Magnesium in PDB 3e8m: Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily

The structure of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily, PDB code: 3e8m was solved by Z.Lu, L.Wang, D.Dunaway-Mariano, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.78 / 1.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.243, 107.482, 75.093, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 14.1

The structure of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily (pdb code 3e8m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily, PDB code: 3e8m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg165 b:10.0 occ:1.00 OD1 A:ASP10 2.0 10.6 1.0 O A:HOH188 2.1 11.2 1.0 OD1 A:ASP103 2.1 10.9 1.0 O A:HOH185 2.1 10.9 1.0 O A:ASP12 2.1 9.3 1.0 O A:HOH190 2.1 10.8 1.0 CG A:ASP103 3.1 10.7 1.0 CG A:ASP10 3.1 9.8 1.0 C A:ASP12 3.3 8.7 1.0 OD2 A:ASP103 3.4 11.5 1.0 HB2 A:ASP12 3.5 11.4 1.0 OD2 A:ASP10 3.6 10.2 1.0 H A:ASP103 3.9 11.3 1.0 HB2 A:ASP104 3.9 15.6 1.0 HA3 A:GLY13 3.9 10.7 1.0 H A:ASP12 4.0 10.4 1.0 OD2 A:ASP107 4.1 10.2 1.0 O A:HOH196 4.1 14.6 1.0 CA A:ASP12 4.1 8.6 1.0 N A:ASP12 4.1 8.7 1.0 HZ1 A:LYS80 4.2 13.3 1.0 HG23 A:VAL14 4.2 12.1 1.0 CB A:ASP12 4.2 9.4 1.0 HB3 A:ASP10 4.3 11.7 1.0 CB A:ASP10 4.3 9.7 1.0 N A:GLY13 4.4 8.5 1.0 O A:HOH183 4.4 10.1 1.0 O B:HOH191 4.4 13.4 1.0 O A:HOH225 4.4 17.9 1.0 CB A:ASP103 4.4 11.3 1.0 HG21 B:THR34 4.5 12.0 1.0 HB3 A:ASP104 4.5 15.6 1.0 HZ3 A:LYS80 4.5 13.3 1.0 CA A:GLY13 4.6 8.8 1.0 N A:ASP103 4.6 9.4 1.0 HB3 A:ASP103 4.6 13.6 1.0 HB3 A:ASP12 4.6 11.4 1.0 CB A:ASP104 4.7 12.9 1.0 H A:ASP104 4.7 12.7 1.0 NZ A:LYS80 4.7 11.1 1.0 HZ2 A:LYS80 4.7 13.3 1.0 HB2 A:ASP10 4.7 11.7 1.0 CL A:CL166 4.8 11.5 1.0 C A:ILE11 4.8 8.6 1.0 N A:ASP104 4.9 10.6 1.0 H A:ILE11 4.9 10.2 1.0 CA A:ASP103 4.9 9.9 1.0 H A:VAL14 4.9 10.4 1.0

Magnesium binding site 2 out of 4 in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg165 b:10.2 occ:1.00 OD1 B:ASP10 2.0 11.2 1.0 O B:HOH189 2.1 12.2 1.0 OD1 B:ASP103 2.1 11.5 1.0 O B:HOH188 2.1 11.9 1.0 O B:ASP12 2.2 9.6 1.0 O B:HOH186 2.2 11.7 1.0 CG B:ASP103 3.1 11.3 1.0 CG B:ASP10 3.1 10.0 1.0 C B:ASP12 3.3 8.6 1.0 OD2 B:ASP103 3.4 12.7 1.0 HB2 B:ASP12 3.6 11.5 1.0 OD2 B:ASP10 3.6 10.7 1.0 HB2 B:ASP104 3.9 17.2 1.0 HA3 B:GLY13 3.9 10.8 1.0 H B:ASP103 3.9 11.9 1.0 O B:HOH214 4.0 16.6 1.0 OD2 B:ASP107 4.1 10.6 1.0 H B:ASP12 4.1 10.5 1.0 CA B:ASP12 4.1 8.6 1.0 N B:ASP12 4.2 8.7 1.0 HG23 B:VAL14 4.2 11.7 1.0 HZ1 B:LYS80 4.2 15.0 1.0 CB B:ASP12 4.3 9.5 1.0 O B:HOH180 4.3 10.7 1.0 N B:GLY13 4.3 8.6 1.0 HB3 B:ASP10 4.3 12.0 1.0 O B:HOH219 4.4 20.9 1.0 CB B:ASP10 4.4 10.0 1.0 O D:HOH297 4.4 15.5 1.0 CB B:ASP103 4.4 11.2 1.0 HG21 D:THR34 4.5 13.5 1.0 CA B:GLY13 4.5 8.9 1.0 HB3 B:ASP104 4.5 17.2 1.0 HZ3 B:LYS80 4.6 15.0 1.0 N B:ASP103 4.6 9.9 1.0 HB3 B:ASP103 4.6 13.4 1.0 CB B:ASP104 4.7 14.3 1.0 HB3 B:ASP12 4.7 11.5 1.0 H B:ASP104 4.7 13.0 1.0 HZ2 B:LYS80 4.7 15.0 1.0 HB2 B:ASP10 4.7 12.0 1.0 NZ B:LYS80 4.7 12.5 1.0 CL B:CL166 4.8 12.4 1.0 N B:ASP104 4.8 10.8 1.0 C B:ILE11 4.8 8.6 1.0 H B:VAL14 4.9 10.2 1.0 H B:ILE11 4.9 10.2 1.0 CA B:ASP103 4.9 10.2 1.0

Magnesium binding site 3 out of 4 in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg165 b:10.7 occ:1.00 OD1 C:ASP10 2.0 11.7 1.0 O C:HOH181 2.1 11.6 1.0 OD1 C:ASP103 2.1 11.9 1.0 O C:HOH185 2.1 12.2 1.0 O C:HOH183 2.1 11.3 1.0 O C:ASP12 2.1 10.0 1.0 CG C:ASP103 3.1 11.7 1.0 CG C:ASP10 3.1 10.6 1.0 C C:ASP12 3.3 9.4 1.0 OD2 C:ASP103 3.4 12.7 1.0 HB2 C:ASP12 3.5 11.8 1.0 OD2 C:ASP10 3.6 10.7 1.0 HA3 C:GLY13 3.9 11.5 1.0 HB2 C:ASP104 3.9 18.8 1.0 H C:ASP103 3.9 12.7 1.0 H C:ASP12 4.0 11.2 1.0 O C:HOH206 4.0 17.6 1.0 OD2 C:ASP107 4.1 11.3 1.0 CA C:ASP12 4.1 9.1 1.0 N C:ASP12 4.1 9.3 1.0 HG23 C:VAL14 4.2 12.2 1.0 CB C:ASP12 4.2 9.8 1.0 HZ1 C:LYS80 4.3 15.2 1.0 HB3 C:ASP10 4.3 12.5 1.0 N C:GLY13 4.3 9.2 1.0 O C:HOH177 4.3 11.4 1.0 O A:HOH207 4.4 17.9 1.0 CB C:ASP10 4.4 10.4 1.0 O C:HOH395 4.4 22.5 1.0 CB C:ASP103 4.4 12.2 1.0 HG21 A:THR34 4.5 13.4 1.0 CA C:GLY13 4.5 9.6 1.0 HB3 C:ASP104 4.6 18.8 1.0 N C:ASP103 4.6 10.6 1.0 HB3 C:ASP103 4.6 14.6 1.0 HB3 C:ASP12 4.6 11.8 1.0 HZ3 C:LYS80 4.7 15.2 1.0 CB C:ASP104 4.7 15.6 1.0 H C:ASP104 4.7 13.8 1.0 HB2 C:ASP10 4.7 12.5 1.0 CL C:CL166 4.8 13.1 1.0 HZ2 C:LYS80 4.8 15.2 1.0 NZ C:LYS80 4.8 12.6 1.0 C C:ILE11 4.8 9.2 1.0 H C:ILE11 4.8 11.3 1.0 N C:ASP104 4.8 11.5 1.0 H C:VAL14 4.9 10.7 1.0 CA C:ASP103 4.9 11.0 1.0

Magnesium binding site 4 out of 4 in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg165 b:10.8 occ:1.00 OD2 D:ASP10 2.0 11.9 1.0 OD1 D:ASP103 2.1 11.8 1.0 O D:HOH286 2.1 12.5 1.0 O D:HOH294 2.1 12.2 1.0 O D:ASP12 2.1 10.0 1.0 O D:HOH291 2.1 12.0 1.0 CG D:ASP103 3.0 11.7 1.0 CG D:ASP10 3.1 10.6 1.0 C D:ASP12 3.3 9.2 1.0 OD2 D:ASP103 3.4 12.7 1.0 HB2 D:ASP12 3.5 11.4 1.0 OD1 D:ASP10 3.6 11.3 1.0 HA3 D:GLY13 3.9 11.3 1.0 H D:ASP103 3.9 12.5 1.0 HB2 D:ASP104 3.9 16.5 1.0 O D:HOH300 4.0 16.0 1.0 H D:ASP12 4.1 11.3 1.0 CA D:ASP12 4.1 9.2 1.0 OD2 D:ASP107 4.1 11.4 1.0 N D:ASP12 4.2 9.4 1.0 HZ1 D:LYS80 4.2 15.1 1.0 HG23 D:VAL14 4.2 13.1 1.0 CB D:ASP12 4.2 9.5 1.0 HB3 D:ASP10 4.3 13.1 1.0 N D:GLY13 4.3 9.0 1.0 CB D:ASP10 4.3 10.9 1.0 O D:HOH285 4.4 11.4 1.0 O D:HOH318 4.4 20.0 1.0 CB D:ASP103 4.4 12.1 1.0 O C:HOH204 4.4 15.0 1.0 HG21 C:THR34 4.5 12.7 1.0 HB3 D:ASP104 4.5 16.5 1.0 CA D:GLY13 4.5 9.4 1.0 HZ3 D:LYS80 4.6 15.1 1.0 N D:ASP103 4.6 10.4 1.0 HB3 D:ASP103 4.6 14.5 1.0 HB3 D:ASP12 4.7 11.4 1.0 CB D:ASP104 4.7 13.7 1.0 NZ D:LYS80 4.7 12.5 1.0 H D:ASP104 4.7 14.0 1.0 HB2 D:ASP10 4.7 13.1 1.0 HZ2 D:LYS80 4.7 15.1 1.0 CL D:CL166 4.8 12.8 1.0 C D:ILE11 4.8 9.2 1.0 H D:ILE11 4.8 11.5 1.0 N D:ASP104 4.9 11.7 1.0 CA D:ASP103 4.9 10.7 1.0 H D:VAL14 4.9 10.9 1.0

Z.Lu, L.Wang, D.Dunaway-Mariano, K.N.Allen. Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphatase Defines Specificity Elements in Type C0 Haloalkanoate Dehalogenase Family Members. J.Biol.Chem. V. 284 1224 2009.
ISSN: ISSN 0021-9258
PubMed: 18986982
DOI: 10.1074/JBC.M807056200