Magnesium in PDB 3e81: 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: 3e81 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)	49.06 / 1.63
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.958, 106.602, 74.830, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.7

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:

Vanadium

(V)

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 3e81). 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: 3e81:
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:28.5 occ:1.00 O1 A:VN4170 2.0 24.2 1.0 OD1 A:ASP103 2.1 25.9 1.0 OD1 A:ASP10 2.2 25.0 1.0 O A:ASP12 2.2 22.4 1.0 O A:HOH288 2.2 24.5 1.0 O A:HOH289 2.2 25.8 1.0 CG A:ASP103 3.1 27.4 1.0 CG A:ASP10 3.1 27.7 1.0 C A:ASP12 3.3 22.2 1.0 V A:VN4170 3.4 28.3 1.0 OD2 A:ASP103 3.5 27.9 1.0 OD2 A:ASP10 3.5 23.1 1.0 OD2 A:ASP107 4.0 23.1 1.0 CA A:ASP12 4.1 22.1 1.0 CB A:ASP12 4.2 22.3 1.0 N A:ASP12 4.2 22.1 1.0 N A:GLY13 4.3 22.1 1.0 C9 A:SLB171 4.4 37.8 0.5 CB A:ASP103 4.4 23.8 1.0 CA A:GLY13 4.4 22.3 1.0 N A:ASP103 4.5 21.7 1.0 CB A:ASP10 4.5 22.6 1.0 O9 A:SLB171 4.5 25.9 0.5 O2 A:VN4170 4.5 26.7 1.0 CB A:ASP104 4.6 25.6 1.0 O3 A:VN4170 4.6 28.9 1.0 N A:ASP104 4.7 23.5 1.0 CA A:ASP103 4.8 23.1 1.0 OD1 A:ASN106 4.9 40.9 1.0 C A:ILE11 4.9 21.9 1.0 C A:ASP103 4.9 22.3 1.0 C A:GLY13 5.0 22.4 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:29.6 occ:1.00 O1 B:VN4170 2.0 27.3 1.0 OD1 B:ASP103 2.1 26.2 1.0 O B:HOH261 2.1 25.9 1.0 O B:HOH260 2.2 25.7 1.0 O B:ASP12 2.2 22.2 1.0 OD1 B:ASP10 2.2 26.1 1.0 CG B:ASP103 3.1 26.6 1.0 CG B:ASP10 3.2 27.5 1.0 C B:ASP12 3.4 22.0 1.0 V B:VN4170 3.5 27.9 1.0 OD2 B:ASP103 3.5 27.5 1.0 OD2 B:ASP10 3.6 25.6 1.0 OD2 B:ASP107 4.0 26.2 1.0 O D:HOH225 4.0 44.4 1.0 CA B:ASP12 4.1 21.9 1.0 N B:ASP12 4.3 21.8 1.0 CB B:ASP12 4.3 22.2 1.0 N B:GLY13 4.4 21.8 1.0 C9 B:SLB171 4.4 43.0 0.5 CB B:ASP103 4.4 21.6 1.0 N B:ASP103 4.5 22.1 1.0 CB B:ASP104 4.5 27.8 1.0 O9 B:SLB171 4.5 23.1 0.5 CA B:GLY13 4.5 21.9 1.0 CB B:ASP10 4.5 22.3 1.0 O2 B:VN4170 4.5 24.8 1.0 O3 B:VN4170 4.6 27.8 1.0 N B:ASP104 4.7 24.4 1.0 OD1 B:ASN106 4.8 44.1 1.0 CA B:ASP103 4.8 22.6 1.0 C B:ASP103 4.9 22.6 1.0 C B:ILE11 5.0 21.5 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:29.6 occ:1.00 O1 C:VN4169 1.9 28.4 1.0 OD1 C:ASP103 2.1 27.4 1.0 OD1 C:ASP10 2.1 29.4 1.0 O C:ASP12 2.2 23.7 1.0 O C:HOH257 2.2 28.0 1.0 O C:HOH256 2.2 30.2 1.0 CG C:ASP10 3.1 29.8 1.0 CG C:ASP103 3.2 29.2 1.0 C C:ASP12 3.3 22.8 1.0 V C:VN4169 3.4 32.2 1.0 OD2 C:ASP10 3.5 25.0 1.0 OD2 C:ASP103 3.6 28.0 1.0 OD2 C:ASP107 4.1 28.8 1.0 CA C:ASP12 4.1 22.8 1.0 CB C:ASP12 4.2 23.4 1.0 N C:ASP12 4.2 23.0 1.0 N C:GLY13 4.3 22.4 1.0 C9 C:SLB171 4.4 38.0 0.5 CB C:ASP103 4.4 26.2 1.0 CB C:ASP10 4.5 26.6 1.0 O9 C:SLB171 4.5 29.4 0.5 CA C:GLY13 4.5 22.4 1.0 N C:ASP103 4.5 24.6 1.0 O2 C:VN4169 4.5 27.7 1.0 CB C:ASP104 4.6 30.3 1.0 O3 C:VN4169 4.6 31.5 1.0 N C:ASP104 4.8 23.8 1.0 CA C:ASP103 4.9 23.6 1.0 OD1 C:ASN106 4.9 43.1 1.0 C C:ILE11 4.9 23.6 1.0 C C:ASP103 5.0 22.4 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:31.6 occ:1.00 O1 D:VN4169 2.0 28.3 1.0 OD1 D:ASP103 2.1 26.0 1.0 OD1 D:ASP10 2.1 28.2 1.0 O D:HOH255 2.2 27.0 1.0 O D:HOH256 2.2 28.6 1.0 O D:ASP12 2.2 24.1 1.0 CG D:ASP103 3.1 28.9 1.0 CG D:ASP10 3.1 27.4 1.0 C D:ASP12 3.4 23.2 1.0 OD2 D:ASP103 3.5 27.5 1.0 V D:VN4169 3.5 30.8 1.0 OD2 D:ASP10 3.6 27.4 1.0 OD2 D:ASP107 4.0 27.9 1.0 CA D:ASP12 4.2 23.1 1.0 CB D:ASP12 4.2 23.4 1.0 N D:ASP12 4.3 23.3 1.0 N D:GLY13 4.3 22.9 1.0 CB D:ASP103 4.4 25.2 1.0 N D:ASP103 4.4 26.8 1.0 C9 D:SLB170 4.5 35.5 0.5 CB D:ASP10 4.5 27.9 1.0 CB D:ASP104 4.5 28.6 1.0 CA D:GLY13 4.5 23.0 1.0 O2 D:VN4169 4.6 27.2 1.0 O9 D:SLB170 4.6 28.6 0.5 N D:ASP104 4.7 25.4 1.0 O3 D:VN4169 4.7 30.8 1.0 CA D:ASP103 4.8 25.2 1.0 C D:ASP103 4.9 24.6 1.0 OD1 D:ASN106 4.9 41.9 1.0 C D:ILE11 5.0 23.1 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