HIS26 2.1 25.8 1.0 NE2 G:HIS28 2.2 25.2 1.0 O6B G:REL428 2.5 27.5 1.0 C5 G:REL428 2.9 28.6 1.0 CG G:ASP355 3.0 26.8 1.0 CE1 G:HIS26 3.0 25.1 1.0 C6 G:REL428 3.1 27.9 1.0 CE1 G:HIS28 3.1 25.8 1.0 CD2 G:HIS26 3.2 24.0 1.0 CD2 G:HIS28 3.2 26.1 1.0 OD2 G:ASP355 3.2 27.2 1.0 C4 G:REL428 3.5 28.6 1.0 C2 G:REL428 3.8 28.8 1.0 NE1 G:TRP325 4.2 22.4 1.0 ND1 G:HIS26 4.2 23.4 1.0 ND1 G:HIS28 4.2 25.1 1.0 CG G:HIS26 4.3 24.0 1.0 CG G:HIS28 4.3 27.1 1.0 O6A G:REL428 4.3 26.9 1.0 C3 G:REL428 4.3 29.1 1.0 CE G:MET258 4.4 32.4 1.0 CB G:ASP355 4.4 25.6 1.0 O2 G:REL428 4.5 28.1 1.0 C1 G:REL428 4.7 29.1 1.0 O4 G:REL428 4.7 27.5 1.0 O1 G:REL428 4.8 26.8 1.0 NH1 G:ARG170 4.8 25.4 1.0 CA G:ASP355 4.9 24.0 1.0 CD1 G:TRP325 4.9 19.6 1.0

Zinc binding site 8 out of 12 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 Zinc with other atoms in the Zn binding site number 8 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:Zn430 b:33.8 occ:1.00 NE2 H:HIS28 2.0 27.1 1.0 O5 H:REL428 2.1 29.1 1.0 NE2 H:HIS26 2.2 24.8 1.0 OD1 H:ASP355 2.2 26.6 1.0 O6B H:REL428 2.5 25.2 1.0 CE1 H:HIS26 2.9 23.3 1.0 CD2 H:HIS28 3.0 27.2 1.0 C5 H:REL428 3.0 31.6 1.0 CE1 H:HIS28 3.1 27.2 1.0 CG H:ASP355 3.1 25.2 1.0 C6 H:REL428 3.1 29.8 1.0 OD2 H:ASP355 3.3 27.6 1.0 CD2 H:HIS26 3.3 25.1 1.0 C4 H:REL428 3.6 32.4 1.0 C2 H:REL428 3.9 32.9 1.0 ND1 H:HIS26 4.1 25.7 1.0 ND1 H:HIS28 4.1 28.1 1.0 CG H:HIS28 4.1 27.5 1.0 NE1 H:TRP325 4.2 22.3 1.0 CE H:MET258 4.3 26.8 1.0 CG H:HIS26 4.3 24.5 1.0 C3 H:REL428 4.4 33.1 1.0 O6A H:REL428 4.4 28.1 1.0 CB H:ASP355 4.5 24.7 1.0 O2 H:REL428 4.5 32.2 1.0 C1 H:REL428 4.8 33.0 1.0 O1 H:REL428 4.8 29.8 1.0 O4 H:REL428 4.8 31.6 1.0 CA H:ASP355 4.8 24.4 1.0 NH1 H:ARG170 4.9 28.1 1.0 CD1 H:TRP325 4.9 20.7 1.0

Zinc binding site 9 out of 12 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 Zinc with other atoms in the Zn binding site number 9 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 I:Zn430 b:32.4 occ:1.00 O5 I:REL428 2.0 29.1 1.0 OD1 I:ASP355 2.1 32.4 1.0 NE2 I:HIS26 2.2 27.2 1.0 NE2 I:HIS28 2.2 33.0 1.0 O6B I:REL428 2.4 27.6 1.0 C5 I:REL428 2.9 32.7 1.0 CG I:ASP355 3.0 32.3 1.0 CE1 I:HIS26 3.0 28.3 1.0 C6 I:REL428 3.0 31.8 1.0 CD2 I:HIS28 3.0 30.2 1.0 OD2 I:ASP355 3.2 33.7 1.0 CD2 I:HIS26 3.2 28.2 1.0 CE1 I:HIS28 3.3 33.1 1.0 C4 I:REL428 3.5 32.9 1.0 C2 I:REL428 3.9 32.5 1.0 NE1 I:TRP325 4.1 24.8 1.0 ND1 I:HIS26 4.1 27.5 1.0 CG I:HIS28 4.2 29.9 1.0 O6A I:REL428 4.3 29.7 1.0 CG I:HIS26 4.3 28.2 1.0 ND1 I:HIS28 4.3 30.5 1.0 C3 I:REL428 4.3 32.7 1.0 CB I:ASP355 4.4 29.4 1.0 CE I:MET258 4.4 30.6 1.0 O2 I:REL428 4.6 30.2 1.0 O4 I:REL428 4.7 31.5 1.0 C1 I:REL428 4.7 32.2 1.0 O1 I:REL428 4.8 30.9 1.0 CD1 I:TRP325 4.8 25.8 1.0 CA I:ASP355 4.8 27.4 1.0 NH1 I:ARG170 5.0 30.8 1.0

Zinc binding site 10 out of 12 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 Zinc with other atoms in the Zn binding site number 10 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 J:Zn430 b:25.4 occ:1.00 O5 J:REL428 2.0 25.7 1.0 OD1 J:ASP355 2.1 27.2 1.0 NE2 J:HIS28 2.1 23.7 1.0 NE2 J:HIS26 2.2 25.5 1.0 O6B J:REL428 2.4 26.9 1.0 C5 J:REL428 2.9 28.8 1.0 CG J:ASP355 3.0 26.3 1.0 C6 J:REL428 3.0 29.1 1.0 CE1 J:HIS26 3.1 25.3 1.0 CE1 J:HIS28 3.1 24.4 1.0 CD2 J:HIS28 3.1 23.7 1.0 OD2 J:ASP355 3.2 29.0 1.0 CD2 J:HIS26 3.3 24.1 1.0 C4 J:REL428 3.5 30.1 1.0 C2 J:REL428 3.9 30.9 1.0 NE1 J:TRP325 4.1 18.4 1.0 ND1 J:HIS28 4.2 23.8 1.0 CG J:HIS28 4.2 26.0 1.0 ND1 J:HIS26 4.2 24.4 1.0 CE J:MET258 4.3 26.6 1.0 O6A J:REL428 4.3 27.7 1.0 C3 J:REL428 4.3 30.9 1.0 CB J:ASP355 4.4 24.6 1.0 CG J:HIS26 4.4 24.4 1.0 C1 J:REL428 4.6 31.6 1.0 O1 J:REL428 4.6 28.4 1.0 O2 J:REL428 4.7 31.9 1.0 O4 J:REL428 4.7 28.4 1.0 CA J:ASP355 4.8 22.3 1.0 CD1 J:TRP325 4.8 18.5 1.0 NH1 J:ARG170 4.9 23.8 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