Chlorine in PDB 3umc: Crystal Structure of the L-2-Haloacid Dehalogenase PA0810

All present enzymatic activity of Crystal Structure of the L-2-Haloacid Dehalogenase PA0810:
3.8.1.2;

The structure of Crystal Structure of the L-2-Haloacid Dehalogenase PA0810, PDB code: 3umc was solved by P.Petit, P.W.Y.Chan, A.Savchenko, A.F.Yakunin, E.A.Edwards, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.38 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	73.424, 123.867, 125.599, 90.00, 90.97, 90.00
R / Rfree (%)	19 / 23.6

The structure of Crystal Structure of the L-2-Haloacid Dehalogenase PA0810 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of the L-2-Haloacid Dehalogenase PA0810 (pdb code 3umc). 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 the L-2-Haloacid Dehalogenase PA0810, PDB code: 3umc:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the L-2-Haloacid Dehalogenase PA0810


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 the L-2-Haloacid Dehalogenase PA0810 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl234 b:37.8 occ:1.00 O A:HOH560 2.6 25.5 1.0 OG A:SER121 2.6 21.2 1.0 N A:PHE9 3.2 12.7 1.0 N A:VAL8 3.3 12.8 1.0 CB A:SER121 3.4 15.3 1.0 OD1 A:ASP7 3.5 20.4 1.0 CA A:SER121 3.6 14.8 1.0 O A:HOH343 3.8 31.1 1.0 CB A:VAL8 3.8 13.0 1.0 CA A:VAL8 3.8 13.1 1.0 CB A:PHE9 3.9 15.6 1.0 CG A:PHE9 3.9 18.1 1.0 C A:VAL8 4.0 13.6 1.0 CD2 A:PHE9 4.0 30.5 1.0 N A:ASN122 4.0 14.8 1.0 CA A:PHE9 4.1 13.9 1.0 CG A:ASP7 4.3 14.6 1.0 CG2 A:VAL8 4.4 13.1 1.0 C A:SER121 4.4 15.0 1.0 C A:ASP7 4.4 12.6 1.0 CD1 A:PHE9 4.6 25.1 1.0 O A:LEU120 4.6 14.0 1.0 N A:GLY123 4.7 17.8 1.0 CE2 A:PHE9 4.7 30.6 1.0 N A:SER121 4.8 13.6 1.0 CA A:ASP7 4.8 11.5 1.0 OD2 A:ASP7 4.8 22.3 1.0 CE A:MSE128 4.9 26.4 1.0 O A:PHE9 4.9 13.6 1.0 NZ A:LYS152 5.0 16.5 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the L-2-Haloacid Dehalogenase PA0810


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 the L-2-Haloacid Dehalogenase PA0810 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl234 b:32.1 occ:1.00 OG B:SER121 2.7 18.1 1.0 O B:HOH559 2.9 27.1 1.0 N B:PHE9 3.2 15.7 1.0 N B:VAL8 3.4 14.3 1.0 O B:HOH531 3.4 34.6 1.0 CB B:SER121 3.5 14.0 1.0 O B:HOH275 3.6 26.2 1.0 CA B:SER121 3.8 14.7 1.0 CB B:VAL8 3.8 16.5 1.0 O B:HOH483 3.8 41.0 1.0 CA B:VAL8 3.8 15.9 1.0 OD1 B:ASP7 3.9 24.2 1.0 C B:VAL8 4.0 15.2 1.0 CB B:PHE9 4.1 16.0 1.0 N B:ASN122 4.1 15.2 1.0 CD1 B:PHE9 4.2 19.5 1.0 CA B:PHE9 4.2 15.7 1.0 CG B:PHE9 4.2 18.2 1.0 CG B:ASP7 4.4 21.5 1.0 C B:SER121 4.5 16.4 1.0 N B:GLY123 4.5 16.2 1.0 C B:ASP7 4.6 16.1 1.0 CG2 B:VAL8 4.7 16.3 1.0 OD2 B:ASP7 4.7 28.5 1.0 SE B:MSE128 4.7 36.3 1.0 CE B:MSE128 4.7 18.3 1.0 CA B:ASP7 4.8 15.4 1.0 CG1 B:VAL8 4.9 15.6 1.0 O B:LEU120 4.9 15.5 1.0 O B:PHE9 4.9 15.5 1.0 CE1 B:PHE9 4.9 19.2 1.0 CD2 B:PHE9 4.9 22.9 1.0 N B:SER121 5.0 14.7 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the L-2-Haloacid Dehalogenase PA0810


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 the L-2-Haloacid Dehalogenase PA0810 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl234 b:36.4 occ:1.00 O C:HOH278 2.7 19.3 1.0 OG C:SER121 2.9 22.1 1.0 N C:PHE9 3.1 15.7 1.0 N C:VAL8 3.2 14.2 1.0 OD1 C:ASP7 3.3 25.8 1.0 CB C:VAL8 3.5 13.4 1.0 CA C:VAL8 3.6 13.3 1.0 CB C:SER121 3.6 18.1 1.0 CA C:SER121 3.8 17.3 1.0 C C:VAL8 3.8 15.3 1.0 O C:HOH320 3.9 36.6 1.0 CB C:PHE9 4.0 19.2 1.0 CG C:PHE9 4.1 22.0 1.0 CA C:PHE9 4.1 18.4 1.0 CG C:ASP7 4.1 21.4 1.0 N C:ASN122 4.2 17.7 1.0 CG2 C:VAL8 4.2 11.7 1.0 C C:ASP7 4.3 14.2 1.0 CD1 C:PHE9 4.4 25.0 1.0 C C:SER121 4.5 17.4 1.0 OD2 C:ASP7 4.6 23.2 1.0 CA C:ASP7 4.6 16.0 1.0 O C:LEU120 4.6 17.6 1.0 CD2 C:PHE9 4.7 30.7 1.0 O C:PHE9 4.7 19.6 1.0 CG1 C:VAL8 4.7 14.0 1.0 N C:SER121 4.9 17.3 1.0 N C:GLY123 4.9 16.9 1.0 C C:PHE9 4.9 18.9 1.0 SE C:MSE128 4.9 39.8 1.0 NZ C:LYS152 5.0 22.4 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the L-2-Haloacid Dehalogenase PA0810


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 the L-2-Haloacid Dehalogenase PA0810 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl234 b:40.2 occ:1.00 O D:HOH476 2.8 25.9 1.0 OG D:SER121 2.9 23.1 1.0 N D:PHE9 3.1 24.8 1.0 N D:VAL8 3.1 21.7 1.0 OD1 D:ASP7 3.3 25.7 1.0 CB D:SER121 3.5 22.0 1.0 CA D:VAL8 3.6 22.1 1.0 CB D:VAL8 3.7 21.2 1.0 CA D:SER121 3.8 21.2 1.0 C D:VAL8 3.8 23.9 1.0 CG D:PHE9 4.0 27.6 1.0 CB D:PHE9 4.0 26.2 1.0 CA D:PHE9 4.1 25.7 1.0 CG D:ASP7 4.2 22.8 1.0 CD2 D:PHE9 4.2 32.6 1.0 N D:ASN122 4.2 21.9 1.0 C D:ASP7 4.3 20.6 1.0 CD1 D:PHE9 4.4 31.9 1.0 CG2 D:VAL8 4.4 21.0 1.0 C D:SER121 4.6 22.2 1.0 O D:LEU120 4.6 17.9 1.0 OD2 D:ASP7 4.6 30.7 1.0 CA D:ASP7 4.7 20.6 1.0 O D:PHE9 4.7 26.9 1.0 CE2 D:PHE9 4.8 34.8 1.0 N D:GLY123 4.8 20.0 1.0 N D:SER121 4.9 20.6 1.0 C D:PHE9 4.9 25.8 1.0 CG1 D:VAL8 4.9 18.8 1.0 CE D:MSE128 5.0 31.8 1.0 SE D:MSE128 5.0 40.8 1.0 NZ D:LYS152 5.0 23.4 1.0 CE1 D:PHE9 5.0 32.3 1.0

P.W.Y.Chan, T.K.W.To, P.Petit, C.Tran, M.Waelti, A.Savchenko, A.F.Yakunin, E.A.Edwards, E.F.Pai. Structural Adaptations of L-2-Haloacid Dehalogenases That Enable Hydrolytic Defluorination To Be Published.