Vanadium 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:

Magnesium

(Mg)

4 atoms

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

Vanadium 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 Vanadium with other atoms in the V 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:V170 b:28.3 occ:1.00 V A:VN4170 0.0 28.3 1.0 O1 A:VN4170 1.8 24.2 1.0 O2 A:VN4170 1.8 26.7 1.0 O3 A:VN4170 1.8 28.9 1.0 OD2 A:ASP10 2.1 23.1 1.0 O9 A:SLB171 2.1 25.9 0.5 C9 A:SLB171 3.0 37.8 0.5 CG A:ASP10 3.2 27.7 1.0 MG A:MG165 3.4 28.5 1.0 OD1 A:ASP10 3.4 25.0 1.0 OG1 A:THR54 3.7 23.1 1.0 O A:HOH289 3.7 25.8 1.0 NZ A:LYS80 3.8 29.0 1.0 N A:ASP12 3.8 22.1 1.0 OD1 A:ASP12 3.9 25.6 1.0 N A:ILE11 4.1 22.1 1.0 CB A:ASP12 4.2 22.3 1.0 N A:GLY55 4.2 23.3 1.0 O A:ASP12 4.3 22.4 1.0 CA A:THR54 4.4 22.8 1.0 C8 A:SLB171 4.4 43.1 1.0 CB A:THR54 4.4 22.5 1.0 ND2 A:ASN106 4.4 40.2 1.0 CA A:ASP12 4.5 22.1 1.0 CB A:ASP10 4.5 22.6 1.0 CG A:ASP12 4.5 24.5 1.0 O8 A:SLB171 4.6 49.6 1.0 C A:ILE11 4.7 21.9 1.0 O A:HOH288 4.8 24.5 1.0 CE A:LYS80 4.8 25.6 1.0 C A:THR54 4.8 23.7 1.0 CA A:ILE11 4.9 21.9 1.0 CA A:ASP10 4.9 22.4 1.0 C A:ASP12 4.9 22.2 1.0 O A:LEU53 4.9 23.8 1.0 OD1 A:ASN106 5.0 40.9 1.0 O A:HOH174 5.0 23.6 1.0

Vanadium 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 Vanadium with other atoms in the V 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:V170 b:27.9 occ:1.00 V B:VN4170 0.0 27.9 1.0 O1 B:VN4170 1.8 27.3 1.0 O2 B:VN4170 1.8 24.8 1.0 O3 B:VN4170 1.8 27.8 1.0 OD2 B:ASP10 2.1 25.6 1.0 O9 B:SLB171 2.1 23.1 0.5 C9 B:SLB171 3.0 43.0 0.5 CG B:ASP10 3.2 27.5 1.0 OD1 B:ASP10 3.4 26.1 1.0 MG B:MG165 3.5 29.6 1.0 OG1 B:THR54 3.6 25.1 1.0 O B:HOH261 3.7 25.9 1.0 NZ B:LYS80 3.8 28.1 1.0 N B:ASP12 3.8 21.8 1.0 OD2 B:ASP12 3.9 25.3 1.0 N B:ILE11 4.1 21.7 1.0 N B:GLY55 4.2 23.6 1.0 CB B:ASP12 4.2 22.2 1.0 O B:ASP12 4.3 22.2 1.0 CA B:THR54 4.3 22.9 1.0 CB B:THR54 4.3 23.4 1.0 ND2 B:ASN106 4.4 39.3 1.0 C8 B:SLB171 4.4 44.3 1.0 CA B:ASP12 4.5 21.9 1.0 CB B:ASP10 4.5 22.3 1.0 CG B:ASP12 4.5 24.0 1.0 O8 B:SLB171 4.5 46.3 1.0 O B:HOH260 4.7 25.7 1.0 C B:ILE11 4.8 21.5 1.0 C B:THR54 4.8 25.0 1.0 CE B:LYS80 4.8 27.4 1.0 CA B:ASP10 4.9 21.9 1.0 CA B:ILE11 4.9 21.5 1.0 C B:ASP12 4.9 22.0 1.0 O B:LEU53 4.9 24.8 1.0 OD1 B:ASN106 4.9 44.1 1.0

Vanadium 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 Vanadium with other atoms in the V 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:V169 b:32.2 occ:1.00 V C:VN4169 0.0 32.2 1.0 O1 C:VN4169 1.8 28.4 1.0 O2 C:VN4169 1.8 27.7 1.0 O3 C:VN4169 1.8 31.5 1.0 OD2 C:ASP10 2.1 25.0 1.0 O9 C:SLB171 2.1 29.4 0.5 C9 C:SLB171 3.0 38.0 0.5 CG C:ASP10 3.2 29.8 1.0 OD1 C:ASP10 3.4 29.4 1.0 MG C:MG165 3.4 29.6 1.0 OG1 C:THR54 3.7 29.0 1.0 O C:HOH256 3.7 30.2 1.0 NZ C:LYS80 3.7 28.2 1.0 N C:ASP12 3.8 23.0 1.0 OD1 C:ASP12 3.9 29.4 1.0 CB C:ASP12 4.1 23.4 1.0 N C:ILE11 4.1 23.5 1.0 N C:GLY55 4.2 26.4 1.0 CA C:THR54 4.3 25.6 1.0 O C:ASP12 4.3 23.7 1.0 CB C:THR54 4.3 27.0 1.0 C8 C:SLB171 4.4 41.9 1.0 ND2 C:ASN106 4.5 44.8 1.0 CA C:ASP12 4.5 22.8 1.0 CG C:ASP12 4.5 27.8 1.0 CB C:ASP10 4.5 26.6 1.0 O8 C:SLB171 4.6 46.6 1.0 O C:HOH257 4.7 28.0 1.0 C C:ILE11 4.7 23.6 1.0 CE C:LYS80 4.8 29.3 1.0 C C:THR54 4.8 28.7 1.0 O C:LEU53 4.9 28.2 1.0 CA C:ASP10 4.9 25.7 1.0 CA C:ILE11 4.9 23.5 1.0 OD1 C:ASN106 4.9 43.1 1.0 C C:ASP12 4.9 22.8 1.0

Vanadium 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 Vanadium with other atoms in the V 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:V169 b:30.8 occ:1.00 V D:VN4169 0.0 30.8 1.0 O1 D:VN4169 1.8 28.3 1.0 O2 D:VN4169 1.8 27.2 1.0 O3 D:VN4169 1.8 30.8 1.0 OD2 D:ASP10 2.1 27.4 1.0 O9 D:SLB170 2.1 28.6 0.5 C9 D:SLB170 3.0 35.5 0.5 CG D:ASP10 3.1 27.4 1.0 OD1 D:ASP10 3.4 28.2 1.0 MG D:MG165 3.5 31.6 1.0 OG1 D:THR54 3.7 28.1 1.0 O D:HOH256 3.7 28.6 1.0 NZ D:LYS80 3.7 27.6 1.0 OD2 D:ASP12 3.9 28.6 1.0 N D:ASP12 3.9 23.3 1.0 N D:GLY55 4.1 25.9 1.0 CB D:ASP12 4.1 23.4 1.0 N D:ILE11 4.2 23.7 1.0 O D:ASP12 4.3 24.1 1.0 C8 D:SLB170 4.4 39.5 1.0 CA D:THR54 4.4 28.7 1.0 CB D:ASP10 4.5 27.9 1.0 ND2 D:ASN106 4.5 41.7 1.0 CB D:THR54 4.5 27.5 1.0 CG D:ASP12 4.5 26.7 1.0 CA D:ASP12 4.5 23.1 1.0 O8 D:SLB170 4.6 48.0 1.0 O D:HOH255 4.7 27.0 1.0 C D:ILE11 4.8 23.1 1.0 CE D:LYS80 4.8 28.8 1.0 C D:THR54 4.8 28.6 1.0 O D:LEU53 4.9 27.7 1.0 CA D:ASP10 4.9 24.7 1.0 OD1 D:ASN106 4.9 41.9 1.0 C D:ASP12 4.9 23.2 1.0 CA D:ILE11 4.9 23.3 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