Magnesium in the structure of TAMAVIDIN2, Novel Avidin-Like Biotin-Binding Proteins From An Edible Mushroom (pdb 2zsc)

The binding sites of Magnesium atom in the structure of TAMAVIDIN2, Novel Avidin-Like Biotin-Binding Proteins From An Edible Mushroom (pdb code 2zsc). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2zsc structure was solved by Y.KAKUTA, N.OKINO, M.ITO, T.YAMAMOTO, Y.TAKAKURA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 18.7-1.3 Space group C121 a (A) 78.382 b (A) 80.017 c (A) 55.733 alpha (°) 90.00 beta (°) 132.32 gamma (°) 90.00 Rfactor (%) 19.9 Rfree (%) 23.8 Magnesium Binding Sites: Magnesium binding site 1 out of 3 in 2zsc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2zsc. 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: Asp40, A: Val41, A: Tyr42, A: Val43, A: Tyr45, A: Asn71, A: Gol1813, A: Hoh1969, A: Hoh1986, A: Hoh2022, conact list: Atom Atom Distance (A) Mg O A:Asp40 4.63 Mg O A:Val41 4.99 Mg N A:Val41 4.84 Mg CB A:Val41 4.09 Mg C A:Val41 3.79 Mg CG1 A:Val41 4.37 Mg CA A:Val41 3.62 Mg N A:Tyr42 3.01 Mg CB A:Tyr42 4.03 Mg CD1 A:Tyr42 3.71 Mg C A:Tyr42 4.36 Mg CE1 A:Tyr42 4.67 Mg CG A:Tyr42 4.31 Mg CA A:Tyr42 3.93 Mg N A:Val43 3.93 Mg CB A:Val43 4.77 Mg CG2 A:Val43 3.90 Mg CG1 A:Val43 4.90 Mg CA A:Val43 4.91 Mg CZ A:Tyr45 3.81 Mg CE1 A:Tyr45 3.88 Mg OH A:Tyr45 2.87 Mg CB A:Asn71 4.00 Mg ND2 A:Asn71 3.19 Mg CG A:Asn71 4.09 Mg O2 A:Gol1813 3.42 Mg C2 A:Gol1813 4.21 Mg O A:Hoh1969 2.51 Mg O A:Hoh1986 4.66 Mg O A:Hoh2022 4.42 interactive model: Magnesium binding site 2 out of 3 in 2zsc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2zsc. 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: Hoh3344, B: Hoh3355, B: Hoh3433, B: Hoh3441, B: Hoh3450, B: Hoh3472, B: Hoh3491, B: Hoh3508, B: Hoh3509, B: Hoh3510, B: Hoh3511, conact list: Atom Atom Distance (A) Mg O B:Hoh3344 4.49 Mg O B:Hoh3355 4.52 Mg O B:Hoh3433 2.06 Mg O B:Hoh3441 2.08 Mg O B:Hoh3450 1.99 Mg O B:Hoh3472 4.24 Mg O B:Hoh3491 4.28 Mg O B:Hoh3508 2.00 Mg O B:Hoh3509 2.56 Mg O B:Hoh3510 2.03 Mg O B:Hoh3511 4.10 interactive model: Magnesium binding site 3 out of 3 in 2zsc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2zsc. 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: Asp40, B: Val41, B: Tyr42, B: Val43, B: Tyr45, B: Asn71, B: Hoh3342, B: Hoh3503, conact list: Atom Atom Distance (A) Mg O B:Asp40 4.70 Mg N B:Val41 4.98 Mg CB B:Val41 4.28 Mg C B:Val41 3.96 Mg CG1 B:Val41 4.54 Mg CA B:Val41 3.79 Mg N B:Tyr42 3.17 Mg CB B:Tyr42 4.10 Mg CE2 B:Tyr42 4.60 Mg CD2 B:Tyr42 3.68 Mg C B:Tyr42 4.56 Mg CG B:Tyr42 4.32 Mg CA B:Tyr42 4.06 Mg N B:Val43 4.16 Mg CG2 B:Val43 4.05 Mg CZ B:Tyr45 3.90 Mg CE1 B:Tyr45 3.94 Mg OH B:Tyr45 2.97 Mg CB B:Asn71 4.03 Mg ND2 B:Asn71 3.30 Mg CG B:Asn71 4.17 Mg O B:Hoh3342 4.84 Mg O B:Hoh3503 3.23 interactive model: