Manganese in the structure of Crystal Structure Of The Lectin I From Ulex Europaeus in Complex With the Methyl Glycoside of Alpha-L-Fucose (pdb 1jxn)
The binding sites of Manganese atom in the structure of Crystal Structure Of The Lectin I From Ulex Europaeus in Complex With the Methyl Glycoside of Alpha-L-Fucose (pdb code 1jxn). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1jxn structure was solved by G.F.AUDETTE, D.J.H.OLSON, A.R.S.ROSS, J.W.QUAIL, L.T.J.DELBAERE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 40.0-2.3 | Space group | P1211 | a (A) | 71.810 | b (A) | 69.000 | c (A) | 119.020 | alpha (°) | 90.00 | beta (°) | 106.76 | gamma (°) | 90.00 | Rfactor (%) | 20.2 | Rfree (%) | 28.9 |
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Manganese Binding Sites:Manganese binding site 1 out of 4 in 1jxn
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1jxn. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Phe107, A: Glu125, A: Asp127, A: Trp136, A: Asp137, A: His142, A: Val150, A: Ser152, A: Ca246, A: Hoh515, A: Hoh516, A: Hoh517, | conact list:
Atom | Atom | Distance (A) | Mn | CE1 A:Phe107 | 4.84 | Mn | OE1 A:Glu125 | 2.22 | Mn | OE2 A:Glu125 | 3.03 | Mn | CD A:Glu125 | 2.97 | Mn | CG A:Glu125 | 4.41 | Mn | CB A:Asp127 | 3.55 | Mn | OD2 A:Asp127 | 4.38 | Mn | OD1 A:Asp127 | 2.28 | Mn | CG A:Asp127 | 3.25 | Mn | CD1 A:Trp136 | 4.90 | Mn | NE1 A:Trp136 | 4.85 | Mn | CB A:Asp137 | 4.29 | Mn | OD2 A:Asp137 | 2.38 | Mn | OD1 A:Asp137 | 3.45 | Mn | CG A:Asp137 | 3.13 | Mn | CA A:Asp137 | 4.98 | Mn | NE2 A:His142 | 2.73 | Mn | ND1 A:His142 | 4.34 | Mn | CD2 A:His142 | 4.02 | Mn | CE1 A:His142 | 3.06 | Mn | CG A:His142 | 4.83 | Mn | O A:Val150 | 4.20 | Mn | OG A:Ser152 | 4.30 | Mn | CA A:Ca246 | 4.10 | Mn | O A:Hoh515 | 2.21 | Mn | O A:Hoh516 | 2.18 | Mn | O A:Hoh517 | 3.96 |
| interactive model:
| Manganese binding site 2 out of 4 in 1jxn
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1jxn. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Glu125, B: Asp127, B: Asp137, B: Pro138, B: His142, B: Val150, B: Ser152, B: Ca246, B: Hoh619, B: Hoh620, B: Hoh641, B: Hoh642, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 B:Glu125 | 2.36 | Mn | OE2 B:Glu125 | 3.54 | Mn | CD B:Glu125 | 3.29 | Mn | CG B:Glu125 | 4.65 | Mn | CB B:Asp127 | 3.34 | Mn | OD2 B:Asp127 | 2.42 | Mn | OD1 B:Asp127 | 4.45 | Mn | CG B:Asp127 | 3.26 | Mn | CA B:Asp127 | 4.86 | Mn | CB B:Asp137 | 3.43 | Mn | OD2 B:Asp137 | 2.56 | Mn | OD1 B:Asp137 | 4.45 | Mn | CG B:Asp137 | 3.33 | Mn | CA B:Asp137 | 4.40 | Mn | CD B:Pro138 | 4.61 | Mn | NE2 B:His142 | 2.11 | Mn | ND1 B:His142 | 4.10 | Mn | CD2 B:His142 | 3.28 | Mn | CE1 B:His142 | 2.90 | Mn | CG B:His142 | 4.31 | Mn | O B:Val150 | 4.67 | Mn | OG B:Ser152 | 4.34 | Mn | CA B:Ca246 | 4.49 | Mn | O B:Hoh619 | 4.92 | Mn | O B:Hoh620 | 2.12 | Mn | O B:Hoh641 | 4.07 | Mn | O B:Hoh642 | 2.65 |
| interactive model:
| Manganese binding site 3 out of 4 in 1jxn
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1jxn. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Phe107, C: Glu125, C: Asp127, C: Trp136, C: Asp137, C: Pro138, C: His142, C: Val150, C: Ser152, C: Ca246, C: Hoh916, C: Hoh918, C: Hoh919, | conact list:
Atom | Atom | Distance (A) | Mn | CE1 C:Phe107 | 4.89 | Mn | OE1 C:Glu125 | 2.53 | Mn | OE2 C:Glu125 | 3.02 | Mn | CD C:Glu125 | 3.14 | Mn | CG C:Glu125 | 4.61 | Mn | CB C:Asp127 | 3.78 | Mn | OD2 C:Asp127 | 4.63 | Mn | OD1 C:Asp127 | 2.52 | Mn | CG C:Asp127 | 3.50 | Mn | CD1 C:Trp136 | 4.50 | Mn | NE1 C:Trp136 | 4.34 | Mn | CB C:Asp137 | 4.24 | Mn | OD2 C:Asp137 | 1.94 | Mn | OD1 C:Asp137 | 3.71 | Mn | CG C:Asp137 | 3.09 | Mn | CA C:Asp137 | 4.72 | Mn | CD C:Pro138 | 4.98 | Mn | NE2 C:His142 | 2.48 | Mn | ND1 C:His142 | 4.60 | Mn | CD2 C:His142 | 3.52 | Mn | CE1 C:His142 | 3.42 | Mn | CG C:His142 | 4.67 | Mn | O C:Val150 | 4.34 | Mn | CB C:Ser152 | 4.99 | Mn | OG C:Ser152 | 3.78 | Mn | CA C:Ca246 | 4.26 | Mn | O C:Hoh916 | 4.35 | Mn | O C:Hoh918 | 2.23 | Mn | O C:Hoh919 | 1.98 |
| interactive model:
| Manganese binding site 4 out of 4 in 1jxn
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1jxn. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Glu125, D: Asp127, D: Trp136, D: Asp137, D: Pro138, D: His142, D: Val150, D: Ser152, D: Ca246, D: Hoh820, D: Hoh822, D: Hoh823, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 D:Glu125 | 2.27 | Mn | OE2 D:Glu125 | 3.70 | Mn | CD D:Glu125 | 3.32 | Mn | CG D:Glu125 | 4.59 | Mn | CB D:Asp127 | 3.59 | Mn | OD2 D:Asp127 | 2.44 | Mn | OD1 D:Asp127 | 4.47 | Mn | CG D:Asp127 | 3.35 | Mn | CD1 D:Trp136 | 4.91 | Mn | NE1 D:Trp136 | 4.89 | Mn | CB D:Asp137 | 4.02 | Mn | OD2 D:Asp137 | 3.50 | Mn | OD1 D:Asp137 | 2.12 | Mn | CG D:Asp137 | 2.98 | Mn | CA D:Asp137 | 4.65 | Mn | CD D:Pro138 | 4.77 | Mn | NE2 D:His142 | 1.89 | Mn | ND1 D:His142 | 4.05 | Mn | CD2 D:His142 | 2.87 | Mn | CE1 D:His142 | 2.95 | Mn | CG D:His142 | 4.04 | Mn | O D:Val150 | 4.45 | Mn | OG D:Ser152 | 4.17 | Mn | CA D:Ca246 | 4.39 | Mn | O D:Hoh820 | 4.51 | Mn | O D:Hoh822 | 2.57 | Mn | O D:Hoh823 | 2.15 |
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