Sodium in the structure of Crystal Structure Analysis Of the Bb Segment of Factor B Complexed With 4-Guanidinobenzoic Acid (pdb 1rtk)

The binding sites of Sodium atom in the structure of Crystal Structure Analysis Of the Bb Segment of Factor B Complexed With 4-Guanidinobenzoic Acid (pdb code 1rtk). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1rtk structure was solved by K.PONNURAJ, Y.XU, K.MACON, D.MOORE, J.E.VOLANAKIS, S.V.NARAYANA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.8-2.3 Space group P61 a (A) 98.355 b (A) 98.355 c (A) 125.657 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.8 Rfree (%) 24.5 Sodium Binding Sites: Sodium binding site 1 out of 7 in 1rtk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1rtk. 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: conact list: Atom Atom Distance (A) interactive model: Sodium binding site 2 out of 7 in 1rtk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1rtk. 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: Asp308, A: Trp309, A: Lys312, A: Hoh809, conact list: Atom Atom Distance (A) Na O A:Asp308 4.23 Na CB A:Asp308 4.31 Na C A:Asp308 4.10 Na CA A:Asp308 4.89 Na N A:Trp309 3.87 Na CB A:Trp309 4.24 Na CD1 A:Trp309 4.43 Na CG A:Trp309 4.77 Na CA A:Trp309 3.80 Na CB A:Lys312 4.79 Na CD A:Lys312 4.14 Na NZ A:Lys312 4.94 Na O A:Hoh809 4.92 interactive model: Sodium binding site 3 out of 7 in 1rtk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1rtk. 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: Glu446, A: Ser447, A: Leu450, A: Gln565, conact list: Atom Atom Distance (A) Na CB A:Glu446 4.06 Na C A:Glu446 4.38 Na CA A:Glu446 4.81 Na N A:Ser447 3.83 Na CB A:Ser447 4.11 Na CA A:Ser447 4.04 Na CD1 A:Leu450 4.31 Na CD2 A:Leu450 4.82 Na CG A:Leu450 4.83 Na NE2 A:Gln565 4.86 Na OE1 A:Gln565 3.91 Na CD A:Gln565 4.80 interactive model: Sodium binding site 4 out of 7 in 1rtk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1rtk. 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: Lys594, A: Leu598, A: Asn719, A: Phe721, A: Gln722, conact list: Atom Atom Distance (A) Na CE A:Lys594 4.33 Na CD A:Lys594 3.17 Na CG A:Lys594 3.84 Na NZ A:Lys594 4.52 Na CD1 A:Leu598 4.40 Na ND2 A:Asn719 3.69 Na OD1 A:Asn719 4.69 Na CG A:Asn719 4.58 Na CB A:Phe721 4.11 Na CG A:Phe721 4.58 Na NE2 A:Gln722 3.54 Na CD A:Gln722 4.70 interactive model: Sodium binding site 5 out of 7 in 1rtk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1rtk. 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: Glu576, A: Thr579, A: Arg580, A: Pro586, A: Hoh922, A: Hoh940, conact list: Atom Atom Distance (A) Na O A:Glu576 4.38 Na CB A:Glu576 4.08 Na OE2 A:Glu576 4.55 Na CD A:Glu576 4.59 Na C A:Glu576 4.92 Na CG A:Glu576 4.49 Na CA A:Glu576 4.57 Na CB A:Thr579 4.55 Na CG2 A:Thr579 4.28 Na CD A:Arg580 4.67 Na CZ A:Arg580 4.63 Na CG A:Arg580 4.22 Na NH1 A:Arg580 3.42 Na O A:Pro586 4.94 Na N A:Pro586 4.82 Na CB A:Pro586 4.03 Na C A:Pro586 4.97 Na CA A:Pro586 3.99 Na O A:Hoh922 3.67 Na O A:Hoh940 3.31 interactive model: Sodium binding site 6 out of 7 in 1rtk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1rtk. 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: Gly387, A: Lys388, A: Asp389, A: Arg390, A: Pro393, conact list: Atom Atom Distance (A) Na O A:Gly387 4.37 Na N A:Gly387 4.96 Na C A:Gly387 3.98 Na CA A:Gly387 3.92 Na N A:Lys388 4.27 Na C A:Lys388 4.75 Na CA A:Lys388 5.00 Na O A:Asp389 4.42 Na N A:Asp389 4.34 Na C A:Asp389 4.24 Na CA A:Asp389 4.73 Na N A:Arg390 4.26 Na CA A:Arg390 4.54 Na CB A:Pro393 3.93 Na CG A:Pro393 4.11 Na CA A:Pro393 4.44 interactive model: Sodium binding site 7 out of 7 in 1rtk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 1rtk. 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: Iod741, A: Hoh1010, conact list: Atom Atom Distance (A) Na I A:Iod741 3.38 Na O A:Hoh1010 4.64 interactive model: