The binding sites of Manganese atom in the structure of The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed With A 16NT Dna Duplex. (pdb code 2w42). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2w42 structure was solved by J.S.PARKER, S.M.ROE, D.BARFORD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 98.1-1.9 | Space group | P1 | a (A) | 51.838 | b (A) | 61.384 | c (A) | 103.540 | alpha (°) | 75.80 | beta (°) | 75.86 | gamma (°) | 79.47 | Rfactor (%) | 20.5 | Rfree (%) | 24.3 |
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Manganese binding site 1 out of 2 in 2w42
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2w42. 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: Gln137, A: Gln159, A: Lys163, A: Arg380, A: Leu427, P: Dt1, P: Dt2, P: Dc3, A: Hoh2242, A: Hoh2243, A: Hoh2244, P: Hoh2002, | conact list:
Atom | Atom | Distance (A) | Mn | NE2 A:Gln137 | 4.45 | Mn | OE1 A:Gln137 | 4.65 | Mn | NE2 A:Gln159 | 3.38 | Mn | OE1 A:Gln159 | 2.04 | Mn | CB A:Gln159 | 4.96 | Mn | CD A:Gln159 | 3.01 | Mn | CG A:Gln159 | 4.36 | Mn | CE A:Lys163 | 4.55 | Mn | NZ A:Lys163 | 3.94 | Mn | CZ A:Arg380 | 4.65 | Mn | CG A:Arg380 | 4.89 | Mn | NE A:Arg380 | 4.19 | Mn | NH2 A:Arg380 | 4.18 | Mn | O A:Leu427 | 2.46 | Mn | CB A:Leu427 | 4.76 | Mn | C A:Leu427 | 2.67 | Mn | CA A:Leu427 | 4.19 | Mn | OXT A:Leu427 | 2.24 | Mn | OP1 P:Dt1 | 3.55 | Mn | P P:Dt1 | 3.28 | Mn | OP2 P:Dt1 | 4.29 | Mn | C5' P:Dt1 | 4.28 | Mn | O5' P:Dt1 | 4.24 | Mn | OP3 P:Dt1 | 1.98 | Mn | O3' P:Dt2 | 3.87 | Mn | OP1 P:Dc3 | 2.09 | Mn | P P:Dc3 | 3.52 | Mn | OP2 P:Dc3 | 4.21 | Mn | C5' P:Dc3 | 4.92 | Mn | O5' P:Dc3 | 4.61 | Mn | O A:Hoh2242 | 4.54 | Mn | O A:Hoh2243 | 4.27 | Mn | O A:Hoh2244 | 2.20 | Mn | O P:Hoh2002 | 4.58 |
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| Manganese binding site 2 out of 2 in 2w42
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2w42. 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: Gln137, B: Gln159, B: Lys163, B: Arg380, B: Leu427, R: Dt1, R: Dt2, R: Dc3, B: Hoh2141, B: Hoh2142, B: Hoh2143, R: Hoh2005, | conact list:
Atom | Atom | Distance (A) | Mn | NE2 B:Gln137 | 4.51 | Mn | OE1 B:Gln137 | 4.67 | Mn | NE2 B:Gln159 | 3.58 | Mn | OE1 B:Gln159 | 2.22 | Mn | CD B:Gln159 | 3.21 | Mn | CG B:Gln159 | 4.56 | Mn | CE B:Lys163 | 4.48 | Mn | NZ B:Lys163 | 3.89 | Mn | CZ B:Arg380 | 4.65 | Mn | CG B:Arg380 | 4.73 | Mn | NE B:Arg380 | 4.15 | Mn | NH2 B:Arg380 | 4.29 | Mn | O B:Leu427 | 2.45 | Mn | CB B:Leu427 | 4.68 | Mn | C B:Leu427 | 2.58 | Mn | CA B:Leu427 | 4.07 | Mn | OXT B:Leu427 | 1.93 | Mn | OP1 R:Dt1 | 3.56 | Mn | P R:Dt1 | 3.36 | Mn | OP2 R:Dt1 | 4.33 | Mn | C5' R:Dt1 | 4.42 | Mn | O5' R:Dt1 | 4.32 | Mn | OP3 R:Dt1 | 2.13 | Mn | O3' R:Dt2 | 3.98 | Mn | OP1 R:Dc3 | 2.13 | Mn | P R:Dc3 | 3.41 | Mn | OP2 R:Dc3 | 4.20 | Mn | C5' R:Dc3 | 4.80 | Mn | O5' R:Dc3 | 4.53 | Mn | O B:Hoh2141 | 4.33 | Mn | O B:Hoh2142 | 4.50 | Mn | O B:Hoh2143 | 2.21 | Mn | O R:Hoh2005 | 4.61 |
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