Magnesium in the structure of Crystal Structure Of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, With Bound Nadh (pdb 3iam)

The binding sites of Magnesium atom in the structure of Crystal Structure Of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, With Bound Nadh (pdb code 3iam). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3iam structure was solved by L.A.SAZANOV, J.M.BERRISFORD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.6-3.1 Space group P1211 a (A) 109.002 b (A) 151.015 c (A) 216.624 alpha (°) 90.00 beta (°) 93.07 gamma (°) 90.00 Rfactor (%) 23.1 Rfree (%) 26.2 Magnesium Binding Sites: Magnesium binding site 1 out of 10 in 3iam Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3iam. 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: 3: Arg243, 3: Leu274, 3: Leu275, 3: Asp302, conact list: Atom Atom Distance (A) Mg NH1 3:Arg243 4.50 Mg O 3:Leu274 2.55 Mg N 3:Leu274 4.27 Mg CB 3:Leu274 4.70 Mg C 3:Leu274 3.70 Mg CA 3:Leu274 4.44 Mg N 3:Leu275 4.71 Mg CA 3:Leu275 4.93 Mg CB 3:Asp302 3.30 Mg OD2 3:Asp302 2.60 Mg OD1 3:Asp302 2.07 Mg CG 3:Asp302 2.31 Mg CA 3:Asp302 4.70 interactive model: Magnesium binding site 2 out of 10 in 3iam Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3iam. 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: 3: Lys166, 3: His167, 3: His168, 3: Pro169, 7: Glu32, conact list: Atom Atom Distance (A) Mg O 3:Lys166 4.99 Mg O 3:His167 2.81 Mg NE2 3:His167 4.14 Mg CB 3:His167 4.55 Mg ND1 3:His167 2.52 Mg CD2 3:His167 4.62 Mg C 3:His167 4.03 Mg CE1 3:His167 2.85 Mg CG 3:His167 3.82 Mg CA 3:His167 4.94 Mg N 3:His168 4.94 Mg CA 3:His168 4.93 Mg CD 3:Pro169 4.35 Mg OE1 7:Glu32 4.67 Mg OE2 7:Glu32 3.33 Mg CD 7:Glu32 4.26 interactive model: Magnesium binding site 3 out of 10 in 3iam Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3iam. 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: 5: His144, conact list: Atom Atom Distance (A) Mg NE2 5:His144 2.38 Mg ND1 5:His144 4.23 Mg CD2 5:His144 3.62 Mg CE1 5:His144 2.96 Mg CG 5:His144 4.57 interactive model: Magnesium binding site 4 out of 10 in 3iam Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3iam. 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: 1: Tyr31, 1: His35, conact list: Atom Atom Distance (A) Mg CE1 1:Tyr31 4.92 Mg OH 1:Tyr31 4.95 Mg NE2 1:His35 2.16 Mg ND1 1:His35 3.72 Mg CD2 1:His35 3.52 Mg CE1 1:His35 2.41 Mg CG 1:His35 4.27 interactive model: Magnesium binding site 5 out of 10 in 3iam Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3iam. 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: 4: Val223, 4: Tyr383, 4: Ala384, 4: Lys386, 4: Glu388, conact list: Atom Atom Distance (A) Mg O 4:Val223 4.71 Mg N 4:Val223 4.49 Mg CB 4:Val223 4.03 Mg CG2 4:Val223 2.54 Mg CG1 4:Val223 4.56 Mg CA 4:Val223 4.80 Mg O 4:Tyr383 4.30 Mg O 4:Ala384 3.57 Mg C 4:Ala384 4.55 Mg O 4:Lys386 3.36 Mg N 4:Lys386 4.58 Mg CB 4:Lys386 4.56 Mg C 4:Lys386 4.41 Mg CA 4:Lys386 4.77 Mg OE1 4:Glu388 4.68 Mg OE2 4:Glu388 2.64 Mg CD 4:Glu388 3.52 Mg CG 4:Glu388 3.69 interactive model: Magnesium binding site 6 out of 10 in 3iam Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3iam. 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: 1: His350, 1: Glu351, 2: Ser68, 2: Lys121, 2: Val122, 2: Glu123, 3: Arg205, conact list: Atom Atom Distance (A) Mg NE2 1:His350 3.05 Mg ND1 1:His350 4.58 Mg CD2 1:His350 3.74 Mg CE1 1:His350 3.70 Mg CG 1:His350 4.63 Mg OE2 1:Glu351 4.04 Mg CB 2:Ser68 4.14 Mg OG 2:Ser68 3.67 Mg O 2:Lys121 4.55 Mg N 2:Val122 4.96 Mg CB 2:Val122 4.50 Mg C 2:Val122 4.03 Mg CG1 2:Val122 4.02 Mg CA 2:Val122 3.88 Mg N 2:Glu123 3.47 Mg CB 2:Glu123 3.96 Mg OE2 2:Glu123 4.44 Mg CD 2:Glu123 4.41 Mg CG 2:Glu123 3.40 Mg CA 2:Glu123 4.34 Mg NH2 3:Arg205 4.98 interactive model: Magnesium binding site 7 out of 10 in 3iam Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 3iam. 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: C: Arg243, C: Leu274, C: Leu275, C: Asp302, conact list: Atom Atom Distance (A) Mg NH1 C:Arg243 4.23 Mg O C:Leu274 2.54 Mg N C:Leu274 4.45 Mg CB C:Leu274 4.85 Mg C C:Leu274 3.70 Mg CA C:Leu274 4.53 Mg N C:Leu275 4.67 Mg CD1 C:Leu275 4.88 Mg CA C:Leu275 4.80 Mg CB C:Asp302 3.58 Mg OD2 C:Asp302 2.91 Mg OD1 C:Asp302 2.30 Mg CG C:Asp302 2.62 Mg CA C:Asp302 4.99 interactive model: Magnesium binding site 8 out of 10 in 3iam Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 3iam. 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: C: His167, C: Pro169, G: Glu74, H: Glu32, conact list: Atom Atom Distance (A) Mg O C:His167 3.01 Mg NE2 C:His167 4.47 Mg CB C:His167 4.72 Mg ND1 C:His167 2.81 Mg CD2 C:His167 4.91 Mg C C:His167 4.24 Mg CE1 C:His167 3.20 Mg CG C:His167 4.07 Mg CD C:Pro169 4.28 Mg OE2 G:Glu74 4.96 Mg OE2 H:Glu32 3.62 Mg CD H:Glu32 4.57 interactive model: Magnesium binding site 9 out of 10 in 3iam Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Magnesium in the PDB 3iam. 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: E: His144, conact list: Atom Atom Distance (A) Mg NE2 E:His144 2.70 Mg ND1 E:His144 4.62 Mg CD2 E:His144 3.87 Mg CE1 E:His144 3.38 Mg CG E:His144 4.89 interactive model: Magnesium binding site 10 out of 10 in 3iam Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Magnesium in the PDB 3iam. 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: His35, conact list: Atom Atom Distance (A) Mg NE2 A:His35 2.76 Mg ND1 A:His35 4.08 Mg CD2 A:His35 3.82 Mg CE1 A:His35 3.02 Mg CG A:His35 4.52 interactive model: