Magnesium in the structure of Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse (pdb 1nzb)

The binding sites of Magnesium atom in the structure of Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse (pdb code 1nzb). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1nzb structure was solved by E.ENNIFAR, J.E.W.MEYER, F.BUCHHOLZ, A.F.STEWART, D.SUCK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-3.1 Space group P212121 a (A) 108.890 b (A) 163.530 c (A) 195.790 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.2 Rfree (%) 25.7 Magnesium Binding Sites: Magnesium binding site 1 out of 10 in 1nzb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1nzb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Dt116, C: Dg117, D: Dc120, D: Da121, conact list: Atom Atom Distance (A) Mg N3 C:Dt116 4.90 Mg C2 C:Dt116 4.69 Mg O2 C:Dt116 4.26 Mg N9 C:Dg117 4.81 Mg N3 C:Dg117 3.49 Mg N2 C:Dg117 3.58 Mg C2 C:Dg117 3.50 Mg C6 C:Dg117 4.82 Mg N1 C:Dg117 4.16 Mg C5 C:Dg117 4.74 Mg O4' C:Dg117 4.56 Mg C4 C:Dg117 4.11 Mg N3 D:Dc120 4.76 Mg C2 D:Dc120 4.91 Mg O2 D:Dc120 4.37 Mg N3 D:Da121 4.81 Mg C2 D:Da121 4.41 Mg N1 D:Da121 4.90 interactive model: Magnesium binding site 2 out of 10 in 1nzb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1nzb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Dc106, A: Gln156, A: Arg159, A: Asn160, A: Gly263, A: Ile264, A: Ala267, conact list: Atom Atom Distance (A) Mg P D:Dc106 4.85 Mg OP2 D:Dc106 3.47 Mg NE2 A:Gln156 3.24 Mg OE1 A:Gln156 4.69 Mg CD A:Gln156 3.93 Mg CG A:Gln156 4.37 Mg CZ A:Arg159 4.84 Mg NH2 A:Arg159 3.51 Mg ND2 A:Asn160 3.63 Mg OD1 A:Asn160 4.44 Mg CG A:Asn160 4.48 Mg O A:Gly263 4.66 Mg CG1 A:Ile264 4.23 Mg CA A:Ile264 4.78 Mg CB A:Ala267 4.97 interactive model: Magnesium binding site 3 out of 10 in 1nzb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1nzb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Dc106, D: Dt107, A: Arg259, A: Ala260, A: Gly263, conact list: Atom Atom Distance (A) Mg C6 D:Dc106 4.23 Mg C5 D:Dc106 4.23 Mg C5' D:Dc106 4.57 Mg O5' D:Dc106 4.81 Mg C5 D:Dt107 4.90 Mg C7 D:Dt107 3.47 Mg O A:Arg259 4.35 Mg C A:Arg259 4.73 Mg O A:Ala260 4.86 Mg N A:Ala260 4.55 Mg C A:Ala260 4.90 Mg CB A:Ala260 4.15 Mg CA A:Ala260 3.87 Mg CA A:Gly263 4.60 interactive model: Magnesium binding site 4 out of 10 in 1nzb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1nzb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Da104, D: Da105, D: Dc106, conact list: Atom Atom Distance (A) Mg C8 D:Da104 4.21 Mg C5 D:Da104 4.75 Mg N7 D:Da104 3.91 Mg C8 D:Da105 3.89 Mg C6 D:Da105 3.89 Mg C5 D:Da105 3.66 Mg N6 D:Da105 3.27 Mg N7 D:Da105 2.81 Mg C4 D:Da105 4.94 Mg C4 D:Dc106 4.75 Mg N4 D:Dc106 4.01 interactive model: Magnesium binding site 5 out of 10 in 1nzb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 1nzb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: G: Dt116, G: Dg117, H: Dc120, H: Da121, conact list: Atom Atom Distance (A) Mg N3 G:Dt116 4.79 Mg C2 G:Dt116 4.37 Mg N1 G:Dt116 4.91 Mg O2 G:Dt116 4.05 Mg N9 G:Dg117 4.23 Mg N3 G:Dg117 3.47 Mg N2 G:Dg117 4.02 Mg C8 G:Dg117 4.75 Mg C2 G:Dg117 3.43 Mg C6 G:Dg117 3.76 Mg N1 G:Dg117 3.55 Mg C5 G:Dg117 3.73 Mg C1' G:Dg117 4.85 Mg N7 G:Dg117 4.53 Mg O4' G:Dg117 4.86 Mg C4 G:Dg117 3.55 Mg O6 G:Dg117 4.47 Mg O2 H:Dc120 4.89 Mg N3 H:Da121 4.94 Mg C2 H:Da121 4.37 Mg N1 H:Da121 4.87 interactive model: Magnesium binding site 6 out of 10 in 1nzb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 1nzb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Dt125, C: Da126, D: Dt111, A: His40, A: Lys43, conact list: Atom Atom Distance (A) Mg C5 C:Dt125 4.69 Mg C7 C:Dt125 3.81 Mg C4 C:Dt125 4.51 Mg O4 C:Dt125 3.64 Mg N6 C:Da126 4.83 Mg O4 D:Dt111 4.37 Mg O A:His40 4.37 Mg NE2 A:His40 4.55 Mg CB A:His40 3.95 Mg ND1 A:His40 2.70 Mg CD2 A:His40 4.66 Mg C A:His40 4.73 Mg CE1 A:His40 3.47 Mg CG A:His40 3.64 Mg CA A:His40 4.09 Mg CB A:Lys43 4.21 Mg CD A:Lys43 4.00 Mg CG A:Lys43 4.58 interactive model: Magnesium binding site 7 out of 10 in 1nzb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 1nzb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Leu135, A: His269, A: Tyr273, conact list: Atom Atom Distance (A) Mg CD1 A:Leu135 4.88 Mg CD2 A:Leu135 4.02 Mg CG A:Leu135 4.86 Mg NE2 A:His269 3.26 Mg CD2 A:His269 4.14 Mg CE1 A:His269 4.21 Mg CE2 A:Tyr273 4.53 Mg CD1 A:Tyr273 4.14 Mg CD2 A:Tyr273 4.55 Mg CZ A:Tyr273 4.33 Mg CE1 A:Tyr273 4.12 Mg CG A:Tyr273 4.37 interactive model: Magnesium binding site 8 out of 10 in 1nzb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 1nzb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu138, A: Thr140, A: Asp141, conact list: Atom Atom Distance (A) Mg OE2 A:Glu138 4.31 Mg CD A:Glu138 4.91 Mg OG1 A:Thr140 4.69 Mg OD2 A:Asp141 3.83 Mg OD1 A:Asp141 4.93 Mg CG A:Asp141 4.71 interactive model: Magnesium binding site 9 out of 10 in 1nzb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Magnesium in the PDB 1nzb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: H: Da119, H: Dc120, H: Da121, F: Gln89, F: Leu92, F: Gly93, F: Asn96, conact list: Atom Atom Distance (A) Mg C2' H:Da119 4.92 Mg C6 H:Dc120 4.53 Mg C5 H:Dc120 4.76 Mg OP2 H:Dc120 4.05 Mg N7 H:Da121 4.83 Mg O F:Gln89 4.00 Mg CD2 F:Leu92 4.79 Mg CG F:Leu92 4.85 Mg N F:Gly93 4.67 Mg CA F:Gly93 4.36 Mg ND2 F:Asn96 4.34 interactive model: Magnesium binding site 10 out of 10 in 1nzb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Magnesium in the PDB 1nzb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: G: Dt111, G: Da112, G: Dt113, F: Met44, F: Thr87, F: His91, conact list: Atom Atom Distance (A) Mg C3' G:Dt111 4.68 Mg O3' G:Dt111 4.90 Mg C2' G:Dt111 3.99 Mg C8 G:Da112 4.12 Mg P G:Da112 4.03 Mg N7 G:Da112 4.72 Mg OP2 G:Da112 2.83 Mg C2' G:Da112 4.67 Mg O5' G:Da112 4.06 Mg C7 G:Dt113 3.85 Mg CE F:Met44 4.98 Mg CG2 F:Thr87 3.68 Mg NE2 F:His91 2.28 Mg ND1 F:His91 4.21 Mg CD2 F:His91 3.45 Mg CE1 F:His91 2.98 Mg CG F:His91 4.46 interactive model: