Magnesium in PDB 5esr: Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus

All present enzymatic activity of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus:
3.8.1.5;

The structure of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus, PDB code: 5esr was solved by V.N.Malashkevich, R.Toro, E.C.Mundorff, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.38 / 1.48
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	79.377, 79.643, 94.766, 90.00, 90.00, 90.00
R / Rfree (%)	12.6 / 14.9

The structure of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus also contains other interesting chemical elements:

Cobalt	(Co)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus (pdb code 5esr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus, PDB code: 5esr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:9.3 occ:1.00 O A:ARG185 2.3 8.4 1.0 O A:HOH613 2.3 13.4 1.0 O A:ASN180 2.4 7.7 1.0 O A:THR183 2.4 8.2 1.0 OD1 A:ASN180 2.4 8.2 1.0 OG1 A:THR183 2.5 8.0 1.0 HG1 A:THR183 2.7 9.6 1.0 HA A:ASN180 3.1 8.6 1.0 HA A:ASP186 3.2 11.7 0.6 C A:THR183 3.2 7.9 1.0 HA A:ASP186 3.3 13.2 0.4 C A:ASN180 3.3 7.4 1.0 C A:ARG185 3.3 8.9 1.0 H A:THR183 3.4 8.6 1.0 CG A:ASN180 3.4 7.9 1.0 CB A:THR183 3.5 8.0 1.0 H A:LEU187 3.5 10.0 1.0 CA A:ASN180 3.6 7.2 1.0 HG A:LEU187 3.6 10.7 1.0 HB A:THR183 3.6 9.6 1.0 CA A:THR183 3.7 7.3 1.0 N A:THR183 3.9 7.2 1.0 CA A:ASP186 4.0 9.7 0.6 CA A:ASP186 4.0 11.0 0.4 N A:ASP186 4.0 9.7 1.0 CB A:ASN180 4.1 7.5 1.0 C A:ALA184 4.2 10.5 1.0 N A:ARG185 4.2 8.8 1.0 N A:ALA184 4.2 8.2 1.0 N A:LEU187 4.2 8.3 1.0 O A:ALA184 4.3 11.6 1.0 CA A:ARG185 4.4 9.1 1.0 ND2 A:ASN180 4.4 8.7 1.0 H A:ARG185 4.5 10.6 1.0 HB3 A:ASN180 4.5 9.0 1.0 N A:GLY181 4.5 7.6 1.0 HD21 A:ASN180 4.5 10.5 1.0 CG A:LEU187 4.6 8.9 1.0 O A:LEU179 4.6 6.5 1.0 C A:ASP186 4.6 12.6 1.0 OD1 A:ASP186 4.6 16.1 0.4 CA A:ALA184 4.6 8.8 1.0 HA A:ALA184 4.7 10.6 1.0 HA A:THR183 4.7 8.8 1.0 CG2 A:THR183 4.8 8.2 1.0 HA2 A:GLY181 4.8 10.5 1.0 H A:ASP186 4.8 11.6 0.4 H A:ASP186 4.8 11.6 0.6 HB2 A:ASN180 4.9 9.0 1.0 HG3 A:ARG185 4.9 13.8 1.0 N A:ASN180 4.9 7.1 1.0 HA A:ARG185 4.9 10.9 1.0 HG23 A:THR183 4.9 9.8 1.0 H A:ALA184 4.9 9.8 1.0 HG21 A:THR183 5.0 9.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Haloalkane Dehalogenase (Dcca) From Caulobacter Crescentus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:12.8 occ:0.83 O A:HOH859 1.9 48.4 1.0 O A:HOH737 2.0 40.3 1.0 OD1 A:ASP293 2.0 13.4 1.0 O A:HOH701 2.3 21.0 1.0 HE2 A:HIS74 2.5 26.1 1.0 CG A:ASP293 3.0 15.5 1.0 NE2 A:HIS74 3.1 21.7 1.0 OD2 A:ASP293 3.4 22.2 1.0 HE1 A:HIS74 3.5 32.3 1.0 CE1 A:HIS74 3.6 26.9 1.0 HB3 A:LYS72 3.7 18.8 1.0 O A:LYS72 3.9 23.0 1.0 O A:HOH861 4.1 27.5 1.0 CD2 A:HIS74 4.1 21.4 1.0 HA A:ASP293 4.3 11.9 1.0 O A:ASP293 4.3 11.6 1.0 CB A:ASP293 4.3 8.6 1.0 HB2 A:ALA297 4.4 15.6 1.0 HD2 A:HIS74 4.4 25.7 1.0 HD3 A:LYS72 4.6 32.7 1.0 CB A:LYS72 4.6 15.7 1.0 HB2 A:ASP293 4.6 10.3 1.0 ND1 A:HIS74 4.7 25.3 1.0 CA A:ASP293 4.7 9.9 1.0 C A:ASP293 4.8 12.5 1.0 HB2 A:LYS72 4.8 18.8 1.0 C A:LYS72 4.9 20.9 1.0 CG A:HIS74 5.0 17.6 1.0

L.Carlucci, E.Zhou, V.N.Malashkevich, S.C.Almo, E.C.Mundorff. Biochemical Characterization of Two Haloalkane Dehalogenases: Dcca From Caulobacter Crescentus and Dsaa From Saccharomonospora Azurea. Protein Sci. V. 25 877 2016.
ISSN: ESSN 1469-896X
PubMed: 26833751
DOI: 10.1002/PRO.2895