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:
|
|
|
|
|