Sodium in the structure of Crystal Structure of the Fas/Fadd Death Domain Complex (pdb 3ezq)

The binding sites of Sodium atom in the structure of Crystal Structure of the Fas/Fadd Death Domain Complex (pdb code 3ezq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3ezq structure was solved by R.SCHWARZENBACHER, H.ROBINSON, B.STEC, S.J.RIEDL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.7 Space group P61 a (A) 126.218 b (A) 126.218 c (A) 299.274 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.4 Rfree (%) 27.8 Sodium Binding Sites: Sodium binding site 1 out of 8 in 3ezq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ezq. 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: A: Ala307, A: Ile310, A: Gln311, C: Ala307, C: Gln311, E: Gln311, G: Gln311, conact list: Atom Atom Distance (A) Na O A:Ala307 4.44 Na CG2 A:Ile310 4.96 Na N A:Gln311 4.62 Na CB A:Gln311 4.61 Na CA A:Gln311 4.69 Na O C:Ala307 4.36 Na N C:Gln311 4.55 Na CB C:Gln311 4.44 Na CA C:Gln311 4.55 Na NE2 E:Gln311 4.34 Na NE2 G:Gln311 4.14 interactive model: Sodium binding site 2 out of 8 in 3ezq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3ezq. 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: A: Lys299, A: Asn302, A: Leu303, B: Glu179, B: Gln182, C: Phe327, conact list: Atom Atom Distance (A) Na O A:Lys299 4.93 Na CG A:Lys299 4.84 Na CB A:Asn302 4.47 Na ND2 A:Asn302 4.66 Na CD2 A:Leu303 4.67 Na CG A:Leu303 4.77 Na OE1 B:Glu179 3.47 Na OE2 B:Glu179 4.10 Na CD B:Glu179 4.18 Na OE1 B:Gln182 4.82 Na CB B:Gln182 4.71 Na CD B:Gln182 4.96 Na CG B:Gln182 4.22 Na CB C:Phe327 4.82 Na CD2 C:Phe327 4.78 Na CG C:Phe327 4.85 interactive model: Sodium binding site 3 out of 8 in 3ezq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3ezq. 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: A: Gln311, C: Gln311, E: Ala307, E: Ile310, E: Gln311, G: Ala307, G: Gln311, E: Hoh56, conact list: Atom Atom Distance (A) Na NE2 A:Gln311 3.90 Na NE2 C:Gln311 4.47 Na O E:Ala307 4.11 Na C E:Ala307 4.91 Na CA E:Ala307 4.85 Na CG2 E:Ile310 4.92 Na NE2 E:Gln311 4.83 Na N E:Gln311 4.50 Na CB E:Gln311 4.37 Na CA E:Gln311 4.52 Na O G:Ala307 4.60 Na N G:Gln311 4.81 Na CB G:Gln311 4.73 Na CA G:Gln311 4.79 Na O E:Hoh56 4.74 interactive model: Sodium binding site 4 out of 8 in 3ezq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3ezq. 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: E: Phe327, G: Lys299, G: Asn302, G: Leu303, H: Glu179, H: Gln182, conact list: Atom Atom Distance (A) Na CB E:Phe327 4.37 Na CD2 E:Phe327 4.46 Na CG E:Phe327 4.54 Na CG G:Lys299 4.88 Na CB G:Asn302 4.80 Na ND2 G:Asn302 4.96 Na CD2 G:Leu303 4.67 Na OE1 H:Glu179 3.59 Na OE2 H:Glu179 3.91 Na CD H:Glu179 4.16 Na OE1 H:Gln182 3.63 Na CB H:Gln182 4.76 Na CD H:Gln182 4.35 Na CG H:Gln182 4.26 interactive model: Sodium binding site 5 out of 8 in 3ezq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3ezq. 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: I: Lys299, I: Asn302, I: Leu303, J: Glu179, J: Gln182, K: Phe327, conact list: Atom Atom Distance (A) Na CG I:Lys299 4.87 Na CB I:Asn302 4.78 Na ND2 I:Asn302 4.94 Na CD2 I:Leu303 4.81 Na CG I:Leu303 4.99 Na OE1 J:Glu179 3.63 Na OE2 J:Glu179 3.93 Na CD J:Glu179 4.19 Na OE1 J:Gln182 3.48 Na CB J:Gln182 4.75 Na CD J:Gln182 4.24 Na CG J:Gln182 4.19 Na CB K:Phe327 4.42 Na CD2 K:Phe327 4.51 Na CG K:Phe327 4.58 interactive model: Sodium binding site 6 out of 8 in 3ezq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3ezq. 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: I: Ala307, I: Gln311, K: Ala307, K: Ile310, K: Gln311, M: Gln311, O: Gln311, I: Hoh164, conact list: Atom Atom Distance (A) Na O I:Ala307 4.46 Na N I:Gln311 4.69 Na CB I:Gln311 4.65 Na CA I:Gln311 4.72 Na O K:Ala307 4.22 Na CA K:Ala307 4.96 Na CG2 K:Ile310 4.81 Na N K:Gln311 4.54 Na CB K:Gln311 4.44 Na CA K:Gln311 4.56 Na OE1 M:Gln311 4.40 Na NE2 O:Gln311 4.04 Na O I:Hoh164 4.84 interactive model: Sodium binding site 7 out of 8 in 3ezq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3ezq. 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: I: Gln311, K: Gln311, M: Ala307, M: Gln311, O: Ala307, O: Ile310, O: Gln311, conact list: Atom Atom Distance (A) Na NE2 I:Gln311 4.08 Na NE2 K:Gln311 4.28 Na O M:Ala307 4.48 Na N M:Gln311 4.74 Na OE1 M:Gln311 4.91 Na CB M:Gln311 4.58 Na CA M:Gln311 4.75 Na O O:Ala307 4.29 Na CG2 O:Ile310 4.98 Na N O:Gln311 4.46 Na CB O:Gln311 4.44 Na CA O:Gln311 4.50 interactive model: Sodium binding site 8 out of 8 in 3ezq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3ezq. 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: M: Phe327, O: Lys299, O: Asn302, O: Leu303, P: Glu179, P: Gln182, I: Hoh162, conact list: Atom Atom Distance (A) Na CB M:Phe327 4.93 Na CD2 M:Phe327 4.94 Na CG M:Phe327 4.99 Na O O:Lys299 4.69 Na CG O:Lys299 4.52 Na CA O:Lys299 4.80 Na CB O:Asn302 4.49 Na ND2 O:Asn302 4.68 Na CD2 O:Leu303 4.59 Na CG O:Leu303 4.61 Na OE1 P:Glu179 3.25 Na OE2 P:Glu179 3.71 Na CD P:Glu179 3.89 Na CG P:Gln182 4.55 Na O I:Hoh162 4.13 interactive model: