Magnesium in PDB 3ddh: The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482

The structure of The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482, PDB code: 3ddh was solved by M.E.Cuff, E.Duggan, J.Abdullah, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.40 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.119, 104.222, 121.212, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.3

The structure of The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482 (pdb code 3ddh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482, PDB code: 3ddh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg232 b:19.9 occ:1.00 OD2 A:ASP11 1.9 27.0 1.0 O A:ASP13 2.0 24.1 1.0 O A:HOH325 2.1 20.2 1.0 OD1 A:ASN179 2.1 23.4 1.0 O A:HOH236 2.1 20.8 1.0 O A:HOH247 2.2 18.6 1.0 CG A:ASP11 2.9 26.2 1.0 CG A:ASN179 3.2 22.5 1.0 C A:ASP13 3.2 24.1 1.0 OD1 A:ASP11 3.3 26.1 1.0 ND2 A:ASN179 3.6 20.6 1.0 OG1 A:THR15 3.9 22.7 1.0 OD2 A:ASP184 4.1 24.5 1.0 CA A:ASP13 4.1 25.5 1.0 CB A:ASP14 4.1 23.2 1.0 O A:HOH248 4.2 29.7 1.0 N A:ASP14 4.2 23.9 1.0 O A:HOH272 4.2 39.1 1.0 CB A:ASP11 4.2 24.4 1.0 N A:ASP13 4.3 24.8 1.0 OD2 A:ASP14 4.3 26.9 1.0 CB A:ASP13 4.3 25.3 1.0 CA A:ASP14 4.4 23.3 1.0 C A:ASP14 4.4 22.6 1.0 CB A:ASN179 4.5 23.4 1.0 O A:HOH356 4.5 40.0 1.0 N A:THR15 4.6 22.3 1.0 CG A:ASP14 4.6 26.3 1.0 O A:HOH251 4.7 23.6 1.0 N A:ASN179 4.7 23.6 1.0 C A:ALA12 4.9 23.8 1.0 O A:ASP14 4.9 22.3 1.0 CB A:THR15 4.9 23.0 1.0 N A:SER180 4.9 24.3 1.0 CG A:ASP184 5.0 27.3 1.0

Magnesium binding site 2 out of 4 in the The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg234 b:45.5 occ:1.00 OD1 A:ASP129 2.2 42.0 1.0 CG A:ASP129 2.8 38.4 1.0 OD2 A:ASP129 2.9 40.1 1.0 N A:ALA64 3.0 29.4 1.0 O A:TYR60 3.0 34.7 1.0 N A:LYS63 3.3 30.4 1.0 NZ B:LYS63 3.3 37.5 1.0 CB A:LYS63 3.5 30.3 1.0 C A:GLY61 3.5 32.0 1.0 CA A:GLY61 3.6 32.1 1.0 CA A:LYS63 3.6 30.7 1.0 CE B:LYS63 3.6 35.6 1.0 CB A:ALA64 3.7 27.8 1.0 O A:GLY61 3.7 31.5 1.0 C A:LYS63 3.8 29.8 1.0 C A:TYR60 3.8 33.3 1.0 N A:ALA62 3.8 31.2 1.0 CA A:ALA64 3.9 28.5 1.0 N A:GLY61 4.0 32.4 1.0 CD B:LYS63 4.1 31.4 1.0 C A:ALA62 4.3 31.0 1.0 CB A:ASP129 4.3 35.0 1.0 CG A:LYS63 4.5 31.9 1.0 O B:HOH381 4.6 33.8 1.0 O A:LEU58 4.6 33.2 1.0 CE A:LYS63 4.7 34.1 1.0 CA A:ALA62 4.7 31.3 1.0 N A:ASP129 4.7 34.0 1.0 CA A:ASP129 4.8 33.9 1.0 O A:HOH257 4.8 36.0 1.0 O A:LYS63 5.0 29.1 1.0

Magnesium binding site 3 out of 4 in the The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg232 b:19.1 occ:1.00 O B:HOH449 2.0 15.6 1.0 OD1 B:ASN179 2.0 22.2 1.0 OD2 B:ASP11 2.0 25.2 1.0 O B:ASP13 2.0 24.6 1.0 O B:HOH452 2.1 18.1 1.0 O B:HOH444 2.1 16.2 1.0 CG B:ASP11 3.0 24.6 1.0 CG B:ASN179 3.1 19.6 1.0 C B:ASP13 3.3 24.0 1.0 OD1 B:ASP11 3.3 26.4 1.0 ND2 B:ASN179 3.6 22.0 1.0 OG1 B:THR15 4.0 24.1 1.0 OD2 B:ASP184 4.0 24.1 1.0 CA B:ASP13 4.2 24.1 1.0 CB B:ASP14 4.2 23.9 1.0 O B:HOH378 4.2 28.6 1.0 OD2 B:ASP14 4.2 27.5 1.0 N B:ASP14 4.3 23.4 1.0 CB B:ASP11 4.3 23.5 1.0 N B:ASP13 4.3 23.6 1.0 CB B:ASP13 4.3 24.5 1.0 CB B:ASN179 4.4 21.5 1.0 O B:HOH395 4.4 37.1 1.0 CA B:ASP14 4.5 23.2 1.0 C B:ASP14 4.6 22.7 1.0 N B:ASN179 4.6 22.0 1.0 N B:THR15 4.6 22.2 1.0 O B:HOH344 4.7 23.2 1.0 CG B:ASP14 4.7 26.6 1.0 N B:SER180 4.9 21.9 1.0 C B:ALA12 4.9 23.4 1.0 CA B:ASN179 4.9 22.1 1.0 CB B:THR15 5.0 23.0 1.0 CG B:ASP184 5.0 25.5 1.0

Magnesium binding site 4 out of 4 in the The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg233 b:60.8 occ:1.00 O B:HOH490 2.0 54.1 1.0 O A:HOH354 2.1 44.7 1.0 O B:HOH488 2.3 54.8 1.0 O B:HOH489 2.3 54.6 1.0 O B:HOH475 2.6 37.6 1.0 NZ B:LYS158 3.5 45.5 1.0 OE2 B:GLU159 4.1 47.0 1.0 OE1 A:GLU134 4.1 43.8 1.0 OG B:SER153 4.3 29.2 1.0 O A:HOH368 4.6 48.5 1.0 O B:HOH454 4.7 52.6 1.0 CE B:LYS158 4.8 40.9 1.0

M.E.Cuff, E.Duggan, J.Abdullah, A.Joachimiak. The Structure of A Putative Haloacid Dehalogenase-Like Family Hydrolase From Bacteroides Thetaiotaomicron Vpi-5482 To Be Published.