Tungsten 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:

Magnesium

(Mg)

4 atoms

The binding sites of Tungsten 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 Tungsten atom.
In total 4 binding sites of Tungsten 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 Tungsten binding site number: 1; 2; 3; 4;

Tungsten 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 Tungsten with other atoms in the W 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:W801 b:30.2 occ:1.00 W A:WO4801 0.0 30.2 1.0 O4 A:WO4801 2.0 30.4 1.0 O3 A:WO4801 2.0 30.1 1.0 O1 A:WO4801 2.0 30.4 1.0 O2 A:WO4801 2.1 30.1 1.0 OD2 A:ASP10 2.5 14.8 1.0 OG1 A:THR54 3.3 26.8 1.0 CG A:ASP10 3.5 17.2 1.0 MG A:MG701 3.7 20.0 1.0 OD2 A:ASP12 3.8 31.9 1.0 OD1 A:ASP10 3.8 18.5 1.0 N A:ASP12 3.9 13.5 1.0 N A:GLY55 4.0 16.9 1.0 O B:HOH882 4.0 24.6 1.0 NZ A:LYS80 4.1 18.5 1.0 CB A:ASP12 4.1 17.1 1.0 O B:HOH857 4.2 37.9 1.0 CB A:THR54 4.3 23.9 1.0 CA A:THR54 4.4 14.8 1.0 N A:ILE11 4.4 14.7 1.0 ND2 A:ASN106 4.4 31.9 1.0 CG A:ASP12 4.4 24.1 1.0 O A:ASP12 4.5 15.1 1.0 CA A:ASP12 4.5 14.7 1.0 O B:HOH1001 4.5 19.6 1.0 C A:THR54 4.7 16.7 1.0 O B:HOH990 4.7 24.4 1.0 N A:GLU56 4.7 16.0 1.0 CG A:GLU56 4.8 22.7 1.0 CA A:GLY55 4.8 21.6 1.0 C A:ILE11 4.8 13.6 1.0 CB A:ASP10 4.9 14.0 1.0 OD1 A:ASN106 4.9 35.5 1.0 CE A:LYS80 5.0 15.4 1.0 CA A:ILE11 5.0 15.7 1.0

Tungsten 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 Tungsten with other atoms in the W 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:W802 b:32.1 occ:1.00 W B:WO4802 0.0 32.1 1.0 O2 B:WO4802 2.0 31.9 1.0 O3 B:WO4802 2.0 32.0 1.0 O1 B:WO4802 2.0 32.1 1.0 O4 B:WO4802 2.1 32.4 1.0 OD1 B:ASP10 2.5 16.4 1.0 OG1 B:THR54 3.3 23.4 1.0 O B:HOH900 3.5 36.3 1.0 CG B:ASP10 3.5 20.4 1.0 MG B:MG702 3.6 21.7 1.0 OD2 B:ASP12 3.7 36.0 1.0 OD2 B:ASP10 3.9 20.1 1.0 N B:ASP12 3.9 15.8 1.0 O B:HOH832 4.0 21.8 1.0 O B:HOH1248 4.0 36.3 1.0 N B:GLY55 4.0 16.2 1.0 NZ B:LYS80 4.1 20.6 1.0 CB B:ASP12 4.1 18.2 1.0 CB B:THR54 4.3 22.4 1.0 N B:ILE11 4.4 14.2 1.0 CA B:THR54 4.4 13.3 1.0 CG B:ASP12 4.4 27.1 1.0 ND2 B:ASN106 4.4 31.8 1.0 O B:ASP12 4.4 17.0 1.0 CA B:ASP12 4.5 14.9 1.0 O B:HOH1143 4.7 23.3 1.0 O B:HOH898 4.7 22.1 1.0 C B:THR54 4.7 18.5 1.0 N B:GLU56 4.8 19.4 1.0 C B:ILE11 4.8 18.5 1.0 CB B:ASP10 4.9 13.4 1.0 CE B:LYS80 4.9 14.6 1.0 CA B:GLY55 5.0 17.4 1.0 CG B:GLU56 5.0 23.4 1.0 C B:ASP12 5.0 17.4 1.0 CA B:ILE11 5.0 14.7 1.0

Tungsten 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 Tungsten with other atoms in the W 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:W803 b:33.9 occ:1.00 W C:WO4803 0.0 33.9 1.0 O3 C:WO4803 2.0 32.8 1.0 O4 C:WO4803 2.0 33.5 1.0 O2 C:WO4803 2.0 33.3 1.0 O1 C:WO4803 2.0 34.0 1.0 OD2 C:ASP10 2.5 19.1 1.0 OG1 C:THR54 3.3 31.4 1.0 CG C:ASP10 3.5 24.2 1.0 OD1 C:ASP12 3.7 40.4 1.0 MG C:MG703 3.7 24.9 1.0 OD1 C:ASP10 3.7 27.0 1.0 O B:HOH936 3.8 27.1 1.0 N C:ASP12 3.9 17.5 1.0 N C:GLY55 4.0 24.9 1.0 CB C:ASP12 4.1 24.0 1.0 NZ C:LYS80 4.1 26.6 1.0 O B:HOH937 4.2 39.6 1.0 CB C:THR54 4.3 28.9 1.0 ND2 C:ASN106 4.3 31.1 1.0 O B:HOH1215 4.3 42.4 1.0 CA C:THR54 4.3 25.0 1.0 CG C:ASP12 4.3 31.2 1.0 N C:ILE11 4.3 17.7 1.0 O C:ASP12 4.5 18.9 1.0 CA C:ASP12 4.5 18.7 1.0 O B:HOH917 4.6 29.8 1.0 O B:HOH935 4.6 17.6 1.0 C C:THR54 4.7 25.3 1.0 N C:GLU56 4.8 26.7 1.0 CB C:ASP10 4.8 22.1 1.0 C C:ILE11 4.9 20.4 1.0 CA C:GLY55 4.9 22.9 1.0 OD1 C:ASN106 4.9 27.7 0.7 CG C:GLU56 5.0 31.2 1.0 CA C:ILE11 5.0 18.0 1.0

Tungsten 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 Tungsten with other atoms in the W 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:W804 b:35.4 occ:1.00 W D:WO4804 0.0 35.4 1.0 O3 D:WO4804 2.0 34.9 1.0 O4 D:WO4804 2.0 35.8 1.0 O2 D:WO4804 2.0 35.6 1.0 O1 D:WO4804 2.0 35.3 1.0 OD1 D:ASP10 2.6 21.7 1.0 OG1 D:THR54 3.5 24.9 1.0 CG D:ASP10 3.5 23.6 1.0 MG D:MG704 3.6 28.2 1.0 OD2 D:ASP12 3.8 41.3 1.0 OD2 D:ASP10 3.8 26.1 1.0 N D:ASP12 3.9 21.4 1.0 N D:GLY55 4.0 30.9 1.0 O B:HOH1093 4.0 22.9 1.0 CB D:ASP12 4.0 19.4 1.0 NZ D:LYS80 4.1 28.1 1.0 CG D:ASP12 4.4 31.3 1.0 CA D:THR54 4.4 26.2 1.0 N D:ILE11 4.4 20.0 1.0 CB D:THR54 4.4 25.8 1.0 ND2 D:ASN106 4.4 34.0 1.0 O D:ASP12 4.5 20.1 1.0 CA D:ASP12 4.5 19.8 1.0 O B:HOH1086 4.6 18.6 1.0 C D:THR54 4.7 28.7 1.0 N D:GLU56 4.7 32.7 1.0 O B:HOH851 4.8 25.6 1.0 CA D:GLY55 4.8 33.0 1.0 C D:ILE11 4.9 20.0 1.0 CB D:ASP10 4.9 22.6 1.0 CG D:GLU56 4.9 29.8 1.0 CE D:LYS80 4.9 25.2 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