Magnesium in the structure of Crystal Structure Of Ternary Complex of E.Coli Hppk(W89A) With Mgampcpp and 6-Hydroxymethylpterin (pdb 1tmm)

The binding sites of Magnesium atom in the structure of Crystal Structure Of Ternary Complex of E.Coli Hppk(W89A) With Mgampcpp and 6-Hydroxymethylpterin (pdb code 1tmm). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1tmm structure was solved by J.BLASZCZYK, Y.LI, Y.WU, G.SHI, X.JI, H.YAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.2 Space group P1211 a (A) 47.992 b (A) 47.392 c (A) 71.438 alpha (°) 90.00 beta (°) 104.13 gamma (°) 90.00 Rfactor (%) 13.2 Rfree (%) 16.4 Magnesium Binding Sites: Magnesium binding site 1 out of 5 in 1tmm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1tmm. 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: Glu77, A: Arg82, A: Lys85, A: Asp95, A: Leu96, A: Asp97, A: Mg162, A: Apc171, A: Hhr181, A: Hoh404, A: Hoh408, A: Hoh435, A: Hoh440, conact list: Atom Atom Distance (A) Mg OE2 A:Glu77 4.17 Mg CZ A:Arg82 4.95 Mg NH2 A:Arg82 4.51 Mg NH1 A:Arg82 4.41 Mg NZ A:Lys85 4.03 Mg CB A:Asp95 4.35 Mg OD2 A:Asp95 3.32 Mg C A:Asp95 4.91 Mg OD1 A:Asp95 2.06 Mg CG A:Asp95 3.00 Mg CA A:Asp95 4.73 Mg O A:Leu96 4.23 Mg N A:Leu96 4.70 Mg C A:Leu96 4.54 Mg N A:Asp97 4.79 Mg CB A:Asp97 4.40 Mg OD2 A:Asp97 3.55 Mg OD1 A:Asp97 2.05 Mg CG A:Asp97 3.09 Mg CA A:Asp97 4.69 Mg MG A:Mg162 3.51 Mg N3 A:Apc171 4.82 Mg PG A:Apc171 4.90 Mg O3B A:Apc171 4.49 Mg PA A:Apc171 3.25 Mg C2 A:Apc171 4.78 Mg C3A A:Apc171 3.50 Mg O5' A:Apc171 3.83 Mg O2B A:Apc171 4.01 Mg O3G A:Apc171 4.72 Mg O2A A:Apc171 4.53 Mg O1B A:Apc171 2.09 Mg PB A:Apc171 3.22 Mg O1G A:Apc171 4.67 Mg O1A A:Apc171 2.11 Mg O6A A:Hhr181 4.74 Mg O A:Hoh404 2.08 Mg O A:Hoh408 2.08 Mg O A:Hoh435 4.72 Mg O A:Hoh440 3.90 interactive model: Magnesium binding site 2 out of 5 in 1tmm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1tmm. 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: Asp95, A: Asp97, A: His115, A: Arg121, A: Met124, A: Mg161, A: Apc171, A: Hhr181, A: Hoh407, A: Hoh408, A: Hoh414, A: Hoh440, A: Hoh469, A: Hoh481, A: Hoh496, conact list: Atom Atom Distance (A) Mg CB A:Asp95 4.46 Mg OD2 A:Asp95 2.09 Mg OD1 A:Asp95 3.58 Mg CG A:Asp95 3.14 Mg CB A:Asp97 4.33 Mg OD2 A:Asp97 2.02 Mg OD1 A:Asp97 3.31 Mg CG A:Asp97 2.97 Mg NE2 A:His115 4.74 Mg NH1 A:Arg121 4.16 Mg CE A:Met124 4.99 Mg MG A:Mg161 3.51 Mg PG A:Apc171 3.17 Mg O3B A:Apc171 3.41 Mg O2G A:Apc171 4.43 Mg C3A A:Apc171 4.72 Mg O2B A:Apc171 3.97 Mg O3G A:Apc171 2.02 Mg O1B A:Apc171 2.14 Mg PB A:Apc171 3.23 Mg O1G A:Apc171 3.86 Mg O1A A:Apc171 4.94 Mg N5 A:Hhr181 4.06 Mg O6A A:Hhr181 2.14 Mg C6 A:Hhr181 4.13 Mg C6A A:Hhr181 3.25 Mg O A:Hoh407 4.22 Mg O A:Hoh408 4.59 Mg O A:Hoh414 4.05 Mg O A:Hoh440 4.57 Mg O A:Hoh469 4.18 Mg O A:Hoh481 4.59 Mg O A:Hoh496 2.10 interactive model: Magnesium binding site 3 out of 5 in 1tmm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1tmm. 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: Gly26, A: Asp27, A: Ile28, A: Ser31, A: His32, A: Act167, A: Hoh418, A: Hoh567, A: Hoh644, A: Hoh671, A: Hoh672, A: Hoh730, A: Hoh819, A: Hoh935, A: Hoh983, conact list: Atom Atom Distance (A) Mg O A:Gly26 2.38 Mg C A:Gly26 3.60 Mg CA A:Gly26 4.63 Mg O A:Asp27 4.99 Mg N A:Asp27 4.41 Mg C A:Asp27 4.59 Mg CA A:Asp27 4.39 Mg O A:Ile28 3.77 Mg N A:Ile28 4.83 Mg C A:Ile28 4.82 Mg O A:Ser31 2.28 Mg N A:Ser31 4.51 Mg C A:Ser31 3.49 Mg CA A:Ser31 4.56 Mg N A:His32 4.31 Mg CB A:His32 4.31 Mg CA A:His32 4.18 Mg OXT A:Act167 4.84 Mg O A:Hoh418 4.54 Mg O A:Hoh567 2.45 Mg O A:Hoh644 2.21 Mg O A:Hoh671 2.60 Mg O A:Hoh672 2.60 Mg O A:Hoh730 4.04 Mg O A:Hoh819 4.95 Mg O A:Hoh935 3.33 Mg O A:Hoh983 4.48 interactive model: Magnesium binding site 4 out of 5 in 1tmm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1tmm. 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: Glu277, B: Arg282, B: Lys285, B: Arg292, B: Asp295, B: Leu296, B: Asp297, B: Mg362, B: Apc371, B: Hhr381, B: Hoh431, B: Hoh433, B: Hoh436, B: Hoh449, conact list: Atom Atom Distance (A) Mg OE2 B:Glu277 4.19 Mg CZ B:Arg282 4.94 Mg NH2 B:Arg282 4.56 Mg NH1 B:Arg282 4.30 Mg NZ B:Lys285 4.00 Mg NH1 B:Arg292 4.96 Mg CB B:Asp295 4.39 Mg OD2 B:Asp295 3.28 Mg C B:Asp295 4.97 Mg OD1 B:Asp295 2.09 Mg CG B:Asp295 3.02 Mg CA B:Asp295 4.76 Mg O B:Leu296 4.23 Mg N B:Leu296 4.75 Mg C B:Leu296 4.60 Mg N B:Asp297 4.83 Mg CB B:Asp297 4.41 Mg OD2 B:Asp297 3.56 Mg OD1 B:Asp297 2.04 Mg CG B:Asp297 3.11 Mg CA B:Asp297 4.70 Mg MG B:Mg362 3.50 Mg N3 B:Apc371 4.72 Mg PG B:Apc371 4.98 Mg O3B B:Apc371 4.49 Mg PA B:Apc371 3.25 Mg C2 B:Apc371 4.64 Mg C3A B:Apc371 3.45 Mg O5' B:Apc371 3.79 Mg O2B B:Apc371 3.94 Mg O3G B:Apc371 4.71 Mg O2A B:Apc371 4.50 Mg O1B B:Apc371 2.07 Mg PB B:Apc371 3.18 Mg O1G B:Apc371 4.80 Mg O1A B:Apc371 2.08 Mg O6A B:Hhr381 4.78 Mg O B:Hoh431 2.07 Mg O B:Hoh433 2.09 Mg O B:Hoh436 4.66 Mg O B:Hoh449 4.13 interactive model: Magnesium binding site 5 out of 5 in 1tmm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 1tmm. 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: Arg292, B: Asp295, B: Asp297, B: His315, B: Arg321, B: Met324, B: Mg361, B: Apc371, B: Hhr381, B: Hoh433, B: Hoh449, B: Hoh464, B: Hoh468, B: Hoh499, B: Hoh517, B: Hoh536, conact list: Atom Atom Distance (A) Mg NH1 B:Arg292 4.41 Mg CB B:Asp295 4.47 Mg OD2 B:Asp295 2.10 Mg OD1 B:Asp295 3.60 Mg CG B:Asp295 3.17 Mg CB B:Asp297 4.25 Mg OD2 B:Asp297 1.96 Mg OD1 B:Asp297 3.24 Mg CG B:Asp297 2.93 Mg NE2 B:His315 4.32 Mg NH1 B:Arg321 4.04 Mg CE B:Met324 4.91 Mg MG B:Mg361 3.50 Mg PG B:Apc371 3.22 Mg O3B B:Apc371 3.32 Mg O2G B:Apc371 4.40 Mg C3A B:Apc371 4.65 Mg O2B B:Apc371 3.98 Mg O3G B:Apc371 2.04 Mg O1B B:Apc371 2.16 Mg PB B:Apc371 3.23 Mg O1G B:Apc371 3.93 Mg O1A B:Apc371 4.93 Mg N5 B:Hhr381 4.26 Mg O6A B:Hhr381 2.16 Mg C6 B:Hhr381 4.27 Mg C6A B:Hhr381 3.41 Mg O B:Hoh433 4.53 Mg O B:Hoh449 4.64 Mg O B:Hoh464 4.30 Mg O B:Hoh468 4.72 Mg O B:Hoh499 4.06 Mg O B:Hoh517 2.17 Mg O B:Hoh536 3.99 interactive model: