Magnesium in the structure of X-Ray High Resolution Structure of The Photosynthetic Reaction Center From Rb. Sphaeroides At pH 9 in the Neutral State (pdb 2ux3)

The binding sites of Magnesium atom in the structure of X-Ray High Resolution Structure of The Photosynthetic Reaction Center From Rb. Sphaeroides At pH 9 in the Neutral State (pdb code 2ux3). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2ux3 structure was solved by J.KOEPKE, R.DIEHM, G.FRITZSCH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 119.5-2.5 Space group P3121 a (A) 139.448 b (A) 139.448 c (A) 184.577 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.5 Rfree (%) 22.1 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 2ux3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2ux3. 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: L: His153, L: Leu154, M: Tyr210, L: Bcl1282, L: Bph1284, conact list: Atom Atom Distance (A) Mg NE2 L:His153 2.03 Mg ND1 L:His153 4.14 Mg CD2 L:His153 3.02 Mg CE1 L:His153 3.03 Mg CG L:His153 4.17 Mg CD1 L:Leu154 4.87 Mg CE2 M:Tyr210 4.68 Mg CBC L:Bcl1282 4.78 Mg C2D L:Bcl1282 4.19 Mg NA L:Bcl1282 2.07 Mg CHA L:Bcl1282 3.40 Mg C2A L:Bcl1282 4.41 Mg C4B L:Bcl1282 3.05 Mg C4A L:Bcl1282 3.02 Mg C1D L:Bcl1282 3.07 Mg C3A L:Bcl1282 4.33 Mg C1C L:Bcl1282 2.99 Mg C2C L:Bcl1282 4.32 Mg CBD L:Bcl1282 4.87 Mg NB L:Bcl1282 2.05 Mg C3B L:Bcl1282 4.24 Mg MG L:Bcl1282 0.00 Mg C4D L:Bcl1282 2.90 Mg NC L:Bcl1282 2.06 Mg CBA L:Bcl1282 4.86 Mg CHB L:Bcl1282 3.40 Mg CHC L:Bcl1282 3.31 Mg C3D L:Bcl1282 4.09 Mg C4C L:Bcl1282 3.03 Mg C2B L:Bcl1282 4.24 Mg CHD L:Bcl1282 3.46 Mg ND L:Bcl1282 2.02 Mg C1B L:Bcl1282 3.08 Mg C3C L:Bcl1282 4.36 Mg C1A L:Bcl1282 3.11 Mg CMC L:Bcl1282 4.96 Mg OBB L:Bph1284 4.38 Mg C20 L:Bph1284 4.69 interactive model: Magnesium binding site 2 out of 4 in 2ux3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2ux3. 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: L: Phe167, L: His173, L: Bcl1286, M: Bcl1304, conact list: Atom Atom Distance (A) Mg CD1 L:Phe167 4.74 Mg NE2 L:His173 2.30 Mg ND1 L:His173 4.33 Mg CD2 L:His173 3.40 Mg CE1 L:His173 3.15 Mg CG L:His173 4.49 Mg C2D L:Bcl1286 4.19 Mg NA L:Bcl1286 2.08 Mg CHA L:Bcl1286 3.47 Mg C2A L:Bcl1286 4.44 Mg C4B L:Bcl1286 3.08 Mg C4A L:Bcl1286 3.03 Mg C1D L:Bcl1286 3.08 Mg C3A L:Bcl1286 4.34 Mg C1C L:Bcl1286 2.99 Mg C2C L:Bcl1286 4.33 Mg CBD L:Bcl1286 4.93 Mg NB L:Bcl1286 2.05 Mg C3B L:Bcl1286 4.27 Mg MG L:Bcl1286 0.00 Mg C4D L:Bcl1286 2.93 Mg NC L:Bcl1286 2.06 Mg CHB L:Bcl1286 3.39 Mg CHC L:Bcl1286 3.33 Mg C3D L:Bcl1286 4.10 Mg C4C L:Bcl1286 3.03 Mg C2B L:Bcl1286 4.24 Mg CHD L:Bcl1286 3.40 Mg ND L:Bcl1286 2.02 Mg C1B L:Bcl1286 3.08 Mg C3C L:Bcl1286 4.35 Mg C1A L:Bcl1286 3.14 Mg CBB M:Bcl1304 3.90 Mg CAB M:Bcl1304 3.59 Mg OBB M:Bcl1304 3.34 Mg C3B M:Bcl1304 4.40 interactive model: Magnesium binding site 3 out of 4 in 2ux3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2ux3. 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: L: Phe181, M: His182, M: Bcl1303, M: Bph1313, M: Spo1315, conact list: Atom Atom Distance (A) Mg CE2 L:Phe181 4.82 Mg NE2 M:His182 2.01 Mg ND1 M:His182 4.12 Mg CD2 M:His182 3.02 Mg CE1 M:His182 3.00 Mg CG M:His182 4.17 Mg C2D M:Bcl1303 4.16 Mg NA M:Bcl1303 2.04 Mg CHA M:Bcl1303 3.40 Mg C2A M:Bcl1303 4.38 Mg C4B M:Bcl1303 3.03 Mg C4A M:Bcl1303 3.03 Mg C1D M:Bcl1303 3.07 Mg C3A M:Bcl1303 4.34 Mg C1C M:Bcl1303 2.98 Mg C2C M:Bcl1303 4.33 Mg CBD M:Bcl1303 4.85 Mg NB M:Bcl1303 2.05 Mg C3B M:Bcl1303 4.21 Mg MG M:Bcl1303 0.00 Mg C4D M:Bcl1303 2.88 Mg NC M:Bcl1303 2.04 Mg CBA M:Bcl1303 4.90 Mg CHB M:Bcl1303 3.43 Mg CHC M:Bcl1303 3.27 Mg C3D M:Bcl1303 4.04 Mg C4C M:Bcl1303 3.01 Mg C2B M:Bcl1303 4.23 Mg CHD M:Bcl1303 3.44 Mg ND M:Bcl1303 2.01 Mg C1B M:Bcl1303 3.08 Mg C3C M:Bcl1303 4.34 Mg C1A M:Bcl1303 3.08 Mg OBB M:Bph1313 4.49 Mg C18 M:Spo1315 4.96 interactive model: Magnesium binding site 4 out of 4 in 2ux3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2ux3. 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: M: His202, L: Bcl1286, M: Bcl1304, conact list: Atom Atom Distance (A) Mg NE2 M:His202 2.02 Mg ND1 M:His202 4.07 Mg CD2 M:His202 3.13 Mg CE1 M:His202 2.89 Mg CG M:His202 4.22 Mg CBB L:Bcl1286 3.61 Mg CAB L:Bcl1286 3.67 Mg OBB L:Bcl1286 3.75 Mg C3B L:Bcl1286 4.44 Mg C2D M:Bcl1304 4.24 Mg NA M:Bcl1304 2.08 Mg CHA M:Bcl1304 3.45 Mg C2A M:Bcl1304 4.45 Mg C4B M:Bcl1304 3.03 Mg C4A M:Bcl1304 3.08 Mg C1D M:Bcl1304 3.10 Mg C3A M:Bcl1304 4.41 Mg C1C M:Bcl1304 3.02 Mg C2C M:Bcl1304 4.32 Mg CBD M:Bcl1304 4.91 Mg NB M:Bcl1304 2.03 Mg C3B M:Bcl1304 4.23 Mg MG M:Bcl1304 0.00 Mg C4D M:Bcl1304 2.94 Mg NC M:Bcl1304 2.05 Mg CHB M:Bcl1304 3.42 Mg CHC M:Bcl1304 3.30 Mg C3D M:Bcl1304 4.13 Mg C4C M:Bcl1304 3.05 Mg C2B M:Bcl1304 4.22 Mg CHD M:Bcl1304 3.50 Mg ND M:Bcl1304 2.03 Mg C1B M:Bcl1304 3.06 Mg C3C M:Bcl1304 4.35 Mg C1A M:Bcl1304 3.13 interactive model: