Vanadium in the structure of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex With Metavanadate (pdb 1dkt)

The binding sites of Vanadium atom in the structure of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex With Metavanadate (pdb code 1dkt). This binding sites where shown with 5.0 Angstroms radius around Vanadium atom. The 1dkt structure was solved by Y.BOURNE, A.S.ARVAI, J.A.TAINER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 6.0-2.9 Space group P6122 a (A) 94.000 b (A) 94.000 c (A) 131.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.5 Rfree (%) 25.8 Vanadium Binding Sites: Vanadium binding site 1 out of 7 in 1dkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Vanadium in the PDB 1dkt. 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: Ser51, A: Arg71, A: V7o100, A: Hoh559, A: Hoh561, A: Hoh581, A: Hoh583, conact list: Atom Atom Distance (A) V CB A:Ser51 3.41 V OG A:Ser51 3.30 V CA A:Ser51 4.59 V CZ A:Arg71 4.38 V NH2 A:Arg71 4.53 V NH1 A:Arg71 3.44 V O5 A:V7o100 4.34 V V3 A:V7o100 3.18 V O8 A:V7o100 4.44 V O1 A:V7o100 1.64 V V1 A:V7o100 0.00 V O3 A:V7o100 1.52 V O2 A:V7o100 1.70 V O9 A:V7o100 4.45 V V2 A:V7o100 3.01 V O7 A:V7o100 3.92 V O4 A:V7o100 1.74 V O6 A:V7o100 3.78 V O A:Hoh559 3.93 V O A:Hoh561 3.77 V O A:Hoh581 4.11 V O A:Hoh583 4.17 interactive model: Vanadium binding site 2 out of 7 in 1dkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Vanadium in the PDB 1dkt. 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: Lys11, A: Arg71, A: V7o100, A: Hoh559, A: Hoh560, A: Hoh583, conact list: Atom Atom Distance (A) V CE A:Lys11 4.99 V CZ A:Arg71 3.70 V NE A:Arg71 4.89 V NH2 A:Arg71 2.96 V NH1 A:Arg71 3.72 V O5 A:V7o100 1.56 V V3 A:V7o100 3.14 V O8 A:V7o100 3.32 V O1 A:V7o100 3.81 V V1 A:V7o100 3.01 V O3 A:V7o100 4.20 V O2 A:V7o100 2.97 V O9 A:V7o100 3.79 V V2 A:V7o100 0.00 V O7 A:V7o100 4.75 V O4 A:V7o100 1.88 V O6 A:V7o100 1.58 V O A:Hoh559 4.78 V O A:Hoh560 3.85 V O A:Hoh583 3.81 interactive model: Vanadium binding site 3 out of 7 in 1dkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Vanadium in the PDB 1dkt. 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: Lys11, A: Arg20, A: Ser51, A: Trp54, A: Arg71, A: V7o100, A: Hoh551, A: Hoh559, A: Hoh560, A: Hoh583, conact list: Atom Atom Distance (A) V CE A:Lys11 4.44 V NZ A:Lys11 4.61 V NH1 A:Arg20 4.10 V N A:Ser51 4.71 V CB A:Ser51 3.85 V OG A:Ser51 4.70 V CA A:Ser51 4.88 V CD1 A:Trp54 4.91 V CZ2 A:Trp54 4.84 V CE2 A:Trp54 4.76 V NE1 A:Trp54 3.92 V CZ A:Arg71 3.98 V NH2 A:Arg71 3.66 V NH1 A:Arg71 3.43 V O5 A:V7o100 3.50 V V3 A:V7o100 0.00 V O8 A:V7o100 1.54 V O1 A:V7o100 4.72 V V1 A:V7o100 3.18 V O3 A:V7o100 3.43 V V4 A:V7o100 3.33 V O10 A:V7o100 3.95 V O2 A:V7o100 3.27 V O9 A:V7o100 1.73 V V2 A:V7o100 3.14 V O11 A:V7o100 4.22 V O7 A:V7o100 1.70 V O4 A:V7o100 1.81 V O12 A:V7o100 4.90 V O6 A:V7o100 4.34 V O A:Hoh551 4.30 V O A:Hoh559 3.12 V O A:Hoh560 4.50 V O A:Hoh583 4.94 interactive model: Vanadium binding site 4 out of 7 in 1dkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Vanadium in the PDB 1dkt. 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: Lys11, A: Arg20, B: Arg20, A: V7o100, A: Hoh547, A: Hoh551, A: Hoh552, A: Hoh558, A: Hoh559, A: Hoh560, conact list: Atom Atom Distance (A) V NZ A:Lys11 4.33 V CZ A:Arg20 4.88 V NH2 A:Arg20 4.55 V NH1 A:Arg20 4.52 V NH2 B:Arg20 4.71 V O5 A:V7o100 4.98 V V3 A:V7o100 3.33 V O8 A:V7o100 3.36 V V5 A:V7o100 3.06 V O16 A:V7o100 3.80 V V6 A:V7o100 4.49 V V4 A:V7o100 0.00 V O10 A:V7o100 1.50 V O15 A:V7o100 4.48 V O9 A:V7o100 1.81 V O13 A:V7o100 4.08 V O14 A:V7o100 4.19 V O11 A:V7o100 1.48 V O7 A:V7o100 3.59 V O4 A:V7o100 4.58 V O12 A:V7o100 1.75 V O A:Hoh547 4.68 V O A:Hoh551 3.33 V O A:Hoh552 4.17 V O A:Hoh558 4.86 V O A:Hoh559 2.94 V O A:Hoh560 4.06 interactive model: Vanadium binding site 5 out of 7 in 1dkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Vanadium in the PDB 1dkt. 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: Lys11, B: Arg20, B: Trp54, B: Arg71, A: V7o100, A: Hoh556, A: Hoh558, A: Hoh559, A: Hoh560, A: Hoh583, conact list: Atom Atom Distance (A) V CE B:Lys11 4.83 V NZ B:Lys11 4.24 V NH2 B:Arg20 3.85 V NE1 B:Trp54 4.81 V CZ B:Arg71 4.85 V NH2 B:Arg71 4.38 V NH1 B:Arg71 4.38 V O18 A:V7o100 4.07 V O19 A:V7o100 4.04 V V5 A:V7o100 0.00 V O16 A:V7o100 3.52 V V6 A:V7o100 3.07 V V7 A:V7o100 3.15 V V4 A:V7o100 3.06 V O10 A:V7o100 4.23 V O15 A:V7o100 3.13 V O9 A:V7o100 4.16 V O13 A:V7o100 1.53 V O14 A:V7o100 1.74 V O11 A:V7o100 3.65 V O17 A:V7o100 3.29 V O12 A:V7o100 1.71 V O A:Hoh556 4.40 V O A:Hoh558 4.92 V O A:Hoh559 3.18 V O A:Hoh560 4.06 V O A:Hoh583 4.88 interactive model: Vanadium binding site 6 out of 7 in 1dkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Vanadium in the PDB 1dkt. 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: Arg20, B: Gln50, B: Ser51, B: Trp54, B: Arg71, A: V7o100, A: Hoh560, A: Hoh582, A: Hoh583, conact list: Atom Atom Distance (A) V NH2 B:Arg20 4.69 V C B:Gln50 4.74 V N B:Ser51 3.60 V CB B:Ser51 3.12 V OG B:Ser51 2.98 V CA B:Ser51 3.97 V CD1 B:Trp54 4.30 V NE1 B:Trp54 3.86 V NH1 B:Arg71 3.97 V O18 A:V7o100 2.90 V O19 A:V7o100 4.30 V V5 A:V7o100 3.07 V O16 A:V7o100 1.53 V V6 A:V7o100 0.00 V V7 A:V7o100 2.81 V V4 A:V7o100 4.49 V O15 A:V7o100 1.50 V O13 A:V7o100 3.90 V O14 A:V7o100 1.78 V O11 A:V7o100 4.12 V O17 A:V7o100 3.81 V O12 A:V7o100 3.44 V O A:Hoh560 2.99 V O A:Hoh582 4.81 V O A:Hoh583 4.94 interactive model: Vanadium binding site 7 out of 7 in 1dkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Vanadium in the PDB 1dkt. 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: Ser51, B: Trp54, B: Arg71, A: V7o100, A: Hoh556, A: Hoh557, A: Hoh559, A: Hoh560, A: Hoh581, A: Hoh582, A: Hoh583, B: Hoh555, conact list: Atom Atom Distance (A) V CB B:Ser51 3.94 V OG B:Ser51 3.35 V NE1 B:Trp54 4.78 V CZ B:Arg71 3.84 V NH2 B:Arg71 3.88 V NH1 B:Arg71 2.94 V O18 A:V7o100 1.46 V O19 A:V7o100 1.55 V V5 A:V7o100 3.15 V O16 A:V7o100 4.22 V V6 A:V7o100 2.81 V V7 A:V7o100 0.00 V O15 A:V7o100 3.78 V O13 A:V7o100 3.82 V O14 A:V7o100 1.73 V O17 A:V7o100 1.72 V O12 A:V7o100 4.59 V O A:Hoh556 3.80 V O A:Hoh557 4.28 V O A:Hoh559 4.92 V O A:Hoh560 3.91 V O A:Hoh581 4.82 V O A:Hoh582 4.52 V O A:Hoh583 3.98 V O B:Hoh555 3.89 interactive model: