Magnesium in the structure of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate (pdb 2w0s)

The binding sites of Magnesium atom in the structure of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate (pdb code 2w0s). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2w0s structure was solved by C.CAILLAT, D.TOPALIS, L.A.AGROFOGLIO, S.POCHET, J.BALZARINI, D.DEVILLE-BONNE, P.MEYER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.9-2.9 Space group P212121 a (A) 58.370 b (A) 78.350 c (A) 95.040 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.24 Rfree (%) 28.28 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 2w0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2w0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys17, A: Thr18, A: Tyr35, A: Asn37, A: Asp92, A: Bvp1207, A: So41208, conact list: Atom Atom Distance (A) Mg NZ A:Lys17 4.62 Mg CB A:Thr18 4.25 Mg CG2 A:Thr18 4.38 Mg OG1 A:Thr18 2.99 Mg OH A:Tyr35 4.96 Mg ND2 A:Asn37 3.31 Mg OD1 A:Asn37 3.51 Mg CG A:Asn37 3.84 Mg CB A:Asp92 4.85 Mg OD2 A:Asp92 3.03 Mg OD1 A:Asp92 4.27 Mg CG A:Asp92 3.84 Mg P A:Bvp1207 4.22 Mg O3P A:Bvp1207 4.45 Mg O1P A:Bvp1207 4.29 Mg O2P A:Bvp1207 3.31 Mg O4 A:So41208 3.91 interactive model: Magnesium binding site 2 out of 4 in 2w0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2w0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp13, A: Lys14, A: Glu142, A: Glu145, A: Bvp1207, A: So41208, conact list: Atom Atom Distance (A) Mg CB A:Asp13 4.69 Mg OD2 A:Asp13 4.45 Mg OD1 A:Asp13 2.43 Mg CG A:Asp13 3.69 Mg CE A:Lys14 4.66 Mg NZ A:Lys14 4.61 Mg OE1 A:Glu142 3.45 Mg CB A:Glu142 4.90 Mg CD A:Glu142 4.41 Mg CG A:Glu142 4.96 Mg OE1 A:Glu145 4.72 Mg OE2 A:Glu145 2.53 Mg CD A:Glu145 3.72 Mg CG A:Glu145 4.35 Mg P A:Bvp1207 3.72 Mg O3P A:Bvp1207 3.44 Mg C5' A:Bvp1207 4.23 Mg O1P A:Bvp1207 3.00 Mg O5' A:Bvp1207 4.36 Mg O2 A:So41208 4.71 interactive model: Magnesium binding site 3 out of 4 in 2w0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2w0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Lys17, B: Thr18, B: Tyr35, B: Asn37, B: Phe38, B: Asp92, B: Bvp1207, B: So41208, conact list: Atom Atom Distance (A) Mg NZ B:Lys17 4.36 Mg CB B:Thr18 4.60 Mg CG2 B:Thr18 4.72 Mg OG1 B:Thr18 3.35 Mg OH B:Tyr35 4.83 Mg CB B:Asn37 4.98 Mg ND2 B:Asn37 3.11 Mg OD1 B:Asn37 2.99 Mg CG B:Asn37 3.44 Mg O B:Phe38 4.63 Mg CB B:Asp92 4.18 Mg OD2 B:Asp92 2.66 Mg OD1 B:Asp92 3.76 Mg CG B:Asp92 3.28 Mg P B:Bvp1207 4.12 Mg O3P B:Bvp1207 4.40 Mg O1P B:Bvp1207 3.25 Mg O2P B:Bvp1207 4.01 Mg O4 B:So41208 3.87 interactive model: Magnesium binding site 4 out of 4 in 2w0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2w0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp13, B: Arg41, B: Glu142, B: Glu145, B: Bvp1207, B: So41208, conact list: Atom Atom Distance (A) Mg CB B:Asp13 4.73 Mg OD2 B:Asp13 4.29 Mg OD1 B:Asp13 2.42 Mg CG B:Asp13 3.64 Mg NH2 B:Arg41 4.71 Mg OE1 B:Glu142 3.36 Mg CB B:Glu142 4.98 Mg CD B:Glu142 4.39 Mg OE2 B:Glu145 2.90 Mg CD B:Glu145 4.06 Mg CG B:Glu145 4.57 Mg P B:Bvp1207 3.56 Mg O3P B:Bvp1207 2.55 Mg C5' B:Bvp1207 3.70 Mg C4' B:Bvp1207 4.87 Mg O5' B:Bvp1207 4.05 Mg O2P B:Bvp1207 3.90 Mg O3 B:So41208 4.88 interactive model: