Manganese in the structure of Peanut Lectin-Triclinic Form (pdb 1cq9)
The binding sites of Manganese atom in the structure of Peanut Lectin-Triclinic Form (pdb code 1cq9). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1cq9 structure was solved by R.RAVISHANKAR, K.SUGUNA, A.SUROLIA, M.VIJAYAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 10.0-3.5 | Space group | P1 | a (A) | 53.640 | b (A) | 71.790 | c (A) | 86.420 | alpha (°) | 65.35 | beta (°) | 77.66 | gamma (°) | 72.31 | Rfactor (%) | 21.7 | Rfree (%) | 27.8 |
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Manganese Binding Sites:Manganese binding site 1 out of 4 in 1cq9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1cq9. 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: Glu121, A: Asp123, A: Asp132, A: Pro133, A: His137, A: Val145, A: Ser147, A: Ca237, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 A:Glu121 | 3.39 | Mn | OE2 A:Glu121 | 2.23 | Mn | CD A:Glu121 | 3.18 | Mn | CG A:Glu121 | 4.54 | Mn | CB A:Asp123 | 3.82 | Mn | OD2 A:Asp123 | 4.58 | Mn | OD1 A:Asp123 | 2.54 | Mn | CG A:Asp123 | 3.49 | Mn | CB A:Asp132 | 4.51 | Mn | OD2 A:Asp132 | 3.76 | Mn | OD1 A:Asp132 | 2.31 | Mn | CG A:Asp132 | 3.30 | Mn | CA A:Asp132 | 4.78 | Mn | CD A:Pro133 | 4.62 | Mn | NE2 A:His137 | 2.65 | Mn | ND1 A:His137 | 4.73 | Mn | CD2 A:His137 | 3.58 | Mn | CE1 A:His137 | 3.63 | Mn | CG A:His137 | 4.77 | Mn | O A:Val145 | 4.11 | Mn | OG A:Ser147 | 4.02 | Mn | CA A:Ca237 | 4.42 |
| interactive model:
| Manganese binding site 2 out of 4 in 1cq9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1cq9. 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: Glu121, B: Asp123, B: Asp132, B: Pro133, B: His137, B: Val145, B: Ser147, B: Thr150, B: Ca239, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 B:Glu121 | 3.64 | Mn | OE2 B:Glu121 | 2.55 | Mn | CD B:Glu121 | 3.43 | Mn | CG B:Glu121 | 4.78 | Mn | CB B:Asp123 | 4.11 | Mn | OD1 B:Asp123 | 2.97 | Mn | CG B:Asp123 | 3.90 | Mn | CB B:Asp132 | 4.39 | Mn | OD2 B:Asp132 | 3.80 | Mn | OD1 B:Asp132 | 2.15 | Mn | CG B:Asp132 | 3.25 | Mn | CA B:Asp132 | 4.50 | Mn | CD B:Pro133 | 4.49 | Mn | NE2 B:His137 | 2.57 | Mn | ND1 B:His137 | 4.68 | Mn | CD2 B:His137 | 3.42 | Mn | CE1 B:His137 | 3.63 | Mn | CG B:His137 | 4.64 | Mn | O B:Val145 | 3.86 | Mn | CB B:Ser147 | 4.66 | Mn | OG B:Ser147 | 3.50 | Mn | CG2 B:Thr150 | 4.82 | Mn | CA B:Ca239 | 4.62 |
| interactive model:
| Manganese binding site 3 out of 4 in 1cq9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1cq9. 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: Glu121, C: Asp123, C: Asp132, C: Pro133, C: His137, C: Val145, C: Ser147, C: Ca241, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 C:Glu121 | 3.19 | Mn | OE2 C:Glu121 | 2.33 | Mn | CD C:Glu121 | 3.14 | Mn | CG C:Glu121 | 4.61 | Mn | CB C:Asp123 | 4.16 | Mn | OD2 C:Asp123 | 4.79 | Mn | OD1 C:Asp123 | 2.68 | Mn | CG C:Asp123 | 3.74 | Mn | CB C:Asp132 | 4.68 | Mn | OD2 C:Asp132 | 3.80 | Mn | OD1 C:Asp132 | 2.37 | Mn | CG C:Asp132 | 3.40 | Mn | CA C:Asp132 | 4.86 | Mn | CD C:Pro133 | 4.72 | Mn | NE2 C:His137 | 3.09 | Mn | CD2 C:His137 | 3.88 | Mn | CE1 C:His137 | 4.12 | Mn | O C:Val145 | 3.62 | Mn | C C:Val145 | 4.81 | Mn | CB C:Ser147 | 4.89 | Mn | OG C:Ser147 | 3.73 | Mn | CA C:Ca241 | 4.68 |
| interactive model:
| Manganese binding site 4 out of 4 in 1cq9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1cq9. 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: Glu121, D: Asp123, D: Asp132, D: Pro133, D: His137, D: Val145, D: Ser147, D: Ca243, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 D:Glu121 | 3.66 | Mn | OE2 D:Glu121 | 2.44 | Mn | CD D:Glu121 | 3.39 | Mn | CG D:Glu121 | 4.77 | Mn | CB D:Asp123 | 3.87 | Mn | OD2 D:Asp123 | 4.67 | Mn | OD1 D:Asp123 | 2.50 | Mn | CG D:Asp123 | 3.56 | Mn | CB D:Asp132 | 4.30 | Mn | OD2 D:Asp132 | 3.71 | Mn | OD1 D:Asp132 | 1.99 | Mn | CG D:Asp132 | 3.12 | Mn | CA D:Asp132 | 4.61 | Mn | CD D:Pro133 | 4.47 | Mn | NE2 D:His137 | 2.52 | Mn | ND1 D:His137 | 4.62 | Mn | CD2 D:His137 | 3.42 | Mn | CE1 D:His137 | 3.52 | Mn | CG D:His137 | 4.64 | Mn | O D:Val145 | 3.83 | Mn | OG D:Ser147 | 4.22 | Mn | CA D:Ca243 | 4.38 |
| interactive model:
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