Manganese in the structure of Crystal Structure Analysis of Dahp Synthase in Complex With MN2+ and 2-Phosphoglycolate (pdb 1gg1)
The binding sites of Manganese atom in the structure of Crystal Structure Analysis of Dahp Synthase in Complex With MN2+ and 2-Phosphoglycolate (pdb code 1gg1). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1gg1 structure was solved by T.WAGNER, I.A.SHUMILIN, R.BAUERLE, R.H.KRETSINGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 20.0-2.0 | Space group | C121 | a (A) | 210.357 | b (A) | 53.188 | c (A) | 149.392 | alpha (°) | 90.00 | beta (°) | 116.09 | gamma (°) | 90.00 | Rfactor (%) | 20.9 | Rfree (%) | 23.7 |
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Manganese Binding Sites:Manganese binding site 1 out of 4 in 1gg1
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1gg1. 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: Cys61, A: Arg92, A: Lys97, A: His268, A: Glu302, A: Asp326, A: Pga372, A: Hoh1435, A: Hoh1460, | conact list:
Atom | Atom | Distance (A) | Mn | O A:Cys61 | 4.86 | Mn | CB A:Cys61 | 3.80 | Mn | SG A:Cys61 | 2.79 | Mn | CA A:Cys61 | 4.39 | Mn | NH2 A:Arg92 | 4.24 | Mn | CE A:Lys97 | 4.86 | Mn | NZ A:Lys97 | 3.62 | Mn | NE2 A:His268 | 2.36 | Mn | ND1 A:His268 | 4.42 | Mn | CD2 A:His268 | 3.24 | Mn | CE1 A:His268 | 3.35 | Mn | CG A:His268 | 4.40 | Mn | OE1 A:Glu302 | 2.16 | Mn | OE2 A:Glu302 | 3.47 | Mn | CD A:Glu302 | 3.15 | Mn | CG A:Glu302 | 4.47 | Mn | CB A:Asp326 | 3.72 | Mn | OD2 A:Asp326 | 2.20 | Mn | OD1 A:Asp326 | 4.37 | Mn | CG A:Asp326 | 3.27 | Mn | O2 A:Pga372 | 2.41 | Mn | C1 A:Pga372 | 3.39 | Mn | O1 A:Pga372 | 4.26 | Mn | O1P A:Pga372 | 4.97 | Mn | C2 A:Pga372 | 3.91 | Mn | O A:Hoh1435 | 4.27 | Mn | O A:Hoh1460 | 4.50 |
| interactive model:
| Manganese binding site 2 out of 4 in 1gg1
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1gg1. 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: Cys61, B: Arg92, B: Lys97, B: His268, B: Lys273, B: Glu302, B: Asp326, B: Pga372, B: Hoh2375, B: Hoh2384, B: Hoh2448, B: Hoh2553, B: Hoh2571, | conact list:
Atom | Atom | Distance (A) | Mn | O B:Cys61 | 4.82 | Mn | CB B:Cys61 | 3.72 | Mn | SG B:Cys61 | 2.67 | Mn | C B:Cys61 | 4.95 | Mn | CA B:Cys61 | 4.29 | Mn | CZ B:Arg92 | 4.97 | Mn | NH2 B:Arg92 | 4.17 | Mn | CE B:Lys97 | 4.72 | Mn | NZ B:Lys97 | 3.91 | Mn | NE2 B:His268 | 2.36 | Mn | ND1 B:His268 | 4.42 | Mn | CD2 B:His268 | 3.38 | Mn | CE1 B:His268 | 3.27 | Mn | CG B:His268 | 4.51 | Mn | NZ B:Lys273 | 4.86 | Mn | OE1 B:Glu302 | 3.49 | Mn | OE2 B:Glu302 | 1.97 | Mn | CD B:Glu302 | 3.03 | Mn | CG B:Glu302 | 4.29 | Mn | N B:Asp326 | 4.92 | Mn | CB B:Asp326 | 3.61 | Mn | OD2 B:Asp326 | 2.06 | Mn | OD1 B:Asp326 | 4.16 | Mn | CG B:Asp326 | 3.09 | Mn | CA B:Asp326 | 4.88 | Mn | O2 B:Pga372 | 2.45 | Mn | C1 B:Pga372 | 3.35 | Mn | O1 B:Pga372 | 4.29 | Mn | O1P B:Pga372 | 4.92 | Mn | C2 B:Pga372 | 3.76 | Mn | O B:Hoh2375 | 2.26 | Mn | O B:Hoh2384 | 4.63 | Mn | O B:Hoh2448 | 4.25 | Mn | O B:Hoh2553 | 4.72 | Mn | O B:Hoh2571 | 4.69 |
| interactive model:
| Manganese binding site 3 out of 4 in 1gg1
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1gg1. 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: Cys61, C: Arg92, C: Lys97, C: His268, C: Glu302, C: Asp326, C: Pga372, C: Hoh3375, C: Hoh3376, C: Hoh3397, C: Hoh3442, | conact list:
Atom | Atom | Distance (A) | Mn | CB C:Cys61 | 3.72 | Mn | SG C:Cys61 | 2.79 | Mn | CA C:Cys61 | 4.33 | Mn | NH2 C:Arg92 | 4.41 | Mn | CE C:Lys97 | 4.69 | Mn | NZ C:Lys97 | 3.83 | Mn | NE2 C:His268 | 2.50 | Mn | ND1 C:His268 | 4.62 | Mn | CD2 C:His268 | 3.22 | Mn | CE1 C:His268 | 3.63 | Mn | CG C:His268 | 4.47 | Mn | OE1 C:Glu302 | 3.20 | Mn | OE2 C:Glu302 | 2.04 | Mn | CD C:Glu302 | 2.95 | Mn | CG C:Glu302 | 4.34 | Mn | CB C:Asp326 | 3.45 | Mn | OD2 C:Asp326 | 1.86 | Mn | OD1 C:Asp326 | 4.04 | Mn | CG C:Asp326 | 2.95 | Mn | CA C:Asp326 | 4.83 | Mn | O2 C:Pga372 | 2.27 | Mn | C1 C:Pga372 | 3.26 | Mn | O1 C:Pga372 | 4.13 | Mn | O1P C:Pga372 | 4.90 | Mn | C2 C:Pga372 | 3.82 | Mn | O C:Hoh3375 | 2.48 | Mn | O C:Hoh3376 | 4.57 | Mn | O C:Hoh3397 | 4.31 | Mn | O C:Hoh3442 | 4.59 |
| interactive model:
| Manganese binding site 4 out of 4 in 1gg1
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1gg1. 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: Cys61, D: Arg92, D: Lys97, D: His268, D: Lys273, D: Glu302, D: Asp326, D: Pga372, D: Hoh4375, D: Hoh4394, D: Hoh4430, D: Hoh4534, D: Hoh4535, | conact list:
Atom | Atom | Distance (A) | Mn | O D:Cys61 | 4.78 | Mn | CB D:Cys61 | 3.72 | Mn | SG D:Cys61 | 2.64 | Mn | C D:Cys61 | 4.96 | Mn | CA D:Cys61 | 4.32 | Mn | NH2 D:Arg92 | 4.27 | Mn | CE D:Lys97 | 4.69 | Mn | NZ D:Lys97 | 3.87 | Mn | NE2 D:His268 | 2.35 | Mn | ND1 D:His268 | 4.45 | Mn | CD2 D:His268 | 3.21 | Mn | CE1 D:His268 | 3.39 | Mn | CG D:His268 | 4.40 | Mn | NZ D:Lys273 | 4.86 | Mn | OE1 D:Glu302 | 2.14 | Mn | OE2 D:Glu302 | 3.29 | Mn | CD D:Glu302 | 3.04 | Mn | CG D:Glu302 | 4.39 | Mn | N D:Asp326 | 4.96 | Mn | CB D:Asp326 | 3.64 | Mn | OD2 D:Asp326 | 2.13 | Mn | OD1 D:Asp326 | 4.24 | Mn | CG D:Asp326 | 3.17 | Mn | CA D:Asp326 | 4.91 | Mn | O2 D:Pga372 | 2.47 | Mn | C1 D:Pga372 | 3.42 | Mn | O1 D:Pga372 | 4.21 | Mn | C2 D:Pga372 | 4.01 | Mn | O D:Hoh4375 | 2.19 | Mn | O D:Hoh4394 | 4.40 | Mn | O D:Hoh4430 | 4.07 | Mn | O D:Hoh4534 | 4.50 | Mn | O D:Hoh4535 | 4.60 |
| interactive model:
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