Manganese in the structure of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions (pdb 1id3)

The binding sites of Manganese atom in the structure of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions (pdb code 1id3). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1id3 structure was solved by C.L.WHITE, R.K.SUTO, K.LUGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-3.1 Space group P212121 a (A) 104.922 b (A) 110.398 c (A) 192.617 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.3 Rfree (%) 29.2 Manganese Binding Sites: Manganese binding site 1 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1id3. 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: Da133, I: Dg134, I: Dg135, conact list: Atom Atom Distance (A) Mn N9 I:Da133 4.77 Mn C8 I:Da133 3.74 Mn C5 I:Da133 4.43 Mn N7 I:Da133 3.48 Mn N9 I:Dg134 4.91 Mn C8 I:Dg134 3.82 Mn C6 I:Dg134 3.56 Mn N1 I:Dg134 4.94 Mn C5 I:Dg134 3.42 Mn N7 I:Dg134 2.68 Mn C4 I:Dg134 4.73 Mn O6 I:Dg134 3.04 Mn C6 I:Dg135 4.89 Mn O6 I:Dg135 3.79 interactive model: Manganese binding site 2 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1id3. 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: Dc69, I: Dg70, I: Dg71, conact list: Atom Atom Distance (A) Mn C6 I:Dc69 4.12 Mn N1 I:Dc69 4.79 Mn C5 I:Dc69 4.52 Mn C2' I:Dc69 4.22 Mn N9 I:Dg70 4.90 Mn C8 I:Dg70 3.73 Mn C6 I:Dg70 3.86 Mn C5 I:Dg70 3.59 Mn N7 I:Dg70 2.69 Mn C4 I:Dg70 4.84 Mn O6 I:Dg70 3.41 Mn O6 I:Dg71 4.27 interactive model: Manganese binding site 3 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1id3. 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, conact list: Atom Atom Distance (A) Mn C2' I:Dt120 4.55 Mn N9 I:Dg121 4.53 Mn C8 I:Dg121 3.46 Mn C6 I:Dg121 3.24 Mn N1 I:Dg121 4.63 Mn C5 I:Dg121 3.04 Mn N7 I:Dg121 2.29 Mn C4 I:Dg121 4.34 Mn OP2 I:Dg121 4.56 Mn O6 I:Dg121 2.82 Mn O6 I:Dg122 4.32 interactive model: Manganese binding site 4 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1id3. 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: Dg78, J: Da213, J: Dg214, J: Dc215, conact list: Atom Atom Distance (A) Mn C6 I:Dg78 4.00 Mn N1 I:Dg78 4.95 Mn C5 I:Dg78 4.70 Mn N7 I:Dg78 4.75 Mn O6 I:Dg78 3.06 Mn C2' J:Da213 4.84 Mn C6 J:Dg214 4.29 Mn C5 J:Dg214 4.47 Mn N7 J:Dg214 3.91 Mn O6 J:Dg214 3.47 Mn N4 J:Dc215 4.25 interactive model: Manganese binding site 5 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 1id3. 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: Dt266, J: Dg267, J: Dg268, conact list: Atom Atom Distance (A) Mn C6 J:Dt266 4.34 Mn N1 J:Dt266 4.90 Mn C5 J:Dt266 4.86 Mn C1' J:Dt266 4.98 Mn C7 J:Dt266 4.92 Mn C2' J:Dt266 3.98 Mn N9 J:Dg267 4.64 Mn C8 J:Dg267 3.53 Mn C6 J:Dg267 3.52 Mn N1 J:Dg267 4.90 Mn C5 J:Dg267 3.26 Mn N7 J:Dg267 2.44 Mn C4 J:Dg267 4.52 Mn OP2 J:Dg267 4.41 Mn O6 J:Dg267 3.11 Mn O6 J:Dg268 4.70 interactive model: Manganese binding site 6 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 1id3. 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 N9 J:Da279 4.94 Mn C8 J:Da279 3.74 Mn C5 J:Da279 4.70 Mn N7 J:Da279 3.52 Mn OP2 J:Da279 4.58 Mn C8 J:Dg280 4.24 Mn C6 J:Dg280 3.22 Mn N1 J:Dg280 4.57 Mn C5 J:Dg280 3.42 Mn N7 J:Dg280 2.99 Mn C4 J:Dg280 4.79 Mn O6 J:Dg280 2.47 Mn O6 J:Dg281 4.45 interactive model: Manganese binding site 7 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 1id3. 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: Dc76, J: Dc215, J: Dg216, J: Dg217, J: Hoh7, conact list: Atom Atom Distance (A) Mn N4 I:Dc76 4.84 Mn C2' J:Dc215 4.70 Mn N9 J:Dg216 3.95 Mn C8 J:Dg216 2.78 Mn C6 J:Dg216 4.00 Mn C5 J:Dg216 3.27 Mn N7 J:Dg216 2.18 Mn C4 J:Dg216 4.19 Mn OP2 J:Dg216 4.64 Mn O6 J:Dg216 4.02 Mn C6 J:Dg217 4.19 Mn C5 J:Dg217 4.72 Mn N7 J:Dg217 4.60 Mn O6 J:Dg217 3.30 Mn O J:Hoh7 3.61 interactive model: Manganese binding site 8 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 1id3. 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: Dt167, J: Dc168, conact list: Atom Atom Distance (A) Mn O3' J:Dt167 4.66 Mn OP1 J:Dc168 3.18 Mn P J:Dc168 4.30 Mn OP2 J:Dc168 4.75 interactive model: Manganese binding site 9 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Manganese in the PDB 1id3. 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: Dt45, I: Dg46, J: Da245, J: Dg246, J: Dc247, conact list: Atom Atom Distance (A) Mn C6 I:Dt45 4.97 Mn C5 I:Dt45 4.24 Mn C7 I:Dt45 3.45 Mn C4 I:Dt45 4.80 Mn O4 I:Dt45 4.77 Mn O6 I:Dg46 4.21 Mn C8 J:Da245 4.21 Mn N7 J:Da245 4.03 Mn N9 J:Dg246 4.97 Mn C8 J:Dg246 3.90 Mn C6 J:Dg246 3.57 Mn N1 J:Dg246 4.94 Mn C5 J:Dg246 3.47 Mn N7 J:Dg246 2.77 Mn C4 J:Dg246 4.77 Mn O6 J:Dg246 3.02 Mn N4 J:Dc247 4.57 interactive model: Manganese binding site 10 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Manganese in the PDB 1id3. 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, I: Dc108, I: Da109, J: Dt184, J: Dg185, J: Dg186, conact list: Atom Atom Distance (A) Mn N3 I:Dc107 4.93 Mn N3 I:Dc108 4.04 Mn C2 I:Dc108 4.69 Mn O2 I:Dc108 4.59 Mn C4 I:Dc108 4.79 Mn N4 I:Dc108 4.72 Mn C2 I:Da109 4.11 Mn N1 I:Da109 4.50 Mn N3 J:Dt184 4.43 Mn C2 J:Dt184 3.64 Mn N1 J:Dt184 4.34 Mn C1' J:Dt184 4.31 Mn O2 J:Dt184 2.86 Mn C2' J:Dt184 4.91 Mn N9 J:Dg185 4.37 Mn N3 J:Dg185 2.48 Mn N2 J:Dg185 2.51 Mn C2 J:Dg185 2.76 Mn C6 J:Dg185 4.93 Mn N1 J:Dg185 4.00 Mn C5 J:Dg185 4.71 Mn C1' J:Dg185 4.39 Mn O4' J:Dg185 4.05 Mn C4 J:Dg185 3.63 Mn N3 J:Dg186 3.95 Mn N2 J:Dg186 3.68 Mn C2 J:Dg186 3.36 Mn C6 J:Dg186 3.63 Mn N1 J:Dg186 3.17 Mn C5 J:Dg186 4.15 Mn C4 J:Dg186 4.22 Mn O6 J:Dg186 4.10 interactive model: Manganese binding site 11 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Manganese in the PDB 1id3. 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: Da202, J: Da203, conact list: Atom Atom Distance (A) Mn N9 J:Da202 4.68 Mn C3' J:Da202 4.19 Mn C8 J:Da202 4.34 Mn C1' J:Da202 4.53 Mn C2' J:Da202 3.27 Mn O5' J:Da202 4.64 Mn N9 J:Da203 4.80 Mn C8 J:Da203 3.57 Mn P J:Da203 4.84 Mn N7 J:Da203 3.84 Mn OP2 J:Da203 3.92 Mn O5' J:Da203 4.66 interactive model: Manganese binding site 12 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Manganese in the PDB 1id3. 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: Arg89, C: Asn90, C: Asp91, C: Asp92, C: Asn95, conact list: Atom Atom Distance (A) Mn O C:Arg89 3.42 Mn C C:Arg89 4.50 Mn O C:Asn90 5.00 Mn N C:Asn90 4.95 Mn C C:Asn90 4.64 Mn OD1 C:Asn90 4.84 Mn CA C:Asn90 4.43 Mn N C:Asp91 4.98 Mn OD1 C:Asp92 4.58 Mn ND2 C:Asn95 4.88 interactive model: Manganese binding site 13 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Manganese in the PDB 1id3. 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: Glu62, C: Leu66, C: Asp91, C: Glu93, C: Hoh137, conact list: Atom Atom Distance (A) Mn OE2 C:Glu62 4.17 Mn CD1 C:Leu66 4.81 Mn CB C:Asp91 4.52 Mn OD2 C:Asp91 3.41 Mn OD1 C:Asp91 2.15 Mn CG C:Asp91 3.14 Mn N C:Glu93 4.87 Mn OE1 C:Glu93 1.85 Mn CB C:Glu93 4.29 Mn OE2 C:Glu93 3.73 Mn CD C:Glu93 3.02 Mn CG C:Glu93 4.03 Mn O C:Hoh137 4.16 interactive model: Manganese binding site 14 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Manganese in the PDB 1id3. 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: Glu108, D: Lys111, D: His112, conact list: Atom Atom Distance (A) Mn OE1 D:Glu108 3.01 Mn CB D:Glu108 4.96 Mn OE2 D:Glu108 1.37 Mn CD D:Glu108 2.43 Mn CG D:Glu108 3.67 Mn CD D:Lys111 4.95 Mn NE2 D:His112 1.87 Mn ND1 D:His112 3.88 Mn CD2 D:His112 2.95 Mn CE1 D:His112 2.74 Mn CG D:His112 4.01 interactive model: Manganese binding site 15 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Manganese in the PDB 1id3. 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: Dt8, E: Arg49, E: Arg53, conact list: Atom Atom Distance (A) Mn OP1 I:Dt8 3.63 Mn P I:Dt8 4.14 Mn OP2 I:Dt8 3.64 Mn O E:Arg49 4.30 Mn CB E:Arg49 4.95 Mn CD E:Arg49 3.68 Mn C E:Arg49 4.91 Mn CG E:Arg49 3.85 Mn CB E:Arg53 3.96 Mn CD E:Arg53 3.79 Mn CG E:Arg53 3.88 Mn NE E:Arg53 4.58 Mn CA E:Arg53 4.96 interactive model: Manganese binding site 16 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Manganese in the PDB 1id3. 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: G: Asp91, G: Asp92, G: Glu93, conact list: Atom Atom Distance (A) Mn CB G:Asp91 4.97 Mn OD2 G:Asp91 3.76 Mn OD1 G:Asp91 2.81 Mn CG G:Asp91 3.63 Mn N G:Asp92 4.80 Mn N G:Glu93 4.41 Mn OE1 G:Glu93 4.92 Mn CB G:Glu93 3.96 Mn CD G:Glu93 4.44 Mn CG G:Glu93 3.29 Mn CA G:Glu93 4.84 interactive model: Manganese binding site 17 out of 17 in 1id3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Manganese in the PDB 1id3. 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: Da111, G: Gly45, G: Ser46, G: Gly47, G: Ala48, H: Ile92, H: Ser93, H: Ala94, I: Hoh156, conact list: Atom Atom Distance (A) Mn OP1 I:Da111 4.07 Mn O G:Gly45 4.19 Mn N G:Gly45 4.41 Mn C G:Gly45 3.53 Mn CA G:Gly45 3.31 Mn N G:Ser46 3.64 Mn OG G:Ser46 4.72 Mn C G:Ser46 4.50 Mn CA G:Ser46 4.59 Mn N G:Gly47 3.49 Mn C G:Gly47 4.40 Mn CA G:Gly47 4.12 Mn N G:Ala48 3.72 Mn CB G:Ala48 4.41 Mn CA G:Ala48 4.61 Mn O H:Ile92 4.31 Mn C H:Ile92 4.88 Mn O H:Ser93 4.37 Mn N H:Ser93 4.53 Mn CB H:Ser93 3.68 Mn OG H:Ser93 4.78 Mn C H:Ser93 3.50 Mn CA H:Ser93 3.25 Mn N H:Ala94 3.38 Mn CB H:Ala94 4.45 Mn CA H:Ala94 4.40 Mn O I:Hoh156 4.59 interactive model: