Magnesium in the structure of Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt At 1.58 A Resolution (pdb 3b9t)

The binding sites of Magnesium atom in the structure of Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt At 1.58 A Resolution (pdb code 3b9t). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3b9t structure was solved by JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.8-1.6 Space group P1 a (A) 62.165 b (A) 82.723 c (A) 83.576 alpha (°) 107.82 beta (°) 105.81 gamma (°) 95.18 Rfactor (%) 13.8 Rfree (%) 17.7 Magnesium Binding Sites: Magnesium binding site 1 out of 8 in 3b9t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3b9t. 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: His110, A: His160, A: Asp316, A: Asp341, A: His343, A: Glu350, A: Ala355, A: Glu357, A: Mg485, A: Edo494, A: Hoh501, conact list: Atom Atom Distance (A) Mg NE2 A:His110 4.58 Mg CE1 A:His110 4.05 Mg NE2 A:His160 4.69 Mg CD2 A:His160 4.64 Mg OD1 A:Asp316 4.39 Mg O A:Asp341 4.37 Mg CB A:Asp341 4.13 Mg OD2 A:Asp341 2.60 Mg C A:Asp341 4.79 Mg OD1 A:Asp341 2.08 Mg CG A:Asp341 2.65 Mg CA A:Asp341 4.73 Mg NE2 A:His343 2.21 Mg ND1 A:His343 4.30 Mg CD2 A:His343 3.05 Mg CE1 A:His343 3.26 Mg CG A:His343 4.23 Mg OE2 A:Glu350 4.01 Mg N A:Ala355 4.71 Mg CB A:Ala355 4.86 Mg OE1 A:Glu357 2.31 Mg CB A:Glu357 4.95 Mg OE2 A:Glu357 2.27 Mg CD A:Glu357 2.62 Mg CG A:Glu357 4.12 Mg MG A:Mg485 3.33 Mg O1 A:Edo494 3.58 Mg O2 A:Edo494 3.54 Mg C2 A:Edo494 2.38 Mg C1 A:Edo494 3.19 Mg O A:Hoh501 4.31 interactive model: Magnesium binding site 2 out of 8 in 3b9t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3b9t. 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: His160, A: Gly291, A: Thr292, A: Asn314, A: Asp316, A: Asp341, A: His343, A: Glu350, A: Asp464, A: Mg484, A: Edo490, A: Edo494, conact list: Atom Atom Distance (A) Mg NE2 A:His160 3.75 Mg CD2 A:His160 4.35 Mg CE1 A:His160 4.54 Mg O A:Gly291 4.46 Mg C A:Gly291 4.39 Mg CA A:Gly291 4.26 Mg OG1 A:Thr292 4.31 Mg O A:Asn314 4.82 Mg CB A:Asn314 4.44 Mg ND2 A:Asn314 3.33 Mg C A:Asn314 4.93 Mg OD1 A:Asn314 2.14 Mg CG A:Asn314 3.05 Mg CA A:Asn314 4.84 Mg N A:Asp316 4.87 Mg CB A:Asp316 3.98 Mg OD2 A:Asp316 2.40 Mg OD1 A:Asp316 1.95 Mg CG A:Asp316 2.49 Mg CA A:Asp316 4.70 Mg CB A:Asp341 4.28 Mg OD2 A:Asp341 2.05 Mg OD1 A:Asp341 3.95 Mg CG A:Asp341 3.23 Mg NE2 A:His343 3.77 Mg CE1 A:His343 3.90 Mg OE1 A:Glu350 4.53 Mg OE2 A:Glu350 3.97 Mg CD A:Glu350 4.68 Mg OD2 A:Asp464 4.51 Mg OD1 A:Asp464 4.59 Mg CG A:Asp464 4.94 Mg MG A:Mg484 3.33 Mg O1 A:Edo490 4.70 Mg O1 A:Edo494 1.81 Mg O2 A:Edo494 4.33 Mg C2 A:Edo494 3.45 Mg C1 A:Edo494 2.89 interactive model: Magnesium binding site 3 out of 8 in 3b9t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3b9t. 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: His110, B: His160, B: Asp316, B: Asp341, B: His343, B: Glu350, B: Ala355, B: Glu357, B: Mg485, B: Edo486, B: Hoh500, conact list: Atom Atom Distance (A) Mg NE2 B:His110 4.50 Mg CE1 B:His110 3.99 Mg NE2 B:His160 4.68 Mg CD2 B:His160 4.62 Mg OD1 B:Asp316 4.47 Mg O B:Asp341 4.42 Mg CB B:Asp341 4.15 Mg OD2 B:Asp341 2.58 Mg C B:Asp341 4.84 Mg OD1 B:Asp341 2.12 Mg CG B:Asp341 2.67 Mg CA B:Asp341 4.78 Mg NE2 B:His343 2.26 Mg ND1 B:His343 4.34 Mg CD2 B:His343 3.12 Mg CE1 B:His343 3.28 Mg CG B:His343 4.30 Mg OE2 B:Glu350 4.14 Mg N B:Ala355 4.69 Mg CB B:Ala355 4.90 Mg OE1 B:Glu357 2.33 Mg CB B:Glu357 4.93 Mg OE2 B:Glu357 2.24 Mg CD B:Glu357 2.58 Mg CG B:Glu357 4.09 Mg MG B:Mg485 3.38 Mg O1 B:Edo486 3.43 Mg O2 B:Edo486 3.45 Mg C2 B:Edo486 2.27 Mg C1 B:Edo486 3.06 Mg O B:Hoh500 4.34 interactive model: Magnesium binding site 4 out of 8 in 3b9t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3b9t. 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: His160, B: Gly291, B: Thr292, B: Asn314, B: Asp316, B: Asp341, B: His343, B: Glu350, B: Asp464, B: Mg484, B: Edo486, B: Edo490, conact list: Atom Atom Distance (A) Mg NE2 B:His160 3.72 Mg CD2 B:His160 4.26 Mg CE1 B:His160 4.52 Mg O B:Gly291 4.34 Mg C B:Gly291 4.35 Mg CA B:Gly291 4.24 Mg N B:Thr292 4.98 Mg OG1 B:Thr292 4.14 Mg O B:Asn314 4.78 Mg CB B:Asn314 4.36 Mg ND2 B:Asn314 3.28 Mg C B:Asn314 4.87 Mg OD1 B:Asn314 2.07 Mg CG B:Asn314 2.98 Mg CA B:Asn314 4.74 Mg N B:Asp316 4.88 Mg CB B:Asp316 4.06 Mg OD2 B:Asp316 2.54 Mg OD1 B:Asp316 2.01 Mg CG B:Asp316 2.58 Mg CA B:Asp316 4.74 Mg CB B:Asp341 4.13 Mg OD2 B:Asp341 1.98 Mg OD1 B:Asp341 3.95 Mg CG B:Asp341 3.17 Mg NE2 B:His343 3.81 Mg CE1 B:His343 3.88 Mg OE1 B:Glu350 4.66 Mg OE2 B:Glu350 4.15 Mg CD B:Glu350 4.83 Mg OD2 B:Asp464 4.56 Mg OD1 B:Asp464 4.67 Mg MG B:Mg484 3.38 Mg O1 B:Edo486 1.73 Mg O2 B:Edo486 4.29 Mg C2 B:Edo486 3.48 Mg C1 B:Edo486 2.89 Mg O2 B:Edo490 4.65 interactive model: Magnesium binding site 5 out of 8 in 3b9t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3b9t. 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: His110, C: His160, C: Asp316, C: Asp341, C: His343, C: Glu350, C: Ala355, C: Glu357, C: Mg485, C: Edo496, C: Hoh500, conact list: Atom Atom Distance (A) Mg NE2 C:His110 4.57 Mg CE1 C:His110 4.09 Mg NE2 C:His160 4.79 Mg CD2 C:His160 4.66 Mg OD1 C:Asp316 4.42 Mg O C:Asp341 4.43 Mg CB C:Asp341 4.19 Mg OD2 C:Asp341 2.60 Mg C C:Asp341 4.88 Mg OD1 C:Asp341 2.15 Mg CG C:Asp341 2.69 Mg CA C:Asp341 4.85 Mg NE2 C:His343 2.25 Mg ND1 C:His343 4.35 Mg CD2 C:His343 3.08 Mg CE1 C:His343 3.31 Mg CG C:His343 4.28 Mg OE2 C:Glu350 4.05 Mg N C:Ala355 4.62 Mg CB C:Ala355 4.85 Mg OE1 C:Glu357 2.26 Mg CB C:Glu357 4.91 Mg OE2 C:Glu357 2.19 Mg CD C:Glu357 2.53 Mg CG C:Glu357 4.03 Mg MG C:Mg485 3.42 Mg O1 C:Edo496 3.36 Mg O2 C:Edo496 3.70 Mg C2 C:Edo496 2.36 Mg C1 C:Edo496 2.83 Mg O C:Hoh500 4.36 interactive model: Magnesium binding site 6 out of 8 in 3b9t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3b9t. 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: His160, C: Gly291, C: Thr292, C: Asn314, C: Asp316, C: Asp341, C: His343, C: Glu350, C: Asp464, C: Mg484, C: Edo489, C: Edo496, conact list: Atom Atom Distance (A) Mg NE2 C:His160 3.70 Mg CD2 C:His160 4.22 Mg CE1 C:His160 4.51 Mg O C:Gly291 4.46 Mg C C:Gly291 4.40 Mg CA C:Gly291 4.33 Mg N C:Thr292 5.00 Mg OG1 C:Thr292 4.21 Mg O C:Asn314 4.75 Mg CB C:Asn314 4.41 Mg ND2 C:Asn314 3.33 Mg C C:Asn314 4.90 Mg OD1 C:Asn314 2.14 Mg CG C:Asn314 3.05 Mg CA C:Asn314 4.80 Mg N C:Asp316 4.92 Mg CB C:Asp316 4.10 Mg OD2 C:Asp316 2.49 Mg OD1 C:Asp316 2.04 Mg CG C:Asp316 2.60 Mg CA C:Asp316 4.79 Mg CB C:Asp341 4.26 Mg OD2 C:Asp341 2.14 Mg OD1 C:Asp341 4.04 Mg CG C:Asp341 3.30 Mg NE2 C:His343 3.90 Mg CE1 C:His343 4.03 Mg OE1 C:Glu350 4.59 Mg OE2 C:Glu350 4.13 Mg CD C:Glu350 4.79 Mg OD2 C:Asp464 4.49 Mg OD1 C:Asp464 4.57 Mg CG C:Asp464 4.90 Mg MG C:Mg484 3.42 Mg O2 C:Edo489 4.46 Mg O1 C:Edo496 1.68 Mg O2 C:Edo496 4.43 Mg C2 C:Edo496 3.56 Mg C1 C:Edo496 2.85 interactive model: Magnesium binding site 7 out of 8 in 3b9t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 3b9t. 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: His110, D: His160, D: Asp316, D: Asp341, D: His343, D: Glu350, D: Ala355, D: Glu357, D: Mg485, D: Edo488, D: Hoh498, conact list: Atom Atom Distance (A) Mg NE2 D:His110 4.56 Mg CE1 D:His110 4.09 Mg NE2 D:His160 4.80 Mg CD2 D:His160 4.69 Mg OD1 D:Asp316 4.42 Mg O D:Asp341 4.42 Mg CB D:Asp341 4.15 Mg OD2 D:Asp341 2.54 Mg C D:Asp341 4.87 Mg OD1 D:Asp341 2.08 Mg CG D:Asp341 2.64 Mg CA D:Asp341 4.80 Mg NE2 D:His343 2.22 Mg ND1 D:His343 4.26 Mg CD2 D:His343 3.11 Mg CE1 D:His343 3.20 Mg CG D:His343 4.26 Mg OE2 D:Glu350 4.02 Mg N D:Ala355 4.68 Mg CB D:Ala355 4.87 Mg OE1 D:Glu357 2.30 Mg CB D:Glu357 4.96 Mg OE2 D:Glu357 2.22 Mg CD D:Glu357 2.57 Mg CG D:Glu357 4.07 Mg MG D:Mg485 3.49 Mg O1 D:Edo488 3.48 Mg O2 D:Edo488 2.77 Mg C2 D:Edo488 2.75 Mg C1 D:Edo488 3.06 Mg O D:Hoh498 4.35 interactive model: Magnesium binding site 8 out of 8 in 3b9t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 3b9t. 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: His160, D: Gly291, D: Thr292, D: Asn314, D: Asp316, D: Asp341, D: His343, D: Glu350, D: Asp464, D: Mg484, D: Edo488, D: Edo493, conact list: Atom Atom Distance (A) Mg NE2 D:His160 3.79 Mg CD2 D:His160 4.28 Mg CE1 D:His160 4.64 Mg O D:Gly291 4.16 Mg C D:Gly291 4.15 Mg CA D:Gly291 4.10 Mg N D:Thr292 4.79 Mg OG1 D:Thr292 3.98 Mg O D:Asn314 4.70 Mg CB D:Asn314 4.25 Mg ND2 D:Asn314 3.25 Mg C D:Asn314 4.76 Mg OD1 D:Asn314 1.92 Mg CG D:Asn314 2.89 Mg CA D:Asn314 4.62 Mg N D:Asp316 4.75 Mg CB D:Asp316 4.05 Mg OD2 D:Asp316 2.57 Mg OD1 D:Asp316 1.96 Mg CG D:Asp316 2.58 Mg CA D:Asp316 4.67 Mg CB D:Asp341 4.15 Mg OD2 D:Asp341 2.03 Mg OD1 D:Asp341 4.02 Mg CG D:Asp341 3.23 Mg NE2 D:His343 3.88 Mg CE1 D:His343 3.93 Mg OE1 D:Glu350 4.67 Mg OE2 D:Glu350 4.29 Mg CD D:Glu350 4.93 Mg OD2 D:Asp464 4.54 Mg OD1 D:Asp464 4.67 Mg CG D:Asp464 4.99 Mg MG D:Mg484 3.49 Mg O1 D:Edo488 1.80 Mg O2 D:Edo488 3.99 Mg C2 D:Edo488 3.85 Mg C1 D:Edo488 2.78 Mg O2 D:Edo493 4.75 interactive model: