Magnesium in the structure of Crystal Structure of Hemolytic Lectin Cel-III (pdb 1vcl)

The binding sites of Magnesium atom in the structure of Crystal Structure of Hemolytic Lectin Cel-III (pdb code 1vcl). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1vcl structure was solved by T.UCHIDA, T.YAMASAKI, S.ETO, H.SUGAWARA, G.KURISU, A.NAKAGAWA, M.KUSUNOKI, T.HATAKEYAMA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 26.2-1.7 Space group P1211 a (A) 52.420 b (A) 65.370 c (A) 126.020 alpha (°) 90.00 beta (°) 98.18 gamma (°) 90.00 Rfactor (%) 16.5 Rfree (%) 20.1 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1vcl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1vcl. 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: Asn32, A: Ile33, A: Ala34, A: Asn72, A: Val73, A: Met74, A: Asp130, A: Ile131, A: Gly132, A: Hoh1390, A: Hoh1581, conact list: Atom Atom Distance (A) Mg CB A:Asn32 4.68 Mg ND2 A:Asn32 4.14 Mg C A:Asn32 4.59 Mg OD1 A:Asn32 2.41 Mg CG A:Asn32 3.52 Mg CA A:Asn32 4.81 Mg O A:Ile33 2.36 Mg N A:Ile33 3.56 Mg CB A:Ile33 4.36 Mg C A:Ile33 3.44 Mg CA A:Ile33 3.96 Mg N A:Ala34 4.58 Mg CB A:Asn72 4.58 Mg ND2 A:Asn72 3.67 Mg C A:Asn72 4.70 Mg OD1 A:Asn72 2.31 Mg CG A:Asn72 3.28 Mg CA A:Asn72 4.78 Mg O A:Val73 2.69 Mg N A:Val73 3.76 Mg CB A:Val73 4.82 Mg C A:Val73 3.77 Mg CA A:Val73 4.30 Mg N A:Met74 4.89 Mg CB A:Asp130 4.76 Mg C A:Asp130 4.59 Mg CA A:Asp130 4.79 Mg O A:Ile131 2.45 Mg N A:Ile131 3.60 Mg CB A:Ile131 4.46 Mg C A:Ile131 3.54 Mg CA A:Ile131 4.04 Mg N A:Gly132 4.70 Mg O A:Hoh1390 2.26 Mg O A:Hoh1581 4.14 interactive model: Magnesium binding site 2 out of 4 in 1vcl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1vcl. 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: Asn177, A: Val178, A: Leu179, A: Asn218, A: Val219, A: Gly220, A: Asp265, A: Val266, A: Gly267, A: Hoh1380, A: Hoh1424, conact list: Atom Atom Distance (A) Mg CB A:Asn177 4.46 Mg ND2 A:Asn177 3.55 Mg C A:Asn177 4.47 Mg OD1 A:Asn177 2.26 Mg CG A:Asn177 3.19 Mg CA A:Asn177 4.63 Mg O A:Val178 2.33 Mg N A:Val178 3.55 Mg CB A:Val178 4.50 Mg C A:Val178 3.42 Mg CA A:Val178 3.98 Mg N A:Leu179 4.57 Mg CA A:Leu179 4.98 Mg CB A:Asn218 4.70 Mg ND2 A:Asn218 3.63 Mg C A:Asn218 4.74 Mg OD1 A:Asn218 2.50 Mg CG A:Asn218 3.38 Mg CA A:Asn218 4.92 Mg O A:Val219 2.56 Mg N A:Val219 3.78 Mg CB A:Val219 4.64 Mg C A:Val219 3.66 Mg CA A:Val219 4.19 Mg N A:Gly220 4.79 Mg CB A:Asp265 4.68 Mg OD2 A:Asp265 4.06 Mg C A:Asp265 4.53 Mg OD1 A:Asp265 2.46 Mg CG A:Asp265 3.55 Mg CA A:Asp265 4.77 Mg O A:Val266 2.43 Mg N A:Val266 3.51 Mg CB A:Val266 4.27 Mg C A:Val266 3.48 Mg CA A:Val266 3.95 Mg N A:Gly267 4.66 Mg O A:Hoh1380 4.23 Mg O A:Hoh1424 3.98 interactive model: Magnesium binding site 3 out of 4 in 1vcl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1vcl. 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: Asn32, B: Ile33, B: Ala34, B: Asn72, B: Val73, B: Met74, B: Asp130, B: Ile131, B: Gly132, B: Hoh2477, B: Hoh2607, conact list: Atom Atom Distance (A) Mg CB B:Asn32 4.65 Mg ND2 B:Asn32 3.70 Mg C B:Asn32 4.61 Mg OD1 B:Asn32 2.47 Mg CG B:Asn32 3.36 Mg CA B:Asn32 4.81 Mg O B:Ile33 2.37 Mg N B:Ile33 3.59 Mg CB B:Ile33 4.43 Mg C B:Ile33 3.47 Mg CA B:Ile33 4.02 Mg N B:Ala34 4.61 Mg CB B:Asn72 4.47 Mg ND2 B:Asn72 3.54 Mg C B:Asn72 4.68 Mg OD1 B:Asn72 2.17 Mg CG B:Asn72 3.14 Mg CA B:Asn72 4.75 Mg O B:Val73 2.67 Mg N B:Val73 3.75 Mg CB B:Val73 4.83 Mg C B:Val73 3.77 Mg CA B:Val73 4.30 Mg N B:Met74 4.90 Mg CB B:Asp130 4.76 Mg C B:Asp130 4.60 Mg CA B:Asp130 4.79 Mg O B:Ile131 2.40 Mg N B:Ile131 3.62 Mg CB B:Ile131 4.45 Mg C B:Ile131 3.48 Mg CA B:Ile131 4.00 Mg N B:Gly132 4.62 Mg O B:Hoh2477 4.01 Mg O B:Hoh2607 2.24 interactive model: Magnesium binding site 4 out of 4 in 1vcl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1vcl. 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: Asn177, B: Val178, B: Leu179, B: Asn218, B: Val219, B: Gly220, B: Asp265, B: Val266, B: Gly267, B: Hoh2254, B: Hoh2312, conact list: Atom Atom Distance (A) Mg CB B:Asn177 4.50 Mg ND2 B:Asn177 3.60 Mg C B:Asn177 4.49 Mg OD1 B:Asn177 2.30 Mg CG B:Asn177 3.23 Mg CA B:Asn177 4.66 Mg O B:Val178 2.43 Mg N B:Val178 3.56 Mg CB B:Val178 4.44 Mg C B:Val178 3.49 Mg CA B:Val178 4.00 Mg N B:Leu179 4.66 Mg CB B:Asn218 4.59 Mg ND2 B:Asn218 3.52 Mg C B:Asn218 4.65 Mg OD1 B:Asn218 2.38 Mg CG B:Asn218 3.25 Mg CA B:Asn218 4.80 Mg O B:Val219 2.48 Mg N B:Val219 3.72 Mg CB B:Val219 4.62 Mg C B:Val219 3.59 Mg CA B:Val219 4.14 Mg N B:Gly220 4.73 Mg CB B:Asp265 4.70 Mg OD2 B:Asp265 4.09 Mg C B:Asp265 4.58 Mg OD1 B:Asp265 2.49 Mg CG B:Asp265 3.57 Mg CA B:Asp265 4.85 Mg O B:Val266 2.39 Mg N B:Val266 3.54 Mg CB B:Val266 4.30 Mg C B:Val266 3.45 Mg CA B:Val266 3.94 Mg N B:Gly267 4.63 Mg O B:Hoh2254 4.20 Mg O B:Hoh2312 3.95 interactive model: