Magnesium in the structure of X-Ray Structure of Gene Product From Arabidopsis Thaliana AT5G08170, Agmatine Iminohydrolase (pdb 1vkp)

The binding sites of Magnesium atom in the structure of X-Ray Structure of Gene Product From Arabidopsis Thaliana AT5G08170, Agmatine Iminohydrolase (pdb code 1vkp). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1vkp structure was solved by G.E.WESENBERG, D.W.SMITH, G.N.PHILLIPS JR., C.A.BINGMAN, S.T.M.ALLARD, CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS(CESG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-1.5 Space group P1211 a (A) 58.020 b (A) 115.813 c (A) 66.634 alpha (°) 90.00 beta (°) 97.10 gamma (°) 90.00 Rfactor (%) 14.6 Rfree (%) 17.4 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 1vkp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1vkp. 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: Ser95, A: Asp119, A: Trp120, A: Asn121, A: Phe122, A: Asp139, A: Leu140, A: Ser143, A: Hoh1025, A: Hoh1040, A: Hoh1056, A: Hoh1091, A: Hoh1181, conact list: Atom Atom Distance (A) Mg O A:Ser95 4.21 Mg O A:Asp119 4.51 Mg CB A:Asp119 4.35 Mg OD2 A:Asp119 4.27 Mg C A:Asp119 3.81 Mg OD1 A:Asp119 2.23 Mg CG A:Asp119 3.46 Mg CA A:Asp119 4.07 Mg N A:Trp120 3.58 Mg CB A:Trp120 4.74 Mg C A:Trp120 3.43 Mg CA A:Trp120 4.09 Mg O A:Trp120 2.30 Mg N A:Asn121 4.53 Mg C A:Asn121 4.86 Mg CA A:Asn121 4.78 Mg CB A:Phe122 4.88 Mg O A:Asp139 4.99 Mg O A:Leu140 4.37 Mg N A:Ser143 4.96 Mg CB A:Ser143 3.90 Mg OG A:Ser143 3.60 Mg O A:Hoh1025 4.22 Mg O A:Hoh1040 2.53 Mg O A:Hoh1056 2.53 Mg O A:Hoh1091 3.83 Mg O A:Hoh1181 2.38 interactive model: Magnesium binding site 2 out of 2 in 1vkp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1vkp. 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: Ser95, B: Asp119, B: Trp120, B: Asn121, B: Phe122, B: Leu140, B: Ser143, B: Hoh922, B: Hoh929, B: Hoh944, B: Hoh973, B: Hoh986, B: Hoh1153, conact list: Atom Atom Distance (A) Mg O B:Ser95 4.26 Mg O B:Asp119 4.52 Mg CB B:Asp119 4.41 Mg OD2 B:Asp119 4.38 Mg C B:Asp119 3.87 Mg OD1 B:Asp119 2.30 Mg CG B:Asp119 3.55 Mg CA B:Asp119 4.09 Mg N B:Trp120 3.60 Mg CB B:Trp120 4.72 Mg C B:Trp120 3.43 Mg CA B:Trp120 4.09 Mg O B:Trp120 2.28 Mg N B:Asn121 4.50 Mg C B:Asn121 4.83 Mg CA B:Asn121 4.76 Mg CB B:Phe122 4.71 Mg O B:Leu140 4.35 Mg N B:Ser143 4.98 Mg CB B:Ser143 3.85 Mg OG B:Ser143 3.66 Mg O B:Hoh922 4.18 Mg O B:Hoh929 2.57 Mg O B:Hoh944 2.52 Mg O B:Hoh973 3.76 Mg O B:Hoh986 2.51 Mg O B:Hoh1153 4.11 interactive model: