Vanadium in 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 3e81)

The binding sites of Vanadium atom in 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). This binding sites where shown with 5.0 Angstroms radius around Vanadium atom. The 3e81 structure was solved by Z.LU, L.WANG, D.DUNAWAY-MARIANO, K.N.ALLEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 49.1-1.6 Space group P21212 a (A) 81.958 b (A) 106.602 c (A) 74.830 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.4 Rfree (%) 20.7 Vanadium Binding Sites: Vanadium binding site 1 out of 4 in 3e81 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Vanadium in the PDB 3e81. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Vanadium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp10, A: Ile11, A: Asp12, A: Leu53, A: Thr54, A: Gly55, A: Lys80, A: Asn106, A: Mg165, A: Vn4170, A: Slb171, A: Hoh174, A: Hoh288, A: Hoh289, conact list: Atom Atom Distance (A) V CB A:Asp10 4.51 V OD2 A:Asp10 2.10 V OD1 A:Asp10 3.44 V CG A:Asp10 3.17 V CA A:Asp10 4.87 V N A:Ile11 4.14 V C A:Ile11 4.74 V CA A:Ile11 4.86 V O A:Asp12 4.27 V N A:Asp12 3.84 V CB A:Asp12 4.15 V C A:Asp12 4.87 V OD1 A:Asp12 3.93 V CG A:Asp12 4.54 V CA A:Asp12 4.50 V O A:Leu53 4.92 V CB A:Thr54 4.42 V OG1 A:Thr54 3.70 V C A:Thr54 4.82 V CA A:Thr54 4.36 V N A:Gly55 4.15 V CE A:Lys80 4.79 V NZ A:Lys80 3.81 V ND2 A:Asn106 4.44 V OD1 A:Asn106 4.98 V MG A:Mg165 3.43 V O1 A:Vn4170 1.76 V O2 A:Vn4170 1.78 V O3 A:Vn4170 1.79 V V A:Vn4170 0.00 V C9 A:Slb171 2.96 V O8 A:Slb171 4.58 V C8 A:Slb171 4.38 V O9 A:Slb171 2.10 V O A:Hoh174 5.00 V O A:Hoh288 4.77 V O A:Hoh289 3.74 interactive model: Vanadium binding site 2 out of 4 in 3e81 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Vanadium in the PDB 3e81. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Vanadium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp10, B: Ile11, B: Asp12, B: Leu53, B: Thr54, B: Gly55, B: Lys80, B: Asn106, B: Mg165, B: Vn4170, B: Slb171, B: Hoh260, B: Hoh261, conact list: Atom Atom Distance (A) V CB B:Asp10 4.52 V OD2 B:Asp10 2.09 V OD1 B:Asp10 3.44 V CG B:Asp10 3.16 V CA B:Asp10 4.86 V N B:Ile11 4.15 V C B:Ile11 4.76 V CA B:Ile11 4.88 V O B:Asp12 4.30 V N B:Asp12 3.84 V CB B:Asp12 4.17 V OD2 B:Asp12 3.91 V C B:Asp12 4.88 V CG B:Asp12 4.53 V CA B:Asp12 4.48 V O B:Leu53 4.91 V CB B:Thr54 4.34 V OG1 B:Thr54 3.60 V C B:Thr54 4.79 V CA B:Thr54 4.31 V N B:Gly55 4.16 V CE B:Lys80 4.83 V NZ B:Lys80 3.83 V ND2 B:Asn106 4.36 V OD1 B:Asn106 4.93 V MG B:Mg165 3.46 V O1 B:Vn4170 1.77 V O2 B:Vn4170 1.78 V O3 B:Vn4170 1.80 V V B:Vn4170 0.00 V C9 B:Slb171 3.00 V O8 B:Slb171 4.54 V C8 B:Slb171 4.38 V O9 B:Slb171 2.11 V O B:Hoh260 4.71 V O B:Hoh261 3.71 interactive model: Vanadium binding site 3 out of 4 in 3e81 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Vanadium in the PDB 3e81. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Vanadium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asp10, C: Ile11, C: Asp12, C: Leu53, C: Thr54, C: Gly55, C: Lys80, C: Asn106, C: Slb171, C: Mg165, C: Vn4169, C: Hoh256, C: Hoh257, conact list: Atom Atom Distance (A) V CB C:Asp10 4.52 V OD2 C:Asp10 2.10 V OD1 C:Asp10 3.42 V CG C:Asp10 3.16 V CA C:Asp10 4.86 V N C:Ile11 4.14 V C C:Ile11 4.74 V CA C:Ile11 4.87 V O C:Asp12 4.32 V N C:Asp12 3.84 V CB C:Asp12 4.11 V C C:Asp12 4.90 V OD1 C:Asp12 3.89 V CG C:Asp12 4.50 V CA C:Asp12 4.48 V O C:Leu53 4.85 V CB C:Thr54 4.33 V OG1 C:Thr54 3.67 V C C:Thr54 4.79 V CA C:Thr54 4.28 V N C:Gly55 4.17 V CE C:Lys80 4.78 V NZ C:Lys80 3.72 V ND2 C:Asn106 4.45 V OD1 C:Asn106 4.88 V C9 C:Slb171 2.97 V O8 C:Slb171 4.61 V C8 C:Slb171 4.37 V O9 C:Slb171 2.11 V MG C:Mg165 3.43 V O1 C:Vn4169 1.75 V O2 C:Vn4169 1.79 V O3 C:Vn4169 1.80 V V C:Vn4169 0.00 V O C:Hoh256 3.68 V O C:Hoh257 4.70 interactive model: Vanadium binding site 4 out of 4 in 3e81 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Vanadium in the PDB 3e81. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Vanadium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asp10, D: Ile11, D: Asp12, D: Leu53, D: Thr54, D: Gly55, D: Lys80, D: Asn106, D: Slb170, D: Mg165, D: Vn4169, D: Hoh255, D: Hoh256, conact list: Atom Atom Distance (A) V CB D:Asp10 4.49 V OD2 D:Asp10 2.09 V OD1 D:Asp10 3.42 V CG D:Asp10 3.14 V CA D:Asp10 4.88 V N D:Ile11 4.18 V C D:Ile11 4.77 V CA D:Ile11 4.92 V O D:Asp12 4.32 V N D:Asp12 3.89 V CB D:Asp12 4.14 V OD2 D:Asp12 3.87 V C D:Asp12 4.91 V CG D:Asp12 4.50 V CA D:Asp12 4.51 V O D:Leu53 4.88 V CB D:Thr54 4.50 V OG1 D:Thr54 3.66 V C D:Thr54 4.82 V CA D:Thr54 4.41 V N D:Gly55 4.11 V CE D:Lys80 4.78 V NZ D:Lys80 3.74 V ND2 D:Asn106 4.50 V OD1 D:Asn106 4.90 V C9 D:Slb170 2.96 V O8 D:Slb170 4.55 V C8 D:Slb170 4.35 V O9 D:Slb170 2.10 V MG D:Mg165 3.48 V O1 D:Vn4169 1.77 V O2 D:Vn4169 1.78 V O3 D:Vn4169 1.80 V V D:Vn4169 0.00 V O D:Hoh255 4.67 V O D:Hoh256 3.73 interactive model: