Magnesium in the structure of The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator. (pdb 1kxg)

The binding sites of Magnesium atom in the structure of The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator. (pdb code 1kxg). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1kxg structure was solved by D.A.OREN, Y.LI, Y.VOLOVIK, T.S.MORRIS, C.DHARIA, K.DAS, O.GALPERINA, R.GENTZ, E.ARNOLD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.6-2.0 Space group P65 a (A) 123.580 b (A) 123.580 c (A) 161.230 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.9 Rfree (%) 20.9 Magnesium Binding Sites: Magnesium binding site 1 out of 7 in 1kxg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1kxg. 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: Gln234, A: Asn243, B: Gln234, B: Asn243, C: Gln234, C: Asn243, B: Mg702, A: Hoh504, B: Hoh1019, C: Hoh1017, conact list: Atom Atom Distance (A) Mg NE2 A:Gln234 3.75 Mg OE1 A:Gln234 2.34 Mg CB A:Gln234 4.83 Mg CD A:Gln234 3.31 Mg CG A:Gln234 4.58 Mg ND2 A:Asn243 4.68 Mg OD1 A:Asn243 4.02 Mg CG A:Asn243 4.36 Mg NE2 B:Gln234 3.68 Mg OE1 B:Gln234 2.49 Mg CD B:Gln234 3.40 Mg CG B:Gln234 4.75 Mg ND2 B:Asn243 4.86 Mg OD1 B:Asn243 4.11 Mg CG B:Asn243 4.50 Mg NE2 C:Gln234 3.71 Mg OE1 C:Gln234 2.45 Mg CD C:Gln234 3.38 Mg CG C:Gln234 4.70 Mg ND2 C:Asn243 4.84 Mg OD1 C:Asn243 4.09 Mg CG C:Asn243 4.51 Mg MG B:Mg702 3.18 Mg O A:Hoh504 2.61 Mg O B:Hoh1019 2.54 Mg O C:Hoh1017 2.71 interactive model: Magnesium binding site 2 out of 7 in 1kxg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1kxg. 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: Lys252, A: Glu254, F: Lys252, F: Glu254, A: Mg903, A: Cit889, F: Mg902, F: Cit888, A: Hoh10, F: Hoh20, F: Hoh395, conact list: Atom Atom Distance (A) Mg CE A:Lys252 4.72 Mg NZ A:Lys252 3.89 Mg OE1 A:Glu254 4.13 Mg CE F:Lys252 4.88 Mg NZ F:Lys252 4.09 Mg OE2 F:Glu254 4.11 Mg MG A:Mg903 4.01 Mg C6 A:Cit889 4.94 Mg O5 A:Cit889 4.87 Mg C5 A:Cit889 3.42 Mg C4 A:Cit889 3.89 Mg C3 A:Cit889 4.05 Mg O7 A:Cit889 2.95 Mg O3 A:Cit889 4.60 Mg O4 A:Cit889 2.45 Mg MG F:Mg902 3.87 Mg C6 F:Cit888 4.77 Mg O5 F:Cit888 4.57 Mg C5 F:Cit888 3.42 Mg C4 F:Cit888 4.05 Mg C3 F:Cit888 4.01 Mg O7 F:Cit888 2.83 Mg O3 F:Cit888 4.53 Mg O4 F:Cit888 2.37 Mg O A:Hoh10 2.85 Mg O F:Hoh20 3.27 Mg O F:Hoh395 2.76 interactive model: Magnesium binding site 3 out of 7 in 1kxg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1kxg. 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: Arg214, A: Lys252, A: Leu253, A: Glu254, A: Asp257, A: Mg901, A: Cit889, F: Cit888, A: Hoh4, A: Hoh10, conact list: Atom Atom Distance (A) Mg CZ A:Arg214 3.57 Mg NE A:Arg214 4.73 Mg NH2 A:Arg214 2.95 Mg NH1 A:Arg214 3.52 Mg O A:Lys252 3.07 Mg CB A:Lys252 4.08 Mg CE A:Lys252 4.74 Mg CD A:Lys252 4.62 Mg C A:Lys252 3.68 Mg CG A:Lys252 3.45 Mg CA A:Lys252 4.54 Mg O A:Leu253 4.68 Mg N A:Leu253 4.21 Mg C A:Leu253 4.22 Mg CA A:Leu253 4.22 Mg N A:Glu254 4.32 Mg OE1 A:Glu254 4.95 Mg CB A:Glu254 4.58 Mg CA A:Glu254 4.96 Mg OD2 A:Asp257 4.98 Mg MG A:Mg901 4.01 Mg C6 A:Cit889 3.75 Mg O5 A:Cit889 3.27 Mg C4 A:Cit889 4.18 Mg C3 A:Cit889 4.21 Mg O7 A:Cit889 3.98 Mg O4 A:Cit889 4.98 Mg O6 A:Cit889 4.44 Mg O5 F:Cit888 4.97 Mg C5 F:Cit888 4.73 Mg O2 F:Cit888 4.58 Mg C4 F:Cit888 5.00 Mg C1 F:Cit888 3.58 Mg O1 F:Cit888 2.83 Mg C3 F:Cit888 4.04 Mg O7 F:Cit888 2.93 Mg O4 F:Cit888 4.17 Mg C2 F:Cit888 3.98 Mg O A:Hoh4 4.76 Mg O A:Hoh10 2.75 interactive model: Magnesium binding site 4 out of 7 in 1kxg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1kxg. 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: Asn235, A: Asn243, B: Gln234, B: Asn235, B: Asn243, C: Gln234, C: Asn235, C: Asn243, A: Mg701, A: Hoh504, A: Hoh507, A: Hoh509, A: Hoh510, A: Hoh511, B: Hoh1019, B: Hoh1020, C: Hoh1017, C: Hoh1018, conact list: Atom Atom Distance (A) Mg O A:Asn235 4.15 Mg ND2 A:Asn243 4.29 Mg OD1 A:Asn243 4.50 Mg CG A:Asn243 4.74 Mg OE1 B:Gln234 4.96 Mg O B:Asn235 4.14 Mg ND2 B:Asn243 4.40 Mg OD1 B:Asn243 4.53 Mg CG B:Asn243 4.80 Mg OE1 C:Gln234 4.98 Mg O C:Asn235 4.16 Mg ND2 C:Asn243 4.36 Mg OD1 C:Asn243 4.50 Mg CG C:Asn243 4.78 Mg MG A:Mg701 3.18 Mg O A:Hoh504 2.54 Mg O A:Hoh507 2.46 Mg O A:Hoh509 4.02 Mg O A:Hoh510 3.84 Mg O A:Hoh511 4.13 Mg O B:Hoh1019 2.36 Mg O B:Hoh1020 2.62 Mg O C:Hoh1017 2.36 Mg O C:Hoh1018 2.52 interactive model: Magnesium binding site 5 out of 7 in 1kxg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 1kxg. 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: D: Asn235, D: Asn243, E: Asn235, E: Asn243, F: Asn235, F: Asn243, D: Mg802, D: Hoh1013, D: Hoh1014, D: Hoh1015, E: Hoh1020, E: Hoh1021, E: Hoh1022, F: Hoh603, F: Hoh608, F: Hoh609, conact list: Atom Atom Distance (A) Mg O D:Asn235 4.10 Mg ND2 D:Asn243 4.36 Mg OD1 D:Asn243 4.55 Mg CG D:Asn243 4.82 Mg O E:Asn235 4.17 Mg ND2 E:Asn243 4.35 Mg OD1 E:Asn243 4.57 Mg CG E:Asn243 4.82 Mg O F:Asn235 4.05 Mg ND2 F:Asn243 4.33 Mg OD1 F:Asn243 4.58 Mg CG F:Asn243 4.81 Mg MG D:Mg802 3.24 Mg O D:Hoh1013 2.50 Mg O D:Hoh1014 2.47 Mg O D:Hoh1015 3.87 Mg O E:Hoh1020 2.43 Mg O E:Hoh1021 2.36 Mg O E:Hoh1022 4.05 Mg O F:Hoh603 2.43 Mg O F:Hoh608 2.53 Mg O F:Hoh609 3.98 interactive model: Magnesium binding site 6 out of 7 in 1kxg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 1kxg. 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: D: Gln234, D: Asn243, E: Gln234, E: Asn243, F: Gln234, F: Asn243, D: Mg801, D: Hoh1013, E: Hoh1020, E: Hoh1021, F: Hoh603, conact list: Atom Atom Distance (A) Mg NE2 D:Gln234 3.67 Mg OE1 D:Gln234 2.42 Mg CB D:Gln234 4.94 Mg CD D:Gln234 3.34 Mg CG D:Gln234 4.65 Mg ND2 D:Asn243 4.81 Mg OD1 D:Asn243 4.17 Mg CG D:Asn243 4.53 Mg NE2 E:Gln234 3.65 Mg OE1 E:Gln234 2.34 Mg CB E:Gln234 4.92 Mg CD E:Gln234 3.29 Mg CG E:Gln234 4.60 Mg ND2 E:Asn243 4.72 Mg OD1 E:Asn243 4.04 Mg CG E:Asn243 4.42 Mg NE2 F:Gln234 3.78 Mg OE1 F:Gln234 2.46 Mg CB F:Gln234 4.96 Mg CD F:Gln234 3.40 Mg CG F:Gln234 4.69 Mg ND2 F:Asn243 4.73 Mg OD1 F:Asn243 4.10 Mg CG F:Asn243 4.45 Mg MG D:Mg801 3.24 Mg O D:Hoh1013 2.56 Mg O E:Hoh1020 2.61 Mg O E:Hoh1021 4.97 Mg O F:Hoh603 2.53 interactive model: Magnesium binding site 7 out of 7 in 1kxg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 1kxg. 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: F: Arg214, F: Lys252, F: Leu253, F: Glu254, F: Asp257, A: Mg901, A: Cit889, F: Cit888, F: Hoh349, F: Hoh395, conact list: Atom Atom Distance (A) Mg CZ F:Arg214 3.60 Mg NE F:Arg214 4.73 Mg NH2 F:Arg214 2.85 Mg NH1 F:Arg214 3.70 Mg O F:Lys252 3.16 Mg CB F:Lys252 4.08 Mg CE F:Lys252 4.77 Mg CD F:Lys252 4.63 Mg C F:Lys252 3.72 Mg CG F:Lys252 3.46 Mg CA F:Lys252 4.57 Mg O F:Leu253 4.71 Mg N F:Leu253 4.21 Mg C F:Leu253 4.23 Mg CA F:Leu253 4.25 Mg N F:Glu254 4.29 Mg CB F:Glu254 4.54 Mg OE2 F:Glu254 4.91 Mg CA F:Glu254 4.91 Mg OD1 F:Asp257 4.99 Mg MG A:Mg901 3.87 Mg C5 A:Cit889 4.54 Mg O2 A:Cit889 4.50 Mg C4 A:Cit889 4.93 Mg C1 A:Cit889 3.69 Mg O1 A:Cit889 3.19 Mg C3 A:Cit889 4.07 Mg O7 A:Cit889 2.93 Mg O4 A:Cit889 4.09 Mg C2 A:Cit889 4.07 Mg C6 F:Cit888 3.81 Mg O5 F:Cit888 3.15 Mg C4 F:Cit888 4.57 Mg C3 F:Cit888 4.38 Mg O7 F:Cit888 4.08 Mg O4 F:Cit888 4.90 Mg O6 F:Cit888 4.56 Mg O F:Hoh349 4.90 Mg O F:Hoh395 2.69 interactive model: