Magnesium in the structure of Carboxyethylarginine Synthase From Streptomyces Clavuligerus: Putative Reaction Intermediate Complex (pdb 2ihu)

The binding sites of Magnesium atom in the structure of Carboxyethylarginine Synthase From Streptomyces Clavuligerus: Putative Reaction Intermediate Complex (pdb code 2ihu). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2ihu structure was solved by M.E.CAINES, C.J.SCHOFIELD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.1-2.0 Space group P212121 a (A) 119.691 b (A) 127.863 c (A) 197.150 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.1 Rfree (%) 20.1 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 2ihu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2ihu. 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: Gly462, A: Asp463, A: Gly464, A: Val488, A: Asn490, A: Asp491, A: Thr492, A: Asn493, A: Gly494, A: Tp9600, A: Hoh1755, conact list: Atom Atom Distance (A) Mg C A:Gly462 4.81 Mg CA A:Gly462 4.82 Mg N A:Asp463 4.04 Mg CB A:Asp463 4.48 Mg OD2 A:Asp463 3.67 Mg OD1 A:Asp463 2.21 Mg CG A:Asp463 3.23 Mg CA A:Asp463 4.70 Mg N A:Gly464 4.31 Mg O A:Val488 4.41 Mg N A:Asn490 4.03 Mg CB A:Asn490 4.43 Mg ND2 A:Asn490 4.29 Mg C A:Asn490 4.67 Mg OD1 A:Asn490 2.23 Mg CG A:Asn490 3.44 Mg CA A:Asn490 4.54 Mg N A:Asp491 4.70 Mg O A:Thr492 2.27 Mg N A:Thr492 4.04 Mg CB A:Thr492 4.67 Mg C A:Thr492 3.47 Mg CA A:Thr492 4.26 Mg N A:Asn493 4.49 Mg C A:Asn493 4.89 Mg CA A:Asn493 4.69 Mg N A:Gly494 4.03 Mg CA A:Gly494 4.69 Mg O3B A:Tp9600 2.21 Mg PA A:Tp9600 3.39 Mg O2A A:Tp9600 4.65 Mg O1B A:Tp9600 4.18 Mg PB A:Tp9600 3.48 Mg O2B A:Tp9600 4.69 Mg O7 A:Tp9600 4.10 Mg O3A A:Tp9600 3.67 Mg O1A A:Tp9600 2.14 Mg O A:Hoh1755 2.35 interactive model: Magnesium binding site 2 out of 4 in 2ihu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2ihu. 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: Gly462, B: Asp463, B: Gly464, B: Val488, B: Asn490, B: Asp491, B: Thr492, B: Asn493, B: Gly494, B: Tyr561, B: Tp9600, B: Hoh868, conact list: Atom Atom Distance (A) Mg C B:Gly462 4.82 Mg CA B:Gly462 4.78 Mg N B:Asp463 4.04 Mg CB B:Asp463 4.53 Mg OD2 B:Asp463 3.70 Mg OD1 B:Asp463 2.28 Mg CG B:Asp463 3.28 Mg CA B:Asp463 4.73 Mg N B:Gly464 4.34 Mg O B:Val488 4.48 Mg N B:Asn490 4.11 Mg CB B:Asn490 4.52 Mg ND2 B:Asn490 4.25 Mg C B:Asn490 4.74 Mg OD1 B:Asn490 2.25 Mg CG B:Asn490 3.46 Mg CA B:Asn490 4.60 Mg N B:Asp491 4.78 Mg O B:Thr492 2.28 Mg N B:Thr492 3.99 Mg CB B:Thr492 4.59 Mg C B:Thr492 3.45 Mg CA B:Thr492 4.21 Mg N B:Asn493 4.48 Mg C B:Asn493 4.87 Mg CA B:Asn493 4.68 Mg N B:Gly494 4.01 Mg CA B:Gly494 4.65 Mg CE2 B:Tyr561 4.91 Mg OH B:Tyr561 4.60 Mg O3B B:Tp9600 2.18 Mg PA B:Tp9600 3.39 Mg O2A B:Tp9600 4.66 Mg O1B B:Tp9600 4.08 Mg PB B:Tp9600 3.41 Mg O2B B:Tp9600 4.61 Mg O7 B:Tp9600 4.11 Mg O3A B:Tp9600 3.61 Mg O1A B:Tp9600 2.19 Mg O B:Hoh868 2.17 interactive model: Magnesium binding site 3 out of 4 in 2ihu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2ihu. 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: Gly462, C: Asp463, C: Gly464, C: Val488, C: Asn490, C: Asp491, C: Thr492, C: Asn493, C: Gly494, C: Tyr561, C: Tp9600, C: Hoh1733, conact list: Atom Atom Distance (A) Mg C C:Gly462 4.83 Mg CA C:Gly462 4.82 Mg N C:Asp463 4.09 Mg CB C:Asp463 4.55 Mg OD2 C:Asp463 3.79 Mg OD1 C:Asp463 2.29 Mg CG C:Asp463 3.33 Mg CA C:Asp463 4.74 Mg N C:Gly464 4.30 Mg O C:Val488 4.51 Mg N C:Asn490 4.15 Mg CB C:Asn490 4.49 Mg ND2 C:Asn490 4.23 Mg C C:Asn490 4.72 Mg OD1 C:Asn490 2.27 Mg CG C:Asn490 3.45 Mg CA C:Asn490 4.62 Mg N C:Asp491 4.76 Mg O C:Thr492 2.22 Mg N C:Thr492 3.95 Mg CB C:Thr492 4.58 Mg C C:Thr492 3.41 Mg CA C:Thr492 4.17 Mg N C:Asn493 4.44 Mg C C:Asn493 4.87 Mg CA C:Asn493 4.62 Mg N C:Gly494 4.04 Mg CA C:Gly494 4.75 Mg CE2 C:Tyr561 4.74 Mg OH C:Tyr561 4.65 Mg O3B C:Tp9600 2.47 Mg O3B C:Tp9600 2.01 Mg PA C:Tp9600 3.39 Mg PA C:Tp9600 3.49 Mg O2B C:Tp9600 4.83 Mg O2B C:Tp9600 4.51 Mg O7 C:Tp9600 3.94 Mg O7 C:Tp9600 4.11 Mg O3A C:Tp9600 3.70 Mg O3A C:Tp9600 3.72 Mg O2A C:Tp9600 4.70 Mg O2A C:Tp9600 4.78 Mg O1B C:Tp9600 4.50 Mg O1B C:Tp9600 4.10 Mg PB C:Tp9600 3.70 Mg PB C:Tp9600 3.37 Mg O1A C:Tp9600 2.19 Mg O1A C:Tp9600 2.29 Mg O C:Hoh1733 2.39 interactive model: Magnesium binding site 4 out of 4 in 2ihu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2ihu. 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: Gly462, D: Asp463, D: Gly464, D: Val488, D: Asn490, D: Asp491, D: Thr492, D: Asn493, D: Gly494, D: Tyr561, D: Tp9600, D: Hoh827, conact list: Atom Atom Distance (A) Mg C D:Gly462 4.82 Mg CA D:Gly462 4.85 Mg N D:Asp463 4.07 Mg CB D:Asp463 4.58 Mg OD2 D:Asp463 3.86 Mg OD1 D:Asp463 2.36 Mg CG D:Asp463 3.38 Mg CA D:Asp463 4.74 Mg N D:Gly464 4.30 Mg O D:Val488 4.49 Mg N D:Asn490 4.09 Mg CB D:Asn490 4.44 Mg ND2 D:Asn490 4.19 Mg C D:Asn490 4.70 Mg OD1 D:Asn490 2.23 Mg CG D:Asn490 3.40 Mg CA D:Asn490 4.56 Mg N D:Asp491 4.76 Mg O D:Thr492 2.26 Mg N D:Thr492 4.00 Mg CB D:Thr492 4.59 Mg C D:Thr492 3.45 Mg CA D:Thr492 4.21 Mg N D:Asn493 4.47 Mg C D:Asn493 4.89 Mg CA D:Asn493 4.65 Mg N D:Gly494 4.07 Mg CA D:Gly494 4.74 Mg CE2 D:Tyr561 4.91 Mg OH D:Tyr561 4.87 Mg O3B D:Tp9600 2.25 Mg PA D:Tp9600 3.43 Mg O2A D:Tp9600 4.72 Mg O1B D:Tp9600 4.32 Mg PB D:Tp9600 3.52 Mg O2B D:Tp9600 4.67 Mg O7 D:Tp9600 4.13 Mg O3A D:Tp9600 3.63 Mg O1A D:Tp9600 2.27 Mg O D:Hoh827 2.04 interactive model: