Sodium in the structure of Structure Of the Complex of Lac Repressor Headpiece And An 11 Base-Pair Half-Operator Determined By Nuclear Magnetic Resonance Spectroscopy and Restrained Molecular Dynamics (pdb 1lcd)

The binding sites of Sodium atom in the structure of Structure Of the Complex of Lac Repressor Headpiece And An 11 Base-Pair Half-Operator Determined By Nuclear Magnetic Resonance Spectroscopy and Restrained Molecular Dynamics (pdb code 1lcd). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1lcd structure was solved by V.P.CHUPRINA, J.A.C.RULLMANN, R.M.J.N.LAMERICHS, J.H.VAN BOOM, R.BOELENS, R.KAPTEIN, with NMR in Solution technique. Sodium Binding Sites: Sodium binding site 1 out of 1 in 1lcd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1lcd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Dc3, C: Dt4, A: Val24, A: Asn25, A: Tyr47, A: Pro49, A: Asn50, C: Hoh923, A: Hoh53, A: Hoh57, A: Hoh58, C: Dc3, C: Dt4, A: Val24, A: Asn25, A: Pro49, A: Asn50, C: Hoh923, C: 1419, A: Hoh55, C: Dc3, C: Dt4, A: Leu6, A: Val24, A: Asn25, A: Tyr47, A: Asn50, C: 703, C: 895, A: Hoh62, conact list: Atom Atom Distance (A) Na C3' C:Dc3 4.21 Na O3' C:Dc3 3.37 Na C5' C:Dc3 4.62 Na C4' C:Dc3 4.73 Na OP1 C:Dt4 2.52 Na P C:Dt4 3.37 Na OP2 C:Dt4 3.86 Na O5' C:Dt4 4.83 Na CB A:Val24 4.49 Na CG2 A:Val24 4.96 Na CG1 A:Val24 3.24 Na HD21 A:Asn25 3.63 Na HD22 A:Asn25 4.72 Na ND2 A:Asn25 4.48 Na OH A:Tyr47 3.98 Na HH A:Tyr47 4.51 Na CB A:Pro49 4.82 Na H A:Asn50 4.84 Na O C:Hoh923 2.13 Na H1 C:Hoh923 2.96 Na H2 C:Hoh923 2.63 Na O A:Hoh53 2.10 Na H1 A:Hoh53 2.56 Na H2 A:Hoh53 2.88 Na O A:Hoh57 2.22 Na H1 A:Hoh57 2.85 Na H2 A:Hoh57 2.90 Na O A:Hoh58 4.76 Na H2 A:Hoh58 4.57 Na C3' C:Dc3 4.21 Na O3' C:Dc3 3.37 Na C5' C:Dc3 4.62 Na C4' C:Dc3 4.73 Na OP1 C:Dt4 2.52 Na P C:Dt4 3.37 Na OP2 C:Dt4 3.86 Na O5' C:Dt4 4.83 Na CB A:Val24 4.49 Na CG2 A:Val24 4.96 Na CG1 A:Val24 3.24 Na HD21 A:Asn25 3.63 Na HD22 A:Asn25 4.72 Na ND2 A:Asn25 4.48 Na CB A:Pro49 4.82 Na H A:Asn50 4.84 Na O C:Hoh923 2.13 Na H1 C:Hoh923 2.96 Na H2 C:Hoh923 2.63 Na C3' C:Dc3 4.21 Na O3' C:Dc3 3.37 Na C5' C:Dc3 4.62 Na C4' C:Dc3 4.73 Na OP1 C:Dt4 2.52 Na P C:Dt4 3.37 Na OP2 C:Dt4 3.86 Na O5' C:Dt4 4.83 Na CB A:Val24 4.49 Na CG2 A:Val24 4.96 Na CG1 A:Val24 3.24 Na HD21 A:Asn25 3.63 Na HD22 A:Asn25 4.72 Na ND2 A:Asn25 4.48 Na OH A:Tyr47 3.98 Na HH A:Tyr47 4.51 Na H A:Asn50 4.84 interactive model: