Manganese in the structure of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T (pdb 3a6n)

The binding sites of Manganese atom in the structure of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T (pdb code 3a6n). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3a6n structure was solved by H.TACHIWANA, W.KAGAWA, A.OSAKABE, K.KOICHIRO, T.SHIGA, H.KIMURA, H.KURUMIZAKA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.7 Space group P212121 a (A) 105.476 b (A) 109.521 c (A) 181.052 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.8 Rfree (%) 26.4 Manganese Binding Sites: Manganese binding site 1 out of 8 in 3a6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3a6n. 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: Glu64, D: Gln44, D: Val45, D: His46, C: Hoh134, D: Hoh123, conact list: Atom Atom Distance (A) Mn OE1 C:Glu64 4.15 Mn OE2 C:Glu64 4.28 Mn CD C:Glu64 4.66 Mn O D:Gln44 4.33 Mn O D:Val45 2.30 Mn N D:Val45 4.90 Mn CB D:Val45 4.54 Mn C D:Val45 3.27 Mn CA D:Val45 3.73 Mn NE2 D:His46 4.85 Mn N D:His46 4.40 Mn CD2 D:His46 4.40 Mn CA D:His46 4.87 Mn O C:Hoh134 4.26 Mn O D:Hoh123 2.02 interactive model: Manganese binding site 2 out of 8 in 3a6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3a6n. 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: I: Dg68, J: Dg224, J: Dc225, conact list: Atom Atom Distance (A) Mn C6 I:Dg68 3.84 Mn N1 I:Dg68 4.86 Mn C5 I:Dg68 4.55 Mn N7 I:Dg68 4.57 Mn O6 I:Dg68 2.78 Mn C6 J:Dg224 4.69 Mn C5 J:Dg224 4.73 Mn N7 J:Dg224 4.09 Mn O6 J:Dg224 4.02 Mn C4 J:Dc225 4.79 Mn N4 J:Dc225 3.56 interactive model: Manganese binding site 3 out of 8 in 3a6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3a6n. 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: I: Dt120, I: Dg121, I: Dg122, J: Dc171, conact list: Atom Atom Distance (A) Mn C6 I:Dt120 3.74 Mn N1 I:Dt120 4.47 Mn C5 I:Dt120 4.00 Mn C1' I:Dt120 4.87 Mn C7 I:Dt120 3.99 Mn C4 I:Dt120 4.98 Mn C2' I:Dt120 4.24 Mn N9 I:Dg121 4.76 Mn C8 I:Dg121 3.63 Mn C6 I:Dg121 3.60 Mn N1 I:Dg121 4.99 Mn C5 I:Dg121 3.36 Mn N7 I:Dg121 2.53 Mn C4 I:Dg121 4.64 Mn O6 I:Dg121 3.15 Mn O6 I:Dg122 4.26 Mn N4 J:Dc171 4.38 interactive model: Manganese binding site 4 out of 8 in 3a6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3a6n. 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: I: Dc132, I: Da133, I: Dg134, conact list: Atom Atom Distance (A) Mn C6 I:Dc132 4.31 Mn C5 I:Dc132 4.16 Mn OP2 I:Dc132 4.79 Mn C8 I:Da133 3.84 Mn C6 I:Da133 4.10 Mn C5 I:Da133 3.76 Mn N6 I:Da133 3.58 Mn N7 I:Da133 2.82 Mn O6 I:Dg134 4.26 interactive model: Manganese binding site 5 out of 8 in 3a6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3a6n. 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: I: Dc107, J: Dt184, J: Dg185, J: Dg186, conact list: Atom Atom Distance (A) Mn N4 I:Dc107 4.23 Mn C3' J:Dt184 4.89 Mn C2' J:Dt184 4.31 Mn N9 J:Dg185 4.77 Mn C8 J:Dg185 3.55 Mn C6 J:Dg185 4.63 Mn C5 J:Dg185 4.03 Mn N7 J:Dg185 2.95 Mn OP2 J:Dg185 3.79 Mn O6 J:Dg185 4.49 Mn C6 J:Dg186 3.53 Mn N1 J:Dg186 4.56 Mn C5 J:Dg186 4.11 Mn N7 J:Dg186 4.13 Mn O6 J:Dg186 2.70 interactive model: Manganese binding site 6 out of 8 in 3a6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3a6n. 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: I: Dc25, J: Dt266, J: Dg267, J: Dg268, conact list: Atom Atom Distance (A) Mn N4 I:Dc25 4.88 Mn C2' J:Dt266 4.63 Mn N9 J:Dg267 4.55 Mn C8 J:Dg267 3.32 Mn C6 J:Dg267 4.30 Mn C5 J:Dg267 3.71 Mn N7 J:Dg267 2.60 Mn C4 J:Dg267 4.75 Mn OP2 J:Dg267 4.12 Mn O6 J:Dg267 4.14 Mn C6 J:Dg268 4.94 Mn O6 J:Dg268 3.98 interactive model: Manganese binding site 7 out of 8 in 3a6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 3a6n. 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: J: Dt216, J: Dg217, J: Da218, conact list: Atom Atom Distance (A) Mn C6 J:Dt216 4.34 Mn N1 J:Dt216 4.76 Mn C5 J:Dt216 4.78 Mn C1' J:Dt216 4.91 Mn C7 J:Dt216 4.99 Mn C2' J:Dt216 4.12 Mn N9 J:Dg217 4.48 Mn C8 J:Dg217 3.28 Mn C6 J:Dg217 3.75 Mn C5 J:Dg217 3.32 Mn N7 J:Dg217 2.30 Mn C4 J:Dg217 4.50 Mn OP2 J:Dg217 4.73 Mn O6 J:Dg217 3.46 Mn N6 J:Da218 4.22 interactive model: Manganese binding site 8 out of 8 in 3a6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 3a6n. 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: J: Da279, J: Dg280, J: Dg281, conact list: Atom Atom Distance (A) Mn C8 J:Da279 4.11 Mn N7 J:Da279 4.14 Mn N9 J:Dg280 4.78 Mn C8 J:Dg280 3.58 Mn C6 J:Dg280 3.87 Mn C5 J:Dg280 3.53 Mn N7 J:Dg280 2.57 Mn C4 J:Dg280 4.76 Mn O6 J:Dg280 3.49 Mn N7 J:Dg281 4.58 Mn O6 J:Dg281 4.19 interactive model: