Nickel in the structure of NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2 (pdb 473d)

The binding sites of Nickel atom in the structure of NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2 (pdb code 473d). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 473d structure was solved by N.G.A.ABRESCIA, L.MALININA, J.A.SUBIRANA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.6 Space group P212121 a (A) 25.180 b (A) 39.110 c (A) 53.470 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Nickel Binding Sites: Nickel binding site 1 out of 4 in 473d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 473d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg10, A: Hoh1000, A: Hoh1001, A: Hoh1002, A: Hoh1003, A: Hoh1004, A: Hoh1022, A: Hoh1035, A: Hoh1061, conact list: Atom Atom Distance (A) Ni N9 A:Dg10 4.20 Ni C8 A:Dg10 2.95 Ni C6 A:Dg10 3.81 Ni C5 A:Dg10 3.22 Ni N7 A:Dg10 2.07 Ni C4 A:Dg10 4.33 Ni O6 A:Dg10 3.62 Ni O A:Hoh1000 2.14 Ni O A:Hoh1001 2.17 Ni O A:Hoh1002 2.13 Ni O A:Hoh1003 2.01 Ni O A:Hoh1004 1.98 Ni O A:Hoh1022 4.18 Ni O A:Hoh1035 4.59 Ni O A:Hoh1061 4.32 interactive model: Nickel binding site 2 out of 4 in 473d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 473d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg2, A: Dt3, A: Hoh1010, A: Hoh1011, A: Hoh1012, A: Hoh1013, A: Hoh1014, B: Hoh1062, conact list: Atom Atom Distance (A) Ni N9 A:Dg2 4.27 Ni OP1 A:Dg2 4.53 Ni C8 A:Dg2 3.05 Ni C6 A:Dg2 3.80 Ni C5 A:Dg2 3.23 Ni P A:Dg2 4.93 Ni N7 A:Dg2 2.14 Ni C4 A:Dg2 4.36 Ni OP2 A:Dg2 4.48 Ni O6 A:Dg2 3.69 Ni O4 A:Dt3 4.81 Ni O A:Hoh1010 2.33 Ni O A:Hoh1011 2.21 Ni O A:Hoh1012 2.17 Ni O A:Hoh1013 2.26 Ni O A:Hoh1014 1.93 Ni O B:Hoh1062 4.82 interactive model: Nickel binding site 3 out of 4 in 473d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Nickel in the PDB 473d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Dg12, B: Dt13, A: Hoh1065, B: Hoh1005, B: Hoh1006, B: Hoh1007, B: Hoh1008, B: Hoh1009, B: Hoh1040, B: Hoh1042, B: Hoh1044, B: Hoh1056, B: Hoh1073, conact list: Atom Atom Distance (A) Ni N9 B:Dg12 4.22 Ni OP1 B:Dg12 4.08 Ni C8 B:Dg12 2.98 Ni C6 B:Dg12 3.82 Ni C5 B:Dg12 3.23 Ni P B:Dg12 4.82 Ni N7 B:Dg12 2.10 Ni C4 B:Dg12 4.35 Ni OP2 B:Dg12 4.81 Ni O6 B:Dg12 3.66 Ni C7 B:Dt13 4.46 Ni C4 B:Dt13 4.91 Ni O4 B:Dt13 4.21 Ni O A:Hoh1065 4.27 Ni O B:Hoh1005 2.04 Ni O B:Hoh1006 2.01 Ni O B:Hoh1007 1.95 Ni O B:Hoh1008 2.01 Ni O B:Hoh1009 2.09 Ni O B:Hoh1040 4.01 Ni O B:Hoh1042 4.01 Ni O B:Hoh1044 4.20 Ni O B:Hoh1056 4.23 Ni O B:Hoh1073 4.12 interactive model: Nickel binding site 4 out of 4 in 473d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Nickel in the PDB 473d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Dg20, B: Hoh1015, B: Hoh1016, B: Hoh1017, B: Hoh1018, B: Hoh1045, B: Hoh1074, conact list: Atom Atom Distance (A) Ni N9 B:Dg20 4.22 Ni C8 B:Dg20 2.96 Ni C6 B:Dg20 3.82 Ni C5 B:Dg20 3.23 Ni N7 B:Dg20 2.08 Ni C4 B:Dg20 4.35 Ni OP2 B:Dg20 4.00 Ni O6 B:Dg20 3.62 Ni O B:Hoh1015 1.98 Ni O B:Hoh1016 2.05 Ni O B:Hoh1017 2.09 Ni O B:Hoh1018 1.97 Ni O B:Hoh1045 4.28 Ni O B:Hoh1074 4.18 interactive model: