Magnesium in the structure of Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7 (pdb 1svt)

The binding sites of Magnesium atom in the structure of Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7 (pdb code 1svt). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1svt structure was solved by C.CHAUDHRY, A.L.HORWICH, A.T.BRUNGER, P.D.ADAMS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 49.4-2.8 Space group P21212 a (A) 255.546 b (A) 266.855 c (A) 187.049 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.7 Rfree (%) 27.4 Magnesium Binding Sites: Magnesium binding site 1 out of 7 in 1svt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1svt. 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: Asp87, A: Gly88, A: Ser151, A: Adp600, A: Af3602, conact list: Atom Atom Distance (A) Mg CB A:Asp87 4.60 Mg OD2 A:Asp87 3.25 Mg OD1 A:Asp87 2.35 Mg CG A:Asp87 3.19 Mg N A:Gly88 4.47 Mg O A:Ser151 4.38 Mg CA A:Ser151 4.89 Mg O3B A:Adp600 3.71 Mg PA A:Adp600 3.15 Mg O2A A:Adp600 1.74 Mg O1B A:Adp600 1.56 Mg PB A:Adp600 2.89 Mg C5' A:Adp600 3.67 Mg O5' A:Adp600 3.96 Mg O2B A:Adp600 4.14 Mg O3A A:Adp600 3.46 Mg O1A A:Adp600 4.39 Mg F3 A:Af3602 4.70 Mg F2 A:Af3602 3.17 Mg AL A:Af3602 2.95 Mg F1 A:Af3602 1.76 interactive model: Magnesium binding site 2 out of 7 in 1svt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1svt. 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: Asp87, B: Gly88, B: Ser151, B: Asp398, B: Adp600, B: Af3602, conact list: Atom Atom Distance (A) Mg CB B:Asp87 4.73 Mg OD2 B:Asp87 3.34 Mg OD1 B:Asp87 2.64 Mg CG B:Asp87 3.35 Mg N B:Gly88 4.66 Mg O B:Ser151 4.33 Mg C B:Ser151 5.00 Mg CA B:Ser151 4.77 Mg OD2 B:Asp398 4.98 Mg O3B B:Adp600 3.99 Mg PA B:Adp600 3.08 Mg O2A B:Adp600 1.61 Mg O1B B:Adp600 1.71 Mg PB B:Adp600 2.98 Mg C5' B:Adp600 3.69 Mg O5' B:Adp600 3.89 Mg O2B B:Adp600 4.14 Mg O3A B:Adp600 3.50 Mg O1A B:Adp600 4.29 Mg F3 B:Af3602 4.92 Mg F2 B:Af3602 3.90 Mg AL B:Af3602 3.23 Mg F1 B:Af3602 1.77 interactive model: Magnesium binding site 3 out of 7 in 1svt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1svt. 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: Asp87, C: Gly88, C: Ser151, C: Asp398, C: Adp600, C: Af3602, conact list: Atom Atom Distance (A) Mg CB C:Asp87 4.75 Mg OD2 C:Asp87 3.43 Mg OD1 C:Asp87 2.27 Mg CG C:Asp87 3.28 Mg N C:Gly88 4.61 Mg O C:Ser151 4.29 Mg CA C:Ser151 4.73 Mg OD2 C:Asp398 4.75 Mg O3B C:Adp600 3.95 Mg PA C:Adp600 3.28 Mg O2A C:Adp600 1.81 Mg O1B C:Adp600 1.76 Mg PB C:Adp600 3.04 Mg C5' C:Adp600 3.81 Mg O5' C:Adp600 4.06 Mg O2B C:Adp600 4.35 Mg O3A C:Adp600 3.58 Mg O1A C:Adp600 4.46 Mg F3 C:Af3602 4.75 Mg F2 C:Af3602 3.46 Mg AL C:Af3602 3.00 Mg F1 C:Af3602 1.63 interactive model: Magnesium binding site 4 out of 7 in 1svt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1svt. 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: Asp87, D: Gly88, D: Ser151, D: Adp600, D: Af3602, D: Hoh611, conact list: Atom Atom Distance (A) Mg CB D:Asp87 4.89 Mg OD2 D:Asp87 3.63 Mg OD1 D:Asp87 2.48 Mg CG D:Asp87 3.47 Mg N D:Gly88 4.55 Mg O D:Ser151 4.68 Mg O3B D:Adp600 3.73 Mg PA D:Adp600 2.93 Mg O2A D:Adp600 1.54 Mg O1B D:Adp600 1.59 Mg PB D:Adp600 2.82 Mg C5' D:Adp600 3.45 Mg C4' D:Adp600 4.91 Mg O5' D:Adp600 3.74 Mg O2B D:Adp600 4.03 Mg O3A D:Adp600 3.34 Mg O1A D:Adp600 4.10 Mg F3 D:Af3602 4.73 Mg F2 D:Af3602 3.10 Mg AL D:Af3602 2.93 Mg F1 D:Af3602 1.73 Mg O D:Hoh611 3.11 interactive model: Magnesium binding site 5 out of 7 in 1svt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 1svt. 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: Asp87, E: Gly88, E: Ser151, E: Asp398, E: Adp600, E: Af3602, E: Hoh608, conact list: Atom Atom Distance (A) Mg CB E:Asp87 4.67 Mg OD2 E:Asp87 3.45 Mg OD1 E:Asp87 2.36 Mg CG E:Asp87 3.28 Mg N E:Gly88 4.37 Mg O E:Ser151 4.50 Mg CA E:Ser151 4.97 Mg OD2 E:Asp398 4.87 Mg O3B E:Adp600 3.69 Mg PA E:Adp600 3.04 Mg O2A E:Adp600 1.67 Mg O1B E:Adp600 1.59 Mg PB E:Adp600 2.83 Mg C5' E:Adp600 3.69 Mg O5' E:Adp600 3.89 Mg O2B E:Adp600 4.12 Mg O3A E:Adp600 3.33 Mg O1A E:Adp600 4.30 Mg F3 E:Af3602 4.66 Mg F2 E:Af3602 3.39 Mg AL E:Af3602 2.93 Mg F1 E:Af3602 1.76 Mg O E:Hoh608 2.20 interactive model: Magnesium binding site 6 out of 7 in 1svt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 1svt. 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: Asp87, F: Gly88, F: Ser151, F: Adp600, F: Af3602, conact list: Atom Atom Distance (A) Mg CB F:Asp87 4.72 Mg OD2 F:Asp87 3.34 Mg OD1 F:Asp87 2.36 Mg CG F:Asp87 3.27 Mg N F:Gly88 4.58 Mg O F:Ser151 4.47 Mg CA F:Ser151 4.91 Mg O3B F:Adp600 3.88 Mg PA F:Adp600 3.04 Mg O2A F:Adp600 1.58 Mg O1B F:Adp600 1.67 Mg PB F:Adp600 2.98 Mg C5' F:Adp600 3.70 Mg O5' F:Adp600 3.93 Mg O2B F:Adp600 4.21 Mg O3A F:Adp600 3.47 Mg O1A F:Adp600 4.18 Mg F3 F:Af3602 4.72 Mg F2 F:Af3602 3.38 Mg AL F:Af3602 2.95 Mg F1 F:Af3602 1.71 interactive model: Magnesium binding site 7 out of 7 in 1svt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 1svt. 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: G: Asp87, G: Gly88, G: Ser151, G: Asp398, G: Adp600, G: Af3602, conact list: Atom Atom Distance (A) Mg CB G:Asp87 4.66 Mg OD2 G:Asp87 3.44 Mg OD1 G:Asp87 2.30 Mg CG G:Asp87 3.27 Mg N G:Gly88 4.49 Mg O G:Ser151 4.48 Mg CA G:Ser151 4.96 Mg OD2 G:Asp398 4.66 Mg O3B G:Adp600 3.88 Mg PA G:Adp600 3.14 Mg O2A G:Adp600 1.72 Mg O1B G:Adp600 1.68 Mg PB G:Adp600 2.99 Mg C5' G:Adp600 3.89 Mg O5' G:Adp600 4.04 Mg O2B G:Adp600 4.31 Mg O3A G:Adp600 3.43 Mg O1A G:Adp600 4.30 Mg F3 G:Af3602 4.64 Mg F2 G:Af3602 3.44 Mg AL G:Af3602 2.93 Mg F1 G:Af3602 1.63 interactive model: