Vanadium in the structure of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi With Bound Vanadate and Adp (pdb 4dz6)

The binding sites of Vanadium atom in the structure of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi With Bound Vanadate and Adp (pdb code 4dz6). This binding sites where shown with 5.0 Angstroms radius around Vanadium atom. The 4dz6 structure was solved by SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 99.5-2.2 Space group P212121 a (A) 78.650 b (A) 81.000 c (A) 181.430 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.3 Rfree (%) 22.3 Vanadium Binding Sites: Vanadium binding site 1 out of 6 in 4dz6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Vanadium in the PDB 4dz6. 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: Lys13, A: Tyr53, A: Arg94, A: Arg111, A: His134, A: Ala135, A: Adp1001, A: Vn41002, conact list: Atom Atom Distance (A) V CE A:Lys13 4.95 V NZ A:Lys13 4.53 V CE1 A:Tyr53 4.75 V OH A:Tyr53 4.37 V NH2 A:Arg94 4.46 V NH2 A:Arg111 4.34 V NE2 A:His134 4.42 V CB A:His134 3.88 V ND1 A:His134 2.48 V CD2 A:His134 4.56 V C A:His134 4.65 V CE1 A:His134 3.26 V CG A:His134 3.49 V CA A:His134 4.02 V O A:Ala135 4.30 V N A:Ala135 4.24 V O3B A:Adp1001 2.01 V C3' A:Adp1001 4.68 V PA A:Adp1001 4.68 V O1B A:Adp1001 3.40 V PB A:Adp1001 3.16 V O3' A:Adp1001 3.84 V C5' A:Adp1001 4.13 V C4' A:Adp1001 4.58 V O5' A:Adp1001 4.94 V O2B A:Adp1001 4.23 V O3A A:Adp1001 4.19 V O1A A:Adp1001 4.11 V O1 A:Vn41002 1.92 V O2 A:Vn41002 1.92 V O3 A:Vn41002 1.91 V V A:Vn41002 0.00 interactive model: Vanadium binding site 2 out of 6 in 4dz6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Vanadium in the PDB 4dz6. 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: Lys13, B: Tyr53, B: Arg94, B: Arg111, B: His134, B: Ala135, B: Vo4201, conact list: Atom Atom Distance (A) V CE B:Lys13 4.75 V NZ B:Lys13 4.13 V CZ B:Tyr53 4.81 V CE1 B:Tyr53 4.44 V OH B:Tyr53 4.18 V NH2 B:Arg94 4.91 V NH2 B:Arg111 4.62 V NE2 B:His134 4.68 V CB B:His134 4.04 V ND1 B:His134 2.70 V CD2 B:His134 4.81 V C B:His134 4.96 V CE1 B:His134 3.51 V CG B:His134 3.72 V CA B:His134 4.19 V O B:Ala135 4.78 V N B:Ala135 4.59 V O1 B:Vo4201 1.91 V O2 B:Vo4201 1.93 V O4 B:Vo4201 1.89 V O3 B:Vo4201 1.92 V V B:Vo4201 0.00 interactive model: Vanadium binding site 3 out of 6 in 4dz6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Vanadium in the PDB 4dz6. 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: Lys13, C: Tyr53, C: Arg94, C: Arg111, C: Ile133, C: His134, C: Ala135, C: Adp1001, C: Vn41002, conact list: Atom Atom Distance (A) V CE C:Lys13 4.95 V NZ C:Lys13 4.53 V CE1 C:Tyr53 4.80 V OH C:Tyr53 4.49 V NH2 C:Arg94 4.45 V NH2 C:Arg111 4.18 V O C:Ile133 4.97 V NE2 C:His134 4.55 V CB C:His134 3.77 V ND1 C:His134 2.53 V CD2 C:His134 4.61 V C C:His134 4.63 V CE1 C:His134 3.42 V CG C:His134 3.48 V CA C:His134 3.96 V O C:Ala135 4.48 V N C:Ala135 4.23 V O3B C:Adp1001 3.21 V C3' C:Adp1001 4.46 V PA C:Adp1001 4.69 V O1B C:Adp1001 1.91 V PB C:Adp1001 3.00 V O3' C:Adp1001 3.61 V C5' C:Adp1001 4.14 V C4' C:Adp1001 4.49 V O5' C:Adp1001 4.93 V O2B C:Adp1001 4.05 V O3A C:Adp1001 4.16 V O1A C:Adp1001 4.07 V O1 C:Vn41002 1.91 V O2 C:Vn41002 1.92 V O3 C:Vn41002 1.91 V V C:Vn41002 0.00 interactive model: Vanadium binding site 4 out of 6 in 4dz6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Vanadium in the PDB 4dz6. 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: Lys13, D: Tyr53, D: Arg111, D: His134, D: Ala135, D: Adp1001, D: Vn41002, conact list: Atom Atom Distance (A) V CE D:Lys13 4.72 V NZ D:Lys13 4.35 V CZ D:Tyr53 4.63 V CE1 D:Tyr53 4.34 V OH D:Tyr53 3.90 V NH2 D:Arg111 4.60 V NE2 D:His134 4.45 V CB D:His134 3.81 V ND1 D:His134 2.42 V CD2 D:His134 4.57 V C D:His134 4.86 V CE1 D:His134 3.27 V CG D:His134 3.46 V CA D:His134 4.11 V O D:Ala135 4.72 V N D:Ala135 4.54 V O3B D:Adp1001 1.98 V C3' D:Adp1001 4.15 V PA D:Adp1001 4.52 V O2A D:Adp1001 4.08 V O1B D:Adp1001 4.22 V PB D:Adp1001 3.09 V O3' D:Adp1001 3.32 V C5' D:Adp1001 3.63 V C4' D:Adp1001 3.98 V O5' D:Adp1001 4.53 V O2B D:Adp1001 3.28 V O3A D:Adp1001 4.07 V O1 D:Vn41002 1.92 V O2 D:Vn41002 1.92 V O3 D:Vn41002 1.90 V V D:Vn41002 0.00 interactive model: Vanadium binding site 5 out of 6 in 4dz6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Vanadium in the PDB 4dz6. 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: E: Lys13, E: Tyr53, E: Arg94, E: Arg111, E: His134, E: Ala135, E: Vo4201, conact list: Atom Atom Distance (A) V CE E:Lys13 4.77 V NZ E:Lys13 4.46 V CZ E:Tyr53 4.74 V CE1 E:Tyr53 4.36 V OH E:Tyr53 4.09 V NH1 E:Arg94 4.70 V NH2 E:Arg111 4.62 V NE2 E:His134 4.40 V CB E:His134 3.73 V ND1 E:His134 2.36 V CD2 E:His134 4.49 V C E:His134 4.68 V CE1 E:His134 3.23 V CG E:His134 3.38 V CA E:His134 3.99 V O E:Ala135 4.50 V N E:Ala135 4.34 V O1 E:Vo4201 1.96 V O2 E:Vo4201 1.95 V O4 E:Vo4201 1.93 V O3 E:Vo4201 1.93 V V E:Vo4201 0.00 interactive model: Vanadium binding site 6 out of 6 in 4dz6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Vanadium in the PDB 4dz6. 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: F: Lys13, F: Tyr53, F: Arg94, F: Arg111, F: Ile133, F: His134, F: Ala135, F: Vo4201, conact list: Atom Atom Distance (A) V CE F:Lys13 4.70 V NZ F:Lys13 4.24 V CE1 F:Tyr53 4.66 V OH F:Tyr53 4.39 V NH1 F:Arg94 4.59 V NH2 F:Arg111 4.34 V O F:Ile133 4.91 V NE2 F:His134 4.88 V CB F:His134 4.13 V ND1 F:His134 2.90 V CD2 F:His134 4.98 V CE1 F:His134 3.72 V CG F:His134 3.87 V CA F:His134 4.25 V O F:Ala135 4.75 V N F:Ala135 4.66 V O1 F:Vo4201 1.92 V O2 F:Vo4201 1.91 V O4 F:Vo4201 1.92 V O3 F:Vo4201 1.92 V V F:Vo4201 0.00 interactive model: