Magnesium in the structure of 1.7 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (pdb 3ed6)

The binding sites of Magnesium atom in the structure of 1.7 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (pdb code 3ed6). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3ed6 structure was solved by A.S.HALAVATY, L.SHUVALOVA, G.MINASOV, I.DUBROVSKA, J.WINSOR, S.N.PETERSON, W.F.ANDERSON, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DESEASES(CSGID), CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES(CSGID), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.7 Space group P21212 a (A) 106.313 b (A) 118.570 c (A) 87.947 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 13.5 Rfree (%) 17 Magnesium Binding Sites: Magnesium binding site 1 out of 5 in 3ed6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3ed6. 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: Val226, A: Asp227, A: Asn248, A: Val249, A: Thr250, A: Asn251, A: Hoh569, A: Hoh580, A: Hoh594, A: Hoh610, A: Hoh745, A: Hoh915, conact list: Atom Atom Distance (A) Mg O A:Val226 4.58 Mg O A:Asp227 4.36 Mg C A:Asp227 4.92 Mg OD1 A:Asp227 4.65 Mg CA A:Asp227 4.65 Mg O A:Asn248 3.89 Mg C A:Asn248 4.86 Mg O A:Val249 2.42 Mg CB A:Val249 4.66 Mg C A:Val249 3.44 Mg CG1 A:Val249 4.95 Mg CA A:Val249 4.61 Mg N A:Thr250 3.99 Mg CB A:Thr250 4.59 Mg CG2 A:Thr250 5.00 Mg OG1 A:Thr250 4.34 Mg C A:Thr250 4.63 Mg CA A:Thr250 3.73 Mg N A:Asn251 4.47 Mg ND2 A:Asn251 4.28 Mg O A:Hoh569 4.97 Mg O A:Hoh580 2.06 Mg O A:Hoh594 2.01 Mg O A:Hoh610 2.25 Mg O A:Hoh745 2.25 Mg O A:Hoh915 2.27 interactive model: Magnesium binding site 2 out of 5 in 3ed6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3ed6. 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: His6, A: Arg191, A: Hoh536, A: Hoh591, A: Hoh819, A: Hoh918, A: Hoh919, A: Hoh920, A: Hoh921, A: Hoh922, A: Hoh924, A: Hoh931, A: Hoh933, A: Hoh1167, conact list: Atom Atom Distance (A) Mg O A:His6 4.66 Mg CB A:His6 4.97 Mg NH1 A:Arg191 4.85 Mg O A:Hoh536 4.42 Mg O A:Hoh591 4.16 Mg O A:Hoh819 2.05 Mg O A:Hoh918 2.06 Mg O A:Hoh919 2.37 Mg O A:Hoh920 2.27 Mg O A:Hoh921 2.09 Mg O A:Hoh922 4.17 Mg O A:Hoh924 4.42 Mg O A:Hoh931 4.24 Mg O A:Hoh933 4.42 Mg O A:Hoh1167 3.90 interactive model: Magnesium binding site 3 out of 5 in 3ed6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3ed6. 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: Asp132, A: Hoh582, A: Hoh598, A: Hoh671, A: Hoh697, A: Hoh926, A: Hoh927, A: Hoh928, A: Hoh929, A: Hoh968, A: Hoh1113, A: Hoh1131, A: Hoh1141, conact list: Atom Atom Distance (A) Mg OD1 A:Asp132 4.58 Mg O A:Hoh582 4.50 Mg O A:Hoh598 4.44 Mg O A:Hoh671 4.41 Mg O A:Hoh671 4.16 Mg O A:Hoh697 4.57 Mg O A:Hoh926 2.07 Mg O A:Hoh927 2.23 Mg O A:Hoh928 2.22 Mg O A:Hoh929 2.11 Mg O A:Hoh968 4.81 Mg O A:Hoh1113 2.47 Mg O A:Hoh1131 4.32 Mg O A:Hoh1141 4.13 interactive model: Magnesium binding site 4 out of 5 in 3ed6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3ed6. 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: Val226, B: Asp227, B: Asn248, B: Val249, B: Thr250, B: Asn251, B: Hoh583, B: Hoh601, B: Hoh607, B: Hoh643, B: Hoh663, B: Hoh694, B: Hoh778, B: Hoh939, conact list: Atom Atom Distance (A) Mg O B:Val226 4.49 Mg O B:Asp227 4.36 Mg C B:Asp227 4.88 Mg OD1 B:Asp227 4.50 Mg CA B:Asp227 4.55 Mg O B:Asn248 3.82 Mg C B:Asn248 4.86 Mg O B:Val249 2.49 Mg CB B:Val249 4.66 Mg C B:Val249 3.50 Mg CG1 B:Val249 4.96 Mg CA B:Val249 4.65 Mg N B:Thr250 4.05 Mg CB B:Thr250 4.65 Mg OG1 B:Thr250 4.40 Mg C B:Thr250 4.75 Mg CA B:Thr250 3.80 Mg N B:Asn251 4.61 Mg ND2 B:Asn251 4.38 Mg O B:Hoh583 1.96 Mg O B:Hoh601 4.81 Mg O B:Hoh607 2.17 Mg O B:Hoh643 2.08 Mg O B:Hoh663 4.83 Mg O B:Hoh694 2.18 Mg O B:Hoh778 4.37 Mg O B:Hoh939 2.26 interactive model: Magnesium binding site 5 out of 5 in 3ed6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3ed6. 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: Lys5, B: His6, B: Hoh677, B: Hoh689, B: Hoh713, B: Hoh807, B: Hoh888, B: Hoh944, B: Hoh945, B: Hoh946, conact list: Atom Atom Distance (A) Mg O B:Lys5 4.09 Mg O B:Lys5 4.14 Mg O B:His6 4.49 Mg ND1 B:His6 4.57 Mg C B:His6 4.67 Mg CA B:His6 4.37 Mg O B:Hoh677 4.72 Mg O B:Hoh689 2.02 Mg O B:Hoh713 1.90 Mg O B:Hoh807 2.15 Mg O B:Hoh888 4.30 Mg O B:Hoh944 2.38 Mg O B:Hoh945 2.19 Mg O B:Hoh946 4.04 interactive model: