Magnesium in PDB 3e84: 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: 3e84 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)	21.93 / 1.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.086, 107.336, 75.310, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.8

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:

Tungsten

(W)

4 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 3e84). 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: 3e84:
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:Mg701 b:20.0 occ:1.00 O3 A:WO4801 1.9 30.1 1.0 OD1 A:ASP10 2.0 18.5 1.0 O B:HOH1001 2.1 19.6 1.0 OD1 A:ASP103 2.2 20.6 1.0 O A:ASP12 2.2 15.1 1.0 O B:HOH882 2.2 24.6 1.0 CG A:ASP10 3.0 17.2 1.0 CG A:ASP103 3.2 21.2 1.0 C A:ASP12 3.4 17.0 1.0 OD2 A:ASP10 3.4 14.8 1.0 OD2 A:ASP103 3.6 21.9 1.0 W A:WO4801 3.7 30.2 1.0 OD2 A:ASP107 4.0 19.9 1.0 CA A:ASP12 4.1 14.7 1.0 N A:ASP12 4.2 13.5 1.0 CB A:ASP12 4.3 17.1 1.0 CB A:ASP10 4.3 14.0 1.0 N A:GLY13 4.4 15.6 1.0 N A:ASP103 4.5 15.3 1.0 CB A:ASP103 4.5 20.6 1.0 CA A:GLY13 4.5 16.0 1.0 CB A:ASP104 4.6 19.0 1.0 O4 A:WO4801 4.6 30.4 1.0 O2 A:WO4801 4.7 30.1 1.0 N A:ASP104 4.7 16.3 1.0 OD1 A:ASN106 4.8 35.5 1.0 C A:ILE11 4.8 13.6 1.0 CA A:ASP103 4.9 16.0 1.0 C A:ASP103 5.0 18.2 1.0 CG A:ASP107 5.0 18.9 1.0 C A:GLY13 5.0 18.3 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:Mg702 b:21.7 occ:1.00 O3 B:WO4802 1.9 32.0 1.0 OD2 B:ASP10 2.1 20.1 1.0 O B:HOH832 2.2 21.8 1.0 OD1 B:ASP103 2.2 19.4 1.0 O B:ASP12 2.2 17.0 1.0 O B:HOH1143 2.2 23.3 1.0 CG B:ASP10 3.1 20.4 1.0 CG B:ASP103 3.2 20.7 1.0 C B:ASP12 3.4 17.4 1.0 OD1 B:ASP10 3.4 16.4 1.0 W B:WO4802 3.6 32.1 1.0 OD2 B:ASP103 3.7 23.5 1.0 OD2 B:ASP107 4.0 18.5 1.0 CA B:ASP12 4.2 14.9 1.0 O B:HOH1038 4.2 48.7 1.0 N B:ASP12 4.3 15.8 1.0 CB B:ASP12 4.3 18.2 1.0 CB B:ASP10 4.4 13.4 1.0 N B:GLY13 4.4 20.4 1.0 N B:ASP103 4.4 17.3 1.0 CB B:ASP103 4.5 15.9 1.0 CB B:ASP104 4.5 26.0 1.0 CA B:GLY13 4.5 16.3 1.0 O2 B:WO4802 4.6 31.9 1.0 O B:HOH900 4.6 36.3 1.0 O1 B:WO4802 4.6 32.1 1.0 N B:ASP104 4.6 22.4 1.0 CA B:ASP103 4.8 17.1 1.0 OD1 B:ASN106 4.9 35.4 1.0 C B:ASP103 4.9 19.7 1.0 C B:ILE11 4.9 18.5 1.0 C B:GLY13 5.0 18.6 1.0 CG2 B:VAL14 5.0 14.8 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:Mg703 b:24.9 occ:1.00 O3 C:WO4803 1.9 32.8 1.0 OD1 C:ASP10 2.0 27.0 1.0 OD1 C:ASP103 2.1 24.4 1.0 O C:ASP12 2.1 18.9 1.0 O B:HOH935 2.2 17.6 1.0 O B:HOH936 2.3 27.1 1.0 CG C:ASP10 3.1 24.2 1.0 CG C:ASP103 3.2 22.5 1.0 C C:ASP12 3.3 18.3 1.0 OD2 C:ASP10 3.6 19.1 1.0 OD2 C:ASP103 3.6 24.4 1.0 W C:WO4803 3.7 33.9 1.0 OD2 C:ASP107 4.0 24.3 1.0 CA C:ASP12 4.0 18.7 1.0 N C:ASP12 4.1 17.5 1.0 O B:HOH937 4.1 39.6 1.0 CB C:ASP12 4.2 24.0 1.0 N C:GLY13 4.3 16.9 1.0 CB C:ASP10 4.3 22.1 1.0 CA C:GLY13 4.4 16.8 1.0 CB C:ASP103 4.4 21.8 1.0 N C:ASP103 4.4 17.7 1.0 CB C:ASP104 4.6 22.3 1.0 O1 C:WO4803 4.6 34.0 1.0 N C:ASP104 4.8 20.4 1.0 C C:ILE11 4.8 20.4 1.0 O4 C:WO4803 4.8 33.5 1.0 CA C:ASP103 4.8 22.1 1.0 C C:GLY13 4.8 17.8 1.0 N C:VAL14 4.9 16.9 1.0 C C:ASP103 4.9 19.3 1.0 CG2 C:VAL14 5.0 18.1 1.0 OD1 C:ASN106 5.0 27.7 0.7

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:Mg704 b:28.2 occ:1.00 O3 D:WO4804 1.9 34.9 1.0 OD2 D:ASP10 2.0 26.1 1.0 OD1 D:ASP103 2.1 22.6 1.0 O B:HOH1086 2.2 18.6 1.0 O D:ASP12 2.2 20.1 1.0 O B:HOH1093 2.3 22.9 1.0 CG D:ASP10 3.1 23.6 1.0 CG D:ASP103 3.2 21.0 1.0 C D:ASP12 3.4 19.7 1.0 OD1 D:ASP10 3.4 21.7 1.0 OD2 D:ASP103 3.6 22.4 1.0 W D:WO4804 3.6 35.4 1.0 OD2 D:ASP107 4.0 25.1 1.0 CA D:ASP12 4.1 19.8 1.0 N D:ASP12 4.2 21.4 1.0 CB D:ASP12 4.2 19.4 1.0 CB D:ASP10 4.4 22.6 1.0 N D:GLY13 4.4 18.1 1.0 CB D:ASP103 4.4 19.5 1.0 N D:ASP103 4.4 18.3 1.0 CA D:GLY13 4.5 16.7 1.0 O1 D:WO4804 4.6 35.3 1.0 O4 D:WO4804 4.6 35.8 1.0 CB D:ASP104 4.6 20.4 1.0 N D:ASP104 4.7 20.7 1.0 CA D:ASP103 4.8 18.1 1.0 C D:ILE11 4.8 20.0 1.0 OD1 D:ASN106 4.9 41.7 1.0 C D:GLY13 4.9 20.0 1.0 C D:ASP103 4.9 21.7 1.0 CG2 D:VAL14 5.0 17.4 1.0 N D:VAL14 5.0 16.9 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