Manganese in the structure of Crystal Structure of Manganese Bound M-Box Rna (pdb 3pdr)

The binding sites of Manganese atom in the structure of Crystal Structure of Manganese Bound M-Box Rna (pdb code 3pdr). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3pdr structure was solved by A RAMESH, W.C.WINKLER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.5-1.9 Space group P212121 a (A) 68.780 b (A) 102.487 c (A) 126.375 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.2 Rfree (%) 22.8 Manganese Binding Sites: Manganese binding site 1 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3pdr. 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: X: C99, X: G100, X: A101, X: C102, X: A103, X: U104, X: Hoh187, X: Hoh222, X: Hoh297, X: Hoh497, conact list: Atom Atom Distance (A) Mn C3' X:C99 4.58 Mn O3' X:C99 4.50 Mn OP2 X:C99 4.77 Mn O5' X:C99 4.80 Mn OP1 X:G100 4.59 Mn C8 X:G100 4.49 Mn P X:G100 3.62 Mn N7 X:G100 4.40 Mn OP2 X:G100 2.20 Mn O5' X:G100 4.12 Mn C3' X:A101 4.37 Mn O3' X:A101 4.48 Mn C5' X:A101 4.55 Mn C4' X:A101 4.80 Mn O5' X:A101 4.91 Mn OP1 X:C102 4.58 Mn C3' X:C102 4.83 Mn P X:C102 3.60 Mn O3' X:C102 4.34 Mn OP2 X:C102 2.21 Mn C5' X:C102 4.57 Mn O5' X:C102 4.13 Mn OP1 X:A103 4.01 Mn P X:A103 3.50 Mn OP2 X:A103 2.18 Mn O5' X:A103 4.55 Mn N3 X:U104 4.38 Mn C5 X:U104 3.71 Mn C4 X:U104 3.20 Mn O4 X:U104 2.19 Mn O X:Hoh187 2.37 Mn O X:Hoh222 4.34 Mn O X:Hoh297 4.17 Mn O X:Hoh497 2.28 interactive model: Manganese binding site 2 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3pdr. 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: X: G22, X: U23, X: C99, X: G100, X: G157, X: Hoh203, X: Hoh209, X: Hoh246, X: Hoh297, X: Hoh304, X: Hoh316, X: Hoh327, X: Hoh518, conact list: Atom Atom Distance (A) Mn OP1 X:G22 4.55 Mn O3' X:G22 3.83 Mn OP1 X:U23 2.05 Mn P X:U23 3.28 Mn OP2 X:U23 3.81 Mn O5' X:U23 4.58 Mn C3' X:C99 4.87 Mn O3' X:C99 3.50 Mn O2' X:C99 4.87 Mn OP1 X:G100 2.10 Mn P X:G100 3.33 Mn OP2 X:G100 4.53 Mn C5' X:G100 3.86 Mn O5' X:G100 4.09 Mn OP1 X:G157 4.33 Mn P X:G157 4.85 Mn OP2 X:G157 4.29 Mn O X:Hoh203 2.31 Mn O X:Hoh209 2.25 Mn O X:Hoh246 4.31 Mn O X:Hoh297 4.17 Mn O X:Hoh304 4.39 Mn O X:Hoh316 2.37 Mn O X:Hoh327 2.26 Mn O X:Hoh518 3.74 interactive model: Manganese binding site 3 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3pdr. 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: X: U23, X: U24, X: A25, X: G26, X: U159, X: C160, X: U161, X: Hoh211, X: Hoh247, X: Hoh266, X: Hoh272, X: Hoh279, X: Hoh328, X: Hoh332, X: Hoh342, X: Hoh498, conact list: Atom Atom Distance (A) Mn C3' X:U23 4.50 Mn O3' X:U23 4.39 Mn C2' X:U23 4.29 Mn OP1 X:U24 4.27 Mn C3' X:U24 4.31 Mn P X:U24 3.54 Mn O3' X:U24 3.76 Mn OP2 X:U24 2.08 Mn C5' X:U24 4.33 Mn C4' X:U24 4.84 Mn O5' X:U24 4.44 Mn OP1 X:A25 2.07 Mn C8 X:A25 4.60 Mn P X:A25 3.40 Mn N7 X:A25 4.41 Mn OP2 X:A25 4.51 Mn O5' X:A25 4.23 Mn C6 X:G26 4.92 Mn C5 X:G26 4.86 Mn N7 X:G26 4.14 Mn O6 X:G26 4.27 Mn O4 X:U159 4.96 Mn N3 X:C160 4.32 Mn O2 X:C160 4.95 Mn N4 X:C160 4.91 Mn N3 X:U161 4.87 Mn C4 X:U161 4.96 Mn O4 X:U161 4.58 Mn O X:Hoh211 3.94 Mn O X:Hoh247 2.30 Mn O X:Hoh266 4.31 Mn O X:Hoh272 2.23 Mn O X:Hoh279 2.38 Mn O X:Hoh328 4.89 Mn O X:Hoh332 4.15 Mn O X:Hoh342 4.48 Mn O X:Hoh498 2.15 interactive model: Manganese binding site 4 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3pdr. 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: X: C69, X: A71, X: A72, X: G73, X: Hoh288, X: Hoh298, X: Hoh299, X: Hoh471, conact list: Atom Atom Distance (A) Mn N3 X:C69 4.13 Mn C2 X:C69 4.66 Mn O2 X:C69 4.34 Mn C3' X:A71 4.46 Mn P X:A71 4.99 Mn O3' X:A71 4.31 Mn OP2 X:A71 4.79 Mn O5' X:A71 4.50 Mn OP1 X:A72 4.37 Mn C8 X:A72 4.74 Mn P X:A72 3.50 Mn N7 X:A72 4.58 Mn OP2 X:A72 2.02 Mn O5' X:A72 4.35 Mn C8 X:G73 4.86 Mn C6 X:G73 4.56 Mn C5 X:G73 4.46 Mn N7 X:G73 4.14 Mn O6 X:G73 4.33 Mn O X:Hoh288 2.57 Mn O X:Hoh298 4.79 Mn O X:Hoh299 2.27 Mn O X:Hoh471 2.35 interactive model: Manganese binding site 5 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3pdr. 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: X: A117, X: A118, X: U119, X: Hoh499, X: Hoh547, conact list: Atom Atom Distance (A) Mn OP1 X:A117 2.96 Mn P X:A117 3.61 Mn O3' X:A117 4.80 Mn OP2 X:A117 3.51 Mn O5' X:A117 4.30 Mn OP1 X:A118 2.32 Mn C3' X:A118 4.80 Mn P X:A118 3.73 Mn O3' X:A118 4.49 Mn OP2 X:A118 4.44 Mn C5' X:A118 4.57 Mn O5' X:A118 4.43 Mn OP1 X:U119 4.16 Mn O2 X:U119 4.59 Mn P X:U119 3.48 Mn O4' X:U119 4.32 Mn OP2 X:U119 2.11 Mn C5' X:U119 3.94 Mn C4' X:U119 4.71 Mn O5' X:U119 4.23 Mn O X:Hoh499 3.54 Mn O X:Hoh547 2.45 interactive model: Manganese binding site 6 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3pdr. 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: X: U34, X: C35, X: C36, X: C143, X: Hoh504, X: Hoh522, X: Hoh523, X: Hoh524, conact list: Atom Atom Distance (A) Mn O3' X:U34 4.54 Mn OP1 X:C35 3.86 Mn C3' X:C35 4.56 Mn P X:C35 3.41 Mn O3' X:C35 4.22 Mn OP2 X:C35 2.22 Mn C5' X:C35 4.34 Mn O5' X:C35 4.24 Mn OP1 X:C36 4.35 Mn C5 X:C36 4.86 Mn P X:C36 3.54 Mn OP2 X:C36 2.10 Mn O5' X:C36 4.50 Mn OP2 X:C143 4.42 Mn O X:Hoh504 2.20 Mn O X:Hoh522 2.44 Mn O X:Hoh523 2.31 Mn O X:Hoh524 2.35 interactive model: Manganese binding site 7 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Manganese in the PDB 3pdr. 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: X: G100, X: A105, X: A106, X: G107, X: Hoh280, X: Hoh500, X: Hoh501, X: Hoh502, X: Hoh503, conact list: Atom Atom Distance (A) Mn N2 X:G100 4.38 Mn O3' X:A105 4.74 Mn OP2 X:A105 4.56 Mn OP1 X:A106 4.13 Mn P X:A106 3.51 Mn OP2 X:A106 2.23 Mn O5' X:A106 4.19 Mn N9 X:G107 4.38 Mn C8 X:G107 3.10 Mn C6 X:G107 4.13 Mn C5 X:G107 3.51 Mn N7 X:G107 2.33 Mn C4 X:G107 4.59 Mn OP2 X:G107 4.60 Mn O6 X:G107 3.94 Mn O X:Hoh280 4.63 Mn O X:Hoh500 2.29 Mn O X:Hoh501 2.15 Mn O X:Hoh502 2.18 Mn O X:Hoh503 2.36 interactive model: Manganese binding site 8 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Manganese in the PDB 3pdr. 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: X: A44, X: G45, X: U138, X: Hoh423, X: Hoh525, X: Hoh526, X: Hoh551, X: Hoh552, conact list: Atom Atom Distance (A) Mn P X:A44 4.92 Mn N7 X:A44 4.87 Mn OP2 X:A44 3.72 Mn N9 X:G45 4.64 Mn C8 X:G45 3.42 Mn C6 X:G45 3.95 Mn C5 X:G45 3.52 Mn N7 X:G45 2.48 Mn C4 X:G45 4.71 Mn OP2 X:G45 4.80 Mn O6 X:G45 3.63 Mn C5 X:U138 4.15 Mn C4 X:U138 4.60 Mn O4 X:U138 4.33 Mn O X:Hoh423 4.79 Mn O X:Hoh525 2.46 Mn O X:Hoh526 2.43 Mn O X:Hoh551 2.52 Mn O X:Hoh552 3.44 interactive model: Manganese binding site 9 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Manganese in the PDB 3pdr. 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: X: G126, X: G127, X: A128, X: U129, X: Hoh505, X: Hoh506, conact list: Atom Atom Distance (A) Mn O3' X:G126 4.69 Mn OP1 X:G127 2.32 Mn P X:G127 3.54 Mn O3' X:G127 4.67 Mn OP2 X:G127 4.39 Mn C5' X:G127 4.08 Mn O5' X:G127 3.91 Mn OP1 X:A128 4.51 Mn C3' X:A128 3.89 Mn P X:A128 3.70 Mn O3' X:A128 4.21 Mn OP2 X:A128 2.25 Mn C5' X:A128 4.40 Mn C4' X:A128 4.59 Mn O5' X:A128 4.42 Mn OP1 X:U129 2.23 Mn P X:U129 3.65 Mn OP2 X:U129 4.54 Mn O5' X:U129 4.65 Mn O X:Hoh505 3.03 Mn O X:Hoh506 2.10 interactive model: Manganese binding site 10 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Manganese in the PDB 3pdr. 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: X: G29, X: A30, X: G31, X: Hoh242, X: Hoh250, X: Hoh313, X: Hoh507, X: Hoh508, X: Hoh509, X: Hoh510, A: Hoh316, conact list: Atom Atom Distance (A) Mn C3' X:G29 4.68 Mn O3' X:G29 4.01 Mn O2' X:G29 4.30 Mn OP1 X:A30 4.71 Mn C3' X:A30 4.58 Mn P X:A30 3.43 Mn O3' X:A30 4.44 Mn OP2 X:A30 2.22 Mn C5' X:A30 4.47 Mn O5' X:A30 3.75 Mn OP1 X:G31 4.31 Mn C8 X:G31 4.51 Mn P X:G31 3.57 Mn N7 X:G31 4.34 Mn OP2 X:G31 2.13 Mn O5' X:G31 4.37 Mn O X:Hoh242 4.61 Mn O X:Hoh250 4.52 Mn O X:Hoh313 4.43 Mn O X:Hoh507 2.23 Mn O X:Hoh508 2.37 Mn O X:Hoh509 2.32 Mn O X:Hoh510 2.25 Mn O A:Hoh316 4.38 interactive model: Manganese binding site 11 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Manganese in the PDB 3pdr. 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: X: G15, X: G16, X: Hoh325, X: Hoh527, conact list: Atom Atom Distance (A) Mn N9 X:G15 4.48 Mn OP1 X:G15 3.90 Mn C8 X:G15 3.24 Mn C6 X:G15 3.94 Mn C5 X:G15 3.42 Mn N7 X:G15 2.34 Mn C4 X:G15 4.58 Mn O6 X:G15 3.70 Mn O6 X:G16 4.90 Mn O X:Hoh325 3.76 Mn O X:Hoh527 2.54 interactive model: Manganese binding site 12 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Manganese in the PDB 3pdr. 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: X: A46, X: U47, X: G126, X: G127, X: A128, X: Hoh542, X: Hoh543, X: Hoh544, X: Hoh545, conact list: Atom Atom Distance (A) Mn N9 X:A46 4.64 Mn C3' X:A46 4.13 Mn C8 X:A46 4.53 Mn C1' X:A46 4.38 Mn O3' X:A46 4.67 Mn OP2 X:A46 4.93 Mn C2' X:A46 3.14 Mn O2' X:A46 2.26 Mn OP1 X:U47 4.03 Mn N9 X:G126 4.46 Mn C8 X:G126 3.22 Mn C6 X:G126 4.04 Mn C5 X:G126 3.48 Mn N7 X:G126 2.39 Mn C4 X:G126 4.58 Mn OP2 X:G126 4.09 Mn O5' X:G126 4.92 Mn O6 X:G126 3.87 Mn C8 X:G127 4.92 Mn N7 X:G127 4.25 Mn O2' X:A128 4.81 Mn O X:Hoh542 2.20 Mn O X:Hoh543 2.32 Mn O X:Hoh544 2.44 Mn O X:Hoh545 2.29 interactive model: Manganese binding site 13 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Manganese in the PDB 3pdr. 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: C99, A: G100, A: A101, A: C102, A: A103, A: U104, A: Hoh195, A: Hoh198, A: Hoh240, A: Hoh365, conact list: Atom Atom Distance (A) Mn C3' A:C99 4.61 Mn O3' A:C99 4.52 Mn OP2 A:C99 4.68 Mn O5' A:C99 4.74 Mn OP1 A:G100 4.52 Mn C8 A:G100 4.38 Mn P A:G100 3.58 Mn N7 A:G100 4.30 Mn OP2 A:G100 2.18 Mn O5' A:G100 4.08 Mn C3' A:A101 4.42 Mn O3' A:A101 4.55 Mn C5' A:A101 4.50 Mn C4' A:A101 4.83 Mn O5' A:A101 4.88 Mn OP1 A:C102 4.45 Mn C3' A:C102 4.81 Mn P A:C102 3.57 Mn O3' A:C102 4.39 Mn OP2 A:C102 2.19 Mn C5' A:C102 4.43 Mn O5' A:C102 4.11 Mn OP1 A:A103 4.22 Mn P A:A103 3.56 Mn OP2 A:A103 2.19 Mn O5' A:A103 4.59 Mn N3 A:U104 4.38 Mn C6 A:U104 4.97 Mn C5 A:U104 3.65 Mn C4 A:U104 3.17 Mn O4 A:U104 2.19 Mn O A:Hoh195 2.40 Mn O A:Hoh198 2.38 Mn O A:Hoh240 4.33 Mn O A:Hoh365 4.06 interactive model: Manganese binding site 14 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Manganese in the PDB 3pdr. 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: G22, A: U23, A: C99, A: G100, A: G157, A: Hoh217, A: Hoh220, A: Hoh224, A: Hoh230, A: Hoh250, A: Hoh287, A: Hoh321, A: Hoh365, A: Hoh472, A: Hoh517, A: Hoh546, conact list: Atom Atom Distance (A) Mn OP1 A:G22 4.45 Mn O3' A:G22 3.90 Mn OP1 A:U23 2.15 Mn P A:U23 3.33 Mn OP2 A:U23 3.85 Mn O5' A:U23 4.63 Mn C3' A:C99 4.82 Mn O3' A:C99 3.45 Mn O2' A:C99 4.87 Mn OP1 A:G100 2.08 Mn P A:G100 3.28 Mn OP2 A:G100 4.49 Mn C5' A:G100 3.83 Mn O5' A:G100 4.04 Mn OP1 A:G157 4.37 Mn P A:G157 4.90 Mn OP2 A:G157 4.34 Mn O A:Hoh217 2.55 Mn O A:Hoh220 2.23 Mn O A:Hoh224 4.47 Mn O A:Hoh230 2.26 Mn O A:Hoh250 4.42 Mn O A:Hoh287 4.12 Mn O A:Hoh321 4.40 Mn O A:Hoh365 4.73 Mn O A:Hoh472 2.27 Mn O A:Hoh517 4.23 Mn O A:Hoh546 2.38 interactive model: Manganese binding site 15 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Manganese in the PDB 3pdr. 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: U23, A: U24, A: A25, A: G26, A: U159, A: C160, A: U161, A: Hoh205, A: Hoh222, A: Hoh225, A: Hoh244, A: Hoh249, A: Hoh255, A: Hoh258, A: Hoh260, A: Hoh274, conact list: Atom Atom Distance (A) Mn C3' A:U23 4.51 Mn O3' A:U23 4.45 Mn C2' A:U23 4.22 Mn O2' A:U23 4.94 Mn OP1 A:U24 4.24 Mn C3' A:U24 4.29 Mn P A:U24 3.54 Mn O3' A:U24 3.68 Mn OP2 A:U24 2.12 Mn C5' A:U24 4.36 Mn C4' A:U24 4.87 Mn O5' A:U24 4.42 Mn OP1 A:A25 2.11 Mn C8 A:A25 4.72 Mn P A:A25 3.36 Mn N7 A:A25 4.61 Mn OP2 A:A25 4.48 Mn O5' A:A25 4.25 Mn C6 A:G26 4.75 Mn C5 A:G26 4.73 Mn N7 A:G26 4.04 Mn O6 A:G26 4.13 Mn O4 A:U159 4.94 Mn N3 A:C160 4.38 Mn C4 A:C160 4.89 Mn N4 A:C160 4.33 Mn O4 A:U161 4.61 Mn O A:Hoh205 4.02 Mn O A:Hoh222 2.37 Mn O A:Hoh225 4.50 Mn O A:Hoh244 2.18 Mn O A:Hoh249 3.84 Mn O A:Hoh255 2.31 Mn O A:Hoh258 2.32 Mn O A:Hoh260 4.46 Mn O A:Hoh274 4.82 interactive model: Manganese binding site 16 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Manganese in the PDB 3pdr. 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: C69, A: A71, A: A72, A: G73, A: Hoh320, A: Hoh332, A: Hoh490, A: Hoh491, conact list: Atom Atom Distance (A) Mn N3 A:C69 4.25 Mn C2 A:C69 4.81 Mn O2 A:C69 4.53 Mn C3' A:A71 4.74 Mn O3' A:A71 4.43 Mn O5' A:A71 4.94 Mn OP1 A:A72 4.27 Mn C8 A:A72 4.86 Mn P A:A72 3.48 Mn N7 A:A72 4.68 Mn OP2 A:A72 2.03 Mn O5' A:A72 4.28 Mn C8 A:G73 4.58 Mn C6 A:G73 4.56 Mn C5 A:G73 4.35 Mn N7 A:G73 3.95 Mn O6 A:G73 4.41 Mn O A:Hoh320 2.24 Mn O A:Hoh332 2.21 Mn O A:Hoh490 2.52 Mn O A:Hoh491 2.65 interactive model: Manganese binding site 17 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Manganese in the PDB 3pdr. 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: A62, A: A63, A: A64, A: U65, A: G76, A: C77, A: C78, A: Hoh263, A: Hoh388, A: Hoh473, A: Hoh474, A: Hoh475, A: Hoh492, conact list: Atom Atom Distance (A) Mn C3' A:A62 4.47 Mn O3' A:A62 4.42 Mn C5' A:A62 4.87 Mn OP1 A:A63 4.38 Mn C8 A:A63 4.26 Mn P A:A63 3.41 Mn N7 A:A63 4.10 Mn OP2 A:A63 2.03 Mn O5' A:A63 3.88 Mn C8 A:A64 4.99 Mn N6 A:A64 4.63 Mn N7 A:A64 4.07 Mn OP2 A:A64 4.68 Mn N3 A:U65 4.96 Mn C4 A:U65 4.78 Mn O4 A:U65 4.15 Mn O6 A:G76 4.59 Mn N3 A:C77 4.35 Mn C2 A:C77 4.90 Mn O2 A:C77 4.49 Mn C2 A:C78 4.70 Mn O2 A:C78 4.17 Mn O A:Hoh263 2.32 Mn O A:Hoh388 4.31 Mn O A:Hoh473 2.26 Mn O A:Hoh474 2.18 Mn O A:Hoh475 2.45 Mn O A:Hoh492 2.18 interactive model: Manganese binding site 18 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Manganese in the PDB 3pdr. 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: A60, A: A61, A: A79, A: A80, A: U81, A: G82, A: Hoh247, A: Hoh367, A: Hoh476, A: Hoh477, A: Hoh487, conact list: Atom Atom Distance (A) Mn N6 A:A60 4.21 Mn C2 A:A61 4.81 Mn N1 A:A61 4.50 Mn C3' A:A79 4.72 Mn O3' A:A79 4.41 Mn O5' A:A79 4.70 Mn OP1 A:A80 3.98 Mn P A:A80 3.44 Mn OP2 A:A80 2.10 Mn O5' A:A80 4.40 Mn N3 A:U81 4.43 Mn C6 A:U81 4.97 Mn C5 A:U81 3.63 Mn C4 A:U81 3.19 Mn O4 A:U81 2.22 Mn O6 A:G82 4.74 Mn O A:Hoh247 2.32 Mn O A:Hoh367 4.30 Mn O A:Hoh476 2.47 Mn O A:Hoh477 2.41 Mn O A:Hoh487 2.29 interactive model: Manganese binding site 19 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 19 of Manganese in the PDB 3pdr. 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: U116, A: A117, A: A118, A: U119, A: Hoh478, A: Hoh493, A: Hoh494, A: Hoh548, A: Hoh550, conact list: Atom Atom Distance (A) Mn O3' A:U116 4.67 Mn OP1 A:A117 2.29 Mn C3' A:A117 4.92 Mn P A:A117 3.53 Mn O3' A:A117 4.37 Mn OP2 A:A117 4.18 Mn C5' A:A117 4.19 Mn O5' A:A117 4.10 Mn OP1 A:A118 2.36 Mn C3' A:A118 4.71 Mn P A:A118 3.72 Mn O3' A:A118 4.20 Mn OP2 A:A118 4.87 Mn C5' A:A118 4.05 Mn C4' A:A118 4.88 Mn O5' A:A118 4.17 Mn OP1 A:U119 4.70 Mn O2 A:U119 4.88 Mn P A:U119 3.72 Mn OP2 A:U119 2.27 Mn C5' A:U119 4.81 Mn O5' A:U119 4.60 Mn O A:Hoh478 2.68 Mn O A:Hoh493 4.67 Mn O A:Hoh494 4.83 Mn O A:Hoh548 3.07 Mn O A:Hoh550 2.51 interactive model: Manganese binding site 20 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 20 of Manganese in the PDB 3pdr. 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: U34, A: C35, A: C36, A: C143, A: Hoh310, A: Hoh481, A: Hoh482, A: Hoh549, conact list: Atom Atom Distance (A) Mn O3' A:U34 4.57 Mn OP1 A:C35 4.00 Mn C3' A:C35 4.50 Mn P A:C35 3.41 Mn O3' A:C35 4.16 Mn OP2 A:C35 2.19 Mn C5' A:C35 4.76 Mn C4' A:C35 4.98 Mn O5' A:C35 4.06 Mn OP1 A:C36 4.26 Mn C5 A:C36 4.98 Mn P A:C36 3.44 Mn OP2 A:C36 2.00 Mn O5' A:C36 4.35 Mn OP1 A:C143 4.92 Mn OP2 A:C143 4.31 Mn O A:Hoh310 2.38 Mn O A:Hoh481 2.33 Mn O A:Hoh482 2.52 Mn O A:Hoh549 2.28 interactive model: Manganese binding site 21 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 21 of Manganese in the PDB 3pdr. 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: G100, A: A105, A: A106, A: G107, A: Hoh313, A: Hoh483, A: Hoh484, A: Hoh485, A: Hoh486, A: Hoh511, conact list: Atom Atom Distance (A) Mn N2 A:G100 4.41 Mn O3' A:A105 4.70 Mn OP2 A:A105 4.64 Mn OP1 A:A106 3.91 Mn P A:A106 3.45 Mn OP2 A:A106 2.26 Mn O5' A:A106 4.18 Mn N9 A:G107 4.42 Mn C8 A:G107 3.12 Mn C6 A:G107 4.18 Mn C5 A:G107 3.55 Mn N7 A:G107 2.36 Mn C4 A:G107 4.63 Mn OP2 A:G107 4.68 Mn O6 A:G107 4.03 Mn O A:Hoh313 4.72 Mn O A:Hoh483 2.14 Mn O A:Hoh484 2.34 Mn O A:Hoh485 2.29 Mn O A:Hoh486 2.19 Mn O A:Hoh511 4.39 interactive model: Manganese binding site 22 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 22 of Manganese in the PDB 3pdr. 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: C59, A: A60, A: A61, A: C77, A: C78, A: Hoh187, A: Hoh231, A: Hoh264, A: Hoh306, A: Hoh488, A: Hoh489, conact list: Atom Atom Distance (A) Mn C3' A:C59 4.60 Mn O3' A:C59 4.60 Mn O5' A:C59 5.00 Mn OP1 A:A60 4.51 Mn C8 A:A60 4.26 Mn P A:A60 3.54 Mn N7 A:A60 4.17 Mn OP2 A:A60 2.25 Mn O5' A:A60 3.89 Mn N6 A:A61 4.74 Mn N7 A:A61 4.42 Mn OP2 A:A61 4.75 Mn OP2 A:C77 4.42 Mn C5 A:C78 4.62 Mn OP2 A:C78 4.37 Mn O A:Hoh187 2.21 Mn O A:Hoh231 2.29 Mn O A:Hoh264 4.20 Mn O A:Hoh306 2.23 Mn O A:Hoh488 2.34 Mn O A:Hoh489 2.30 interactive model: Manganese binding site 23 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 23 of Manganese in the PDB 3pdr. 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: A44, A: G45, A: C137, A: U138, A: Hoh324, A: Hoh495, A: Hoh519, A: Hoh520, conact list: Atom Atom Distance (A) Mn C3' A:A44 4.64 Mn O3' A:A44 4.57 Mn O5' A:A44 4.83 Mn OP1 A:G45 4.53 Mn C8 A:G45 4.43 Mn P A:G45 3.60 Mn N7 A:G45 4.36 Mn OP2 A:G45 2.19 Mn O5' A:G45 4.12 Mn OP2 A:C137 4.57 Mn C5 A:U138 4.67 Mn C4 A:U138 4.88 Mn O4 A:U138 4.37 Mn O A:Hoh324 2.34 Mn O A:Hoh495 2.15 Mn O A:Hoh519 2.56 Mn O A:Hoh520 2.81 interactive model: Manganese binding site 24 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 24 of Manganese in the PDB 3pdr. 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: G126, A: G127, A: A128, A: U129, A: Hoh305, A: Hoh463, A: Hoh496, A: Hoh515, conact list: Atom Atom Distance (A) Mn O3' A:G126 4.54 Mn OP1 A:G127 2.17 Mn C3' A:G127 4.93 Mn P A:G127 3.41 Mn O3' A:G127 4.53 Mn OP2 A:G127 4.20 Mn C5' A:G127 4.03 Mn O5' A:G127 3.89 Mn OP1 A:A128 4.29 Mn C3' A:A128 3.88 Mn P A:A128 3.56 Mn O3' A:A128 4.14 Mn OP2 A:A128 2.12 Mn C5' A:A128 4.45 Mn C4' A:A128 4.62 Mn O5' A:A128 4.37 Mn OP1 A:U129 2.09 Mn P A:U129 3.48 Mn OP2 A:U129 4.24 Mn O5' A:U129 4.54 Mn O A:Hoh305 4.01 Mn O A:Hoh463 4.25 Mn O A:Hoh496 2.31 Mn O A:Hoh515 2.37 interactive model: Manganese binding site 25 out of 25 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 25 of Manganese in the PDB 3pdr. 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: G15, A: G16, A: Hoh186, A: Hoh379, conact list: Atom Atom Distance (A) Mn N9 A:G15 4.43 Mn OP1 A:G15 3.38 Mn C8 A:G15 3.20 Mn C6 A:G15 4.03 Mn C5 A:G15 3.49 Mn P A:G15 4.51 Mn N7 A:G15 2.40 Mn C4 A:G15 4.59 Mn O5' A:G15 4.65 Mn OP3 A:G15 4.92 Mn O6 A:G15 3.77 Mn N7 A:G16 4.95 Mn O A:Hoh186 3.96 Mn O A:Hoh379 4.64 interactive model: