Manganese in the structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex With D-Psicose (pdb 3ito)
The binding sites of Manganese atom in the structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex With D-Psicose (pdb code 3ito). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3ito structure was solved by H.YOSHIDA, M.YAMAJI, T.ISHII, K.IZUMORI, S.KAMITORI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 42.1-1.9 | Space group | P1211 | a (A) | 74.762 | b (A) | 104.732 | c (A) | 115.035 | alpha (°) | 90.00 | beta (°) | 108.24 | gamma (°) | 90.00 | Rfactor (%) | 17.6 | Rfree (%) | 21.1 |
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Manganese Binding Sites:Manganese binding site 1 out of 8 in 3ito
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3ito. 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: Glu219, A: Asp254, A: His257, A: His281, A: Asn327, A: Mn502, A: Psv601, A: Hoh530, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 A:Glu219 | 3.31 | Mn | OE2 A:Glu219 | 2.12 | Mn | CD A:Glu219 | 3.06 | Mn | CG A:Glu219 | 4.46 | Mn | CB A:Asp254 | 3.70 | Mn | OD2 A:Asp254 | 4.35 | Mn | OD1 A:Asp254 | 2.21 | Mn | CG A:Asp254 | 3.26 | Mn | CA A:Asp254 | 4.99 | Mn | NE2 A:His257 | 3.97 | Mn | ND1 A:His257 | 4.59 | Mn | CE1 A:His257 | 3.65 | Mn | NE2 A:His281 | 4.18 | Mn | CB A:His281 | 3.74 | Mn | ND1 A:His281 | 2.17 | Mn | CD2 A:His281 | 4.35 | Mn | CE1 A:His281 | 2.99 | Mn | CG A:His281 | 3.30 | Mn | CB A:Asn327 | 4.07 | Mn | ND2 A:Asn327 | 2.57 | Mn | OD1 A:Asn327 | 4.41 | Mn | CG A:Asn327 | 3.53 | Mn | MN A:Mn502 | 3.93 | Mn | O5 A:Psv601 | 3.90 | Mn | C5 A:Psv601 | 4.51 | Mn | O2 A:Psv601 | 2.09 | Mn | C4 A:Psv601 | 4.58 | Mn | C1 A:Psv601 | 4.41 | Mn | O1 A:Psv601 | 4.94 | Mn | C3 A:Psv601 | 3.42 | Mn | O3 A:Psv601 | 2.54 | Mn | O4 A:Psv601 | 4.98 | Mn | C2 A:Psv601 | 3.22 | Mn | O A:Hoh530 | 3.99 |
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| Manganese binding site 2 out of 8 in 3ito
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3ito. 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: Glu219, A: Lys221, A: Asp254, A: His257, A: Asp289, A: Asp291, A: Asn327, B: Arg65, A: Mn501, A: Psv601, A: Hoh487, A: Hoh530, | conact list:
Atom | Atom | Distance (A) | Mn | OE2 A:Glu219 | 4.75 | Mn | CE A:Lys221 | 4.24 | Mn | CD A:Lys221 | 4.57 | Mn | NZ A:Lys221 | 4.12 | Mn | OD2 A:Asp254 | 4.35 | Mn | OD1 A:Asp254 | 3.67 | Mn | CG A:Asp254 | 4.16 | Mn | NE2 A:His257 | 2.09 | Mn | ND1 A:His257 | 4.14 | Mn | CD2 A:His257 | 3.16 | Mn | CE1 A:His257 | 2.99 | Mn | CG A:His257 | 4.26 | Mn | CB A:Asp289 | 4.41 | Mn | OD2 A:Asp289 | 2.28 | Mn | OD1 A:Asp289 | 3.03 | Mn | CG A:Asp289 | 2.98 | Mn | OD2 A:Asp291 | 4.31 | Mn | OD1 A:Asp291 | 3.87 | Mn | CG A:Asp291 | 4.53 | Mn | ND2 A:Asn327 | 3.84 | Mn | NH2 B:Arg65 | 4.76 | Mn | MN A:Mn501 | 3.93 | Mn | O5 A:Psv601 | 3.43 | Mn | C5 A:Psv601 | 4.86 | Mn | O2 A:Psv601 | 2.43 | Mn | C1 A:Psv601 | 3.09 | Mn | O1 A:Psv601 | 2.29 | Mn | C3 A:Psv601 | 4.58 | Mn | O3 A:Psv601 | 4.98 | Mn | C2 A:Psv601 | 3.12 | Mn | O A:Hoh487 | 2.36 | Mn | O A:Hoh530 | 2.04 |
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| Manganese binding site 3 out of 8 in 3ito
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3ito. 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: Glu219, B: Asp254, B: His257, B: His281, B: Asn327, B: Mn504, B: Psv602, B: Hoh1435, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 B:Glu219 | 3.16 | Mn | OE2 B:Glu219 | 2.23 | Mn | CD B:Glu219 | 3.00 | Mn | CG B:Glu219 | 4.38 | Mn | CB B:Asp254 | 3.78 | Mn | OD2 B:Asp254 | 2.30 | Mn | OD1 B:Asp254 | 4.46 | Mn | CG B:Asp254 | 3.36 | Mn | NE2 B:His257 | 4.13 | Mn | ND1 B:His257 | 4.59 | Mn | CE1 B:His257 | 3.70 | Mn | CB B:His281 | 4.00 | Mn | ND1 B:His281 | 2.97 | Mn | CE1 B:His281 | 3.90 | Mn | CG B:His281 | 3.88 | Mn | CB B:Asn327 | 4.08 | Mn | ND2 B:Asn327 | 2.50 | Mn | OD1 B:Asn327 | 4.61 | Mn | CG B:Asn327 | 3.62 | Mn | MN B:Mn504 | 4.07 | Mn | O5 B:Psv602 | 4.13 | Mn | C5 B:Psv602 | 4.73 | Mn | O2 B:Psv602 | 2.31 | Mn | C4 B:Psv602 | 4.63 | Mn | C1 B:Psv602 | 4.55 | Mn | C3 B:Psv602 | 3.46 | Mn | O3 B:Psv602 | 2.49 | Mn | O4 B:Psv602 | 4.93 | Mn | C2 B:Psv602 | 3.39 | Mn | O B:Hoh1435 | 4.40 |
| interactive model:
| Manganese binding site 4 out of 8 in 3ito
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3ito. 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: Arg65, A: Phe66, B: Glu219, B: Lys221, B: Asp254, B: His257, B: Asp289, B: Asp291, B: Asn327, B: Mn503, B: Psv602, B: Hoh684, B: Hoh1435, | conact list:
Atom | Atom | Distance (A) | Mn | NH2 A:Arg65 | 4.94 | Mn | CZ A:Phe66 | 4.99 | Mn | OE2 B:Glu219 | 4.58 | Mn | CE B:Lys221 | 4.23 | Mn | CD B:Lys221 | 4.61 | Mn | NZ B:Lys221 | 3.98 | Mn | OD2 B:Asp254 | 3.74 | Mn | OD1 B:Asp254 | 4.43 | Mn | CG B:Asp254 | 4.24 | Mn | NE2 B:His257 | 2.03 | Mn | ND1 B:His257 | 4.03 | Mn | CD2 B:His257 | 3.16 | Mn | CE1 B:His257 | 2.85 | Mn | CG B:His257 | 4.21 | Mn | CB B:Asp289 | 4.61 | Mn | OD2 B:Asp289 | 3.23 | Mn | OD1 B:Asp289 | 2.41 | Mn | CG B:Asp289 | 3.17 | Mn | OD2 B:Asp291 | 4.27 | Mn | OD1 B:Asp291 | 3.83 | Mn | CG B:Asp291 | 4.49 | Mn | ND2 B:Asn327 | 3.98 | Mn | MN B:Mn503 | 4.07 | Mn | O5 B:Psv602 | 3.50 | Mn | C5 B:Psv602 | 4.92 | Mn | O2 B:Psv602 | 2.32 | Mn | C1 B:Psv602 | 3.01 | Mn | O1 B:Psv602 | 2.18 | Mn | C3 B:Psv602 | 4.49 | Mn | O3 B:Psv602 | 4.87 | Mn | C2 B:Psv602 | 3.07 | Mn | O B:Hoh684 | 2.39 | Mn | O B:Hoh1435 | 1.97 |
| interactive model:
| Manganese binding site 5 out of 8 in 3ito
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3ito. 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: Glu219, C: Asp254, C: His257, C: His281, C: Asn327, C: Mn506, C: Psv603, C: Hoh1436, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 C:Glu219 | 3.22 | Mn | OE2 C:Glu219 | 2.17 | Mn | CD C:Glu219 | 3.01 | Mn | CG C:Glu219 | 4.37 | Mn | CB C:Asp254 | 3.77 | Mn | OD2 C:Asp254 | 2.30 | Mn | OD1 C:Asp254 | 4.43 | Mn | CG C:Asp254 | 3.34 | Mn | NE2 C:His257 | 4.04 | Mn | ND1 C:His257 | 4.52 | Mn | CE1 C:His257 | 3.61 | Mn | NE2 C:His281 | 4.48 | Mn | CB C:His281 | 3.77 | Mn | ND1 C:His281 | 2.45 | Mn | CD2 C:His281 | 4.57 | Mn | CE1 C:His281 | 3.33 | Mn | CG C:His281 | 3.47 | Mn | CB C:Asn327 | 4.12 | Mn | ND2 C:Asn327 | 2.46 | Mn | OD1 C:Asn327 | 4.59 | Mn | CG C:Asn327 | 3.61 | Mn | MN C:Mn506 | 3.98 | Mn | O5 C:Psv603 | 4.06 | Mn | C5 C:Psv603 | 4.76 | Mn | O2 C:Psv603 | 2.16 | Mn | C4 C:Psv603 | 4.68 | Mn | C1 C:Psv603 | 4.43 | Mn | O1 C:Psv603 | 4.83 | Mn | C3 C:Psv603 | 3.44 | Mn | O3 C:Psv603 | 2.56 | Mn | C2 C:Psv603 | 3.29 | Mn | O C:Hoh1436 | 4.08 |
| interactive model:
| Manganese binding site 6 out of 8 in 3ito
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3ito. 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: Glu219, C: Lys221, C: Asp254, C: His257, C: Asp289, C: Asp291, C: Asn327, D: Arg65, C: Mn505, C: Psv603, C: Hoh1421, C: Hoh1436, | conact list:
Atom | Atom | Distance (A) | Mn | OE2 C:Glu219 | 4.56 | Mn | CE C:Lys221 | 4.30 | Mn | CD C:Lys221 | 4.61 | Mn | NZ C:Lys221 | 4.07 | Mn | OD2 C:Asp254 | 3.67 | Mn | OD1 C:Asp254 | 4.30 | Mn | CG C:Asp254 | 4.14 | Mn | NE2 C:His257 | 1.98 | Mn | ND1 C:His257 | 4.00 | Mn | CD2 C:His257 | 3.11 | Mn | CE1 C:His257 | 2.82 | Mn | CG C:His257 | 4.16 | Mn | CB C:Asp289 | 4.53 | Mn | OD2 C:Asp289 | 2.52 | Mn | OD1 C:Asp289 | 3.03 | Mn | CG C:Asp289 | 3.10 | Mn | OD2 C:Asp291 | 4.39 | Mn | OD1 C:Asp291 | 3.78 | Mn | CG C:Asp291 | 4.52 | Mn | ND2 C:Asn327 | 4.10 | Mn | NH1 D:Arg65 | 4.95 | Mn | MN C:Mn505 | 3.98 | Mn | O5 C:Psv603 | 3.64 | Mn | O2 C:Psv603 | 2.47 | Mn | C1 C:Psv603 | 3.16 | Mn | O1 C:Psv603 | 2.20 | Mn | C3 C:Psv603 | 4.65 | Mn | C2 C:Psv603 | 3.23 | Mn | O C:Hoh1421 | 2.43 | Mn | O C:Hoh1436 | 1.99 |
| interactive model:
| Manganese binding site 7 out of 8 in 3ito
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 3ito. 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: Glu219, D: Leu252, D: Asp254, D: His257, D: His281, D: Asn327, D: Mn508, D: Psv604, D: Hoh457, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 D:Glu219 | 3.32 | Mn | OE2 D:Glu219 | 2.09 | Mn | CD D:Glu219 | 3.05 | Mn | CG D:Glu219 | 4.43 | Mn | CD2 D:Leu252 | 4.88 | Mn | CB D:Asp254 | 3.69 | Mn | OD2 D:Asp254 | 2.16 | Mn | OD1 D:Asp254 | 4.32 | Mn | CG D:Asp254 | 3.23 | Mn | CA D:Asp254 | 4.96 | Mn | NE2 D:His257 | 3.99 | Mn | ND1 D:His257 | 4.60 | Mn | CE1 D:His257 | 3.69 | Mn | NE2 D:His281 | 4.18 | Mn | CB D:His281 | 3.70 | Mn | ND1 D:His281 | 2.17 | Mn | CD2 D:His281 | 4.33 | Mn | CE1 D:His281 | 3.01 | Mn | CG D:His281 | 3.28 | Mn | CB D:Asn327 | 4.12 | Mn | ND2 D:Asn327 | 2.58 | Mn | OD1 D:Asn327 | 4.39 | Mn | CG D:Asn327 | 3.54 | Mn | MN D:Mn508 | 3.81 | Mn | O5 D:Psv604 | 3.81 | Mn | C5 D:Psv604 | 4.42 | Mn | O2 D:Psv604 | 2.04 | Mn | C4 D:Psv604 | 4.44 | Mn | C1 D:Psv604 | 4.35 | Mn | O1 D:Psv604 | 4.81 | Mn | C3 D:Psv604 | 3.32 | Mn | O3 D:Psv604 | 2.42 | Mn | O4 D:Psv604 | 4.79 | Mn | C2 D:Psv604 | 3.14 | Mn | O D:Hoh457 | 3.91 |
| interactive model:
| Manganese binding site 8 out of 8 in 3ito
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 3ito. 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: Arg65, D: Glu219, D: Lys221, D: Asp254, D: His257, D: Asp289, D: Asp291, D: Asn327, D: Mn507, D: Psv604, D: Hoh457, D: Hoh536, | conact list:
Atom | Atom | Distance (A) | Mn | NH2 C:Arg65 | 4.83 | Mn | OE2 D:Glu219 | 4.65 | Mn | CE D:Lys221 | 4.29 | Mn | CD D:Lys221 | 4.68 | Mn | NZ D:Lys221 | 4.24 | Mn | OD2 D:Asp254 | 3.55 | Mn | OD1 D:Asp254 | 4.34 | Mn | CG D:Asp254 | 4.10 | Mn | NE2 D:His257 | 2.11 | Mn | ND1 D:His257 | 4.17 | Mn | CD2 D:His257 | 3.17 | Mn | CE1 D:His257 | 3.02 | Mn | CG D:His257 | 4.27 | Mn | CB D:Asp289 | 4.47 | Mn | OD2 D:Asp289 | 2.23 | Mn | OD1 D:Asp289 | 3.17 | Mn | CG D:Asp289 | 3.05 | Mn | OD2 D:Asp291 | 4.31 | Mn | OD1 D:Asp291 | 3.90 | Mn | CG D:Asp291 | 4.54 | Mn | ND2 D:Asn327 | 3.72 | Mn | CG D:Asn327 | 5.00 | Mn | MN D:Mn507 | 3.81 | Mn | O5 D:Psv604 | 3.46 | Mn | C5 D:Psv604 | 4.87 | Mn | O2 D:Psv604 | 2.35 | Mn | C1 D:Psv604 | 3.12 | Mn | O1 D:Psv604 | 2.27 | Mn | C3 D:Psv604 | 4.54 | Mn | O3 D:Psv604 | 4.89 | Mn | C2 D:Psv604 | 3.11 | Mn | O D:Hoh457 | 2.04 | Mn | O D:Hoh536 | 2.40 |
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