Manganese in the structure of Binding of Cesium Ions to the Nucleosome Core Particle (pdb 3mgs)

The binding sites of Manganese atom in the structure of Binding of Cesium Ions to the Nucleosome Core Particle (pdb code 3mgs). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3mgs structure was solved by K.MOHIDEEN, R.MUHAMMAD, C.A.DAVEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 94.1-3.1 Space group P212121 a (A) 106.510 b (A) 109.668 c (A) 182.609 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.6 Rfree (%) 23.8 Manganese Binding Sites: Manganese binding site 1 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3mgs. 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: Da60, J: Dg61, J: Dg62, conact list: Atom Atom Distance (A) Mn N9 J:Da60 4.99 Mn C8 J:Da60 4.24 Mn N7 J:Da60 4.35 Mn N9 J:Dg61 4.62 Mn C8 J:Dg61 3.39 Mn C6 J:Dg61 4.08 Mn C5 J:Dg61 3.58 Mn N7 J:Dg61 2.53 Mn C4 J:Dg61 4.71 Mn O6 J:Dg61 3.82 Mn O6 J:Dg62 4.23 interactive model: Manganese binding site 2 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3mgs. 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: E: Glu73, E: Gln76, E: Asp77, F: Leu22, conact list: Atom Atom Distance (A) Mn O E:Glu73 4.51 Mn CG E:Glu73 5.00 Mn OE1 E:Gln76 4.16 Mn N E:Asp77 4.75 Mn CB E:Asp77 4.53 Mn OD2 E:Asp77 3.42 Mn OD1 E:Asp77 2.28 Mn CG E:Asp77 3.18 Mn CA E:Asp77 4.80 Mn O F:Leu22 4.17 interactive model: Manganese binding site 3 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3mgs. 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: Dt-29, I: Dg-28, J: Da26, J: Dg27, J: Dc28, conact list: Atom Atom Distance (A) Mn C7 I:Dt-29 4.86 Mn O6 I:Dg-28 4.22 Mn C8 J:Da26 4.55 Mn N7 J:Da26 4.70 Mn N9 J:Dg27 4.61 Mn C8 J:Dg27 3.42 Mn C6 J:Dg27 3.92 Mn C5 J:Dg27 3.51 Mn N7 J:Dg27 2.53 Mn C4 J:Dg27 4.66 Mn O6 J:Dg27 3.60 Mn N4 J:Dc28 4.92 interactive model: Manganese binding site 4 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3mgs. 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: Dc2, J: Dt-4, J: Dg-3, J: Dg-2, conact list: Atom Atom Distance (A) Mn N4 I:Dc2 4.82 Mn C6 J:Dt-4 4.33 Mn N1 J:Dt-4 4.75 Mn C5 J:Dt-4 4.74 Mn C1' J:Dt-4 4.95 Mn C7 J:Dt-4 4.93 Mn C2' J:Dt-4 4.03 Mn N9 J:Dg-3 4.44 Mn C8 J:Dg-3 3.19 Mn C6 J:Dg-3 3.89 Mn C5 J:Dg-3 3.39 Mn N7 J:Dg-3 2.30 Mn C4 J:Dg-3 4.54 Mn O6 J:Dg-3 3.60 Mn C6 J:Dg-2 4.82 Mn O6 J:Dg-2 4.00 interactive model: Manganese binding site 5 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3mgs. 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: Dt47, J: Dg48, J: Dg49, conact list: Atom Atom Distance (A) Mn C2' J:Dt47 4.18 Mn N9 J:Dg48 4.36 Mn C8 J:Dg48 3.16 Mn C6 J:Dg48 3.67 Mn C5 J:Dg48 3.20 Mn N7 J:Dg48 2.18 Mn C4 J:Dg48 4.38 Mn OP2 J:Dg48 4.27 Mn O6 J:Dg48 3.41 Mn O6 J:Dg49 4.10 interactive model: Manganese binding site 6 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3mgs. 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: Dt13, I: Dg14, I: Dc15, J: Da-13, J: Dt-12, I: Cs75, J: Cs74, conact list: Atom Atom Distance (A) Mn O2 I:Dt13 4.05 Mn O4' I:Dg14 4.31 Mn C4' I:Dg14 4.66 Mn O4' I:Dc15 4.62 Mn C5' I:Dc15 4.50 Mn C4' I:Dc15 4.69 Mn N3 J:Da-13 4.47 Mn C2 J:Da-13 4.38 Mn C2 J:Dt-12 4.79 Mn C1' J:Dt-12 4.79 Mn O2 J:Dt-12 4.03 Mn O4' J:Dt-12 4.14 Mn C4' J:Dt-12 4.78 Mn CS I:Cs75 2.71 Mn CS J:Cs74 1.47 interactive model: Manganese binding site 7 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 3mgs. 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: Dt47, I: Dg48, I: Dg49, conact list: Atom Atom Distance (A) Mn C2' I:Dt47 4.10 Mn N9 I:Dg48 4.45 Mn C8 I:Dg48 3.21 Mn C6 I:Dg48 3.97 Mn C5 I:Dg48 3.44 Mn N7 I:Dg48 2.35 Mn C4 I:Dg48 4.57 Mn OP2 I:Dg48 4.95 Mn O6 I:Dg48 3.73 Mn O6 I:Dg49 4.31 interactive model: Manganese binding site 8 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 3mgs. 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: Da60, I: Dg61, I: Dg62, conact list: Atom Atom Distance (A) Mn N9 I:Da60 4.95 Mn C8 I:Da60 4.21 Mn N7 I:Da60 4.31 Mn N9 I:Dg61 4.58 Mn C8 I:Dg61 3.38 Mn C6 I:Dg61 3.86 Mn C5 I:Dg61 3.43 Mn N7 I:Dg61 2.43 Mn C4 I:Dg61 4.62 Mn O6 I:Dg61 3.54 Mn O6 I:Dg62 4.34 interactive model: Manganese binding site 9 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Manganese in the PDB 3mgs. 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: Dc34, J: Dt-36, J: Dg-35, J: Dg-34, conact list: Atom Atom Distance (A) Mn N4 I:Dc34 4.79 Mn C3' J:Dt-36 4.70 Mn O3' J:Dt-36 4.25 Mn C2' J:Dt-36 4.18 Mn N9 J:Dg-35 4.20 Mn C8 J:Dg-35 3.07 Mn C6 J:Dg-35 4.15 Mn C5 J:Dg-35 3.48 Mn P J:Dg-35 5.00 Mn N7 J:Dg-35 2.46 Mn C4 J:Dg-35 4.41 Mn OP2 J:Dg-35 4.29 Mn O6 J:Dg-35 4.11 Mn C8 J:Dg-34 4.77 Mn C6 J:Dg-34 3.37 Mn N1 J:Dg-34 4.51 Mn C5 J:Dg-34 3.74 Mn N7 J:Dg-34 3.61 Mn C4 J:Dg-34 4.98 Mn O6 J:Dg-34 2.67 interactive model: Manganese binding site 10 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Manganese in the PDB 3mgs. 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: Da26, I: Dg27, conact list: Atom Atom Distance (A) Mn N9 I:Da26 4.72 Mn C8 I:Da26 3.98 Mn N7 I:Da26 4.18 Mn C2' I:Da26 4.73 Mn N9 I:Dg27 4.72 Mn C8 I:Dg27 3.44 Mn C6 I:Dg27 4.22 Mn C5 I:Dg27 3.72 Mn N7 I:Dg27 2.59 Mn C4 I:Dg27 4.85 Mn O6 I:Dg27 3.95 interactive model: Manganese binding site 11 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Manganese in the PDB 3mgs. 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: Da4, I: Dg5, J: Dg-6, J: Dc-5, conact list: Atom Atom Distance (A) Mn N7 I:Da4 4.77 Mn C6 I:Dg5 3.82 Mn C5 I:Dg5 4.25 Mn N7 I:Dg5 4.00 Mn O6 I:Dg5 2.89 Mn C6 J:Dg-6 4.69 Mn C5 J:Dg-6 4.80 Mn N7 J:Dg-6 4.17 Mn O6 J:Dg-6 3.94 Mn N4 J:Dc-5 4.23 interactive model: Manganese binding site 12 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Manganese in the PDB 3mgs. 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: Dt-4, I: Dg-3, I: Dg-2, J: Dc2, conact list: Atom Atom Distance (A) Mn C6 I:Dt-4 4.88 Mn C2' I:Dt-4 4.51 Mn N9 I:Dg-3 4.41 Mn C8 I:Dg-3 3.29 Mn C6 I:Dg-3 3.62 Mn N1 I:Dg-3 4.96 Mn C5 I:Dg-3 3.22 Mn N7 I:Dg-3 2.33 Mn C4 I:Dg-3 4.38 Mn OP2 I:Dg-3 4.98 Mn O6 I:Dg-3 3.34 Mn C6 I:Dg-2 4.18 Mn C5 I:Dg-2 4.58 Mn N7 I:Dg-2 4.39 Mn O6 I:Dg-2 3.39 Mn N4 J:Dc2 4.83 interactive model: Manganese binding site 13 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Manganese in the PDB 3mgs. 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: Dt-36, I: Dg-35, I: Dg-34, J: Dc34, conact list: Atom Atom Distance (A) Mn C3' I:Dt-36 4.89 Mn O3' I:Dt-36 4.71 Mn C2' I:Dt-36 4.24 Mn N9 I:Dg-35 4.36 Mn C8 I:Dg-35 3.12 Mn C6 I:Dg-35 3.92 Mn C5 I:Dg-35 3.37 Mn N7 I:Dg-35 2.27 Mn C4 I:Dg-35 4.48 Mn OP2 I:Dg-35 4.71 Mn O6 I:Dg-35 3.71 Mn C8 I:Dg-34 4.87 Mn C6 I:Dg-34 3.53 Mn N1 I:Dg-34 4.71 Mn C5 I:Dg-34 3.87 Mn N7 I:Dg-34 3.70 Mn O6 I:Dg-34 2.78 Mn N4 J:Dc34 4.26 interactive model: Manganese binding site 14 out of 14 in 3mgs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Manganese in the PDB 3mgs. 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: Dg-6, I: Dc-5, J: Da4, J: Dg5, conact list: Atom Atom Distance (A) Mn N7 I:Dg-6 4.70 Mn O6 I:Dg-6 4.39 Mn C4 I:Dc-5 5.00 Mn N4 I:Dc-5 3.72 Mn C8 J:Da4 4.20 Mn C6 J:Da4 4.97 Mn C5 J:Da4 4.46 Mn N6 J:Da4 4.74 Mn N7 J:Da4 3.63 Mn C6 J:Dg5 3.65 Mn N1 J:Dg5 4.86 Mn C5 J:Dg5 4.17 Mn N7 J:Dg5 3.95 Mn O6 J:Dg5 2.60 interactive model: