Sodium in the structure of P3, The Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. (pdb 1hx6)

The binding sites of Sodium atom in the structure of P3, The Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. (pdb code 1hx6). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1hx6 structure was solved by S.D.BENSON, J.K.H.BAMFORD, D.H.BAMFORD, R.M.BURNETT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 53.5-1.6 Space group P212121 a (A) 117.960 b (A) 121.300 c (A) 126.390 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19 Rfree (%) 20.8 Sodium Binding Sites: Sodium binding site 1 out of 7 in 1hx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1hx6. 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: Glu111, A: Glu261, A: Asn262, A: Ser263, A: Hoh1182, A: Hoh1183, A: Hoh1184, A: Hoh1185, A: Hoh1192, A: Hoh1194, A: Hoh1768, conact list: Atom Atom Distance (A) Na O A:Glu111 4.37 Na CG A:Glu111 4.94 Na OE1 A:Glu261 4.55 Na C A:Glu261 4.95 Na O A:Asn262 2.27 Na N A:Asn262 3.81 Na CB A:Asn262 4.53 Na ND2 A:Asn262 4.64 Na C A:Asn262 3.31 Na OD1 A:Asn262 2.81 Na CG A:Asn262 3.77 Na CA A:Asn262 4.05 Na N A:Ser263 4.30 Na N A:Ser263 4.28 Na CA A:Ser263 4.53 Na CA A:Ser263 4.52 Na O A:Hoh1182 4.72 Na O A:Hoh1183 2.51 Na O A:Hoh1184 2.39 Na O A:Hoh1185 4.41 Na O A:Hoh1192 4.03 Na O A:Hoh1194 2.31 Na O A:Hoh1768 4.92 interactive model: Sodium binding site 2 out of 7 in 1hx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1hx6. 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: Asn199, A: Asn200, A: Phe203, A: Ala220, A: Ala221, A: Cys223, A: Hoh1580, A: Hoh1581, A: Hoh1582, A: Hoh1583, A: Hoh1584, A: Hoh1585, A: Hoh1586, A: Hoh1590, A: Hoh1759, conact list: Atom Atom Distance (A) Na O A:Asn199 2.57 Na CB A:Asn199 4.51 Na C A:Asn199 3.67 Na CA A:Asn199 4.61 Na N A:Asn200 4.48 Na ND2 A:Asn200 4.13 Na CA A:Asn200 4.45 Na CD2 A:Phe203 4.78 Na O A:Ala220 4.91 Na O A:Ala221 4.47 Na O A:Cys223 4.70 Na O A:Hoh1580 4.43 Na O A:Hoh1581 2.47 Na O A:Hoh1582 4.01 Na O A:Hoh1583 2.35 Na O A:Hoh1584 2.45 Na O A:Hoh1585 2.17 Na O A:Hoh1586 4.01 Na O A:Hoh1590 2.41 Na O A:Hoh1759 4.43 interactive model: Sodium binding site 3 out of 7 in 1hx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1hx6. 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: Asp143, A: Asn146, A: Ile148, A: Asp149, B: Asp136, A: Hoh1123, A: Hoh1124, A: Hoh1126, A: Hoh1154, B: Hoh1125, B: Hoh1564, conact list: Atom Atom Distance (A) Na CB A:Asp143 4.63 Na OD2 A:Asp143 2.30 Na OD1 A:Asp143 3.61 Na CG A:Asp143 3.29 Na CB A:Asn146 4.15 Na ND2 A:Asn146 4.64 Na OD1 A:Asn146 2.41 Na CG A:Asn146 3.55 Na CA A:Asn146 4.27 Na O A:Ile148 4.41 Na CB A:Asp149 3.61 Na OD2 A:Asp149 4.09 Na OD1 A:Asp149 2.40 Na CG A:Asp149 3.16 Na CA A:Asp149 4.31 Na O B:Asp136 4.66 Na CB B:Asp136 4.92 Na OD2 B:Asp136 4.28 Na CG B:Asp136 4.92 Na O A:Hoh1123 4.14 Na O A:Hoh1124 2.52 Na O A:Hoh1126 3.48 Na O A:Hoh1154 4.35 Na O B:Hoh1125 2.43 Na O B:Hoh1564 2.45 interactive model: Sodium binding site 4 out of 7 in 1hx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1hx6. 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: B: Asp143, B: Asn146, B: Ile148, B: Asp149, C: Asp136, B: Hoh1138, B: Hoh1140, B: Hoh1345, B: Hoh1346, B: Hoh1639, C: Hoh1139, C: Hoh1486, conact list: Atom Atom Distance (A) Na CB B:Asp143 4.59 Na OD2 B:Asp143 2.26 Na OD1 B:Asp143 3.70 Na CG B:Asp143 3.31 Na CB B:Asn146 4.26 Na ND2 B:Asn146 4.73 Na OD1 B:Asn146 2.49 Na CG B:Asn146 3.64 Na CA B:Asn146 4.41 Na O B:Ile148 4.40 Na CB B:Asp149 3.49 Na CB B:Asp149 3.23 Na OD2 B:Asp149 3.91 Na OD2 B:Asp149 4.40 Na OD1 B:Asp149 2.26 Na CG B:Asp149 3.00 Na CG B:Asp149 4.28 Na CA B:Asp149 4.23 Na CA B:Asp149 4.24 Na O C:Asp136 4.70 Na CB C:Asp136 4.83 Na OD2 C:Asp136 4.23 Na CG C:Asp136 4.86 Na O B:Hoh1138 4.13 Na O B:Hoh1140 3.48 Na O B:Hoh1345 2.44 Na O B:Hoh1346 4.61 Na O B:Hoh1639 4.38 Na O C:Hoh1139 2.58 Na O C:Hoh1486 2.53 interactive model: Sodium binding site 5 out of 7 in 1hx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1hx6. 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: B: Asn199, B: Asn200, B: Phe203, B: Ala220, B: Ala221, B: Cys223, B: Hoh1007, B: Hoh1008, B: Hoh1009, B: Hoh1010, B: Hoh1011, B: Hoh1517, B: Hoh1518, B: Hoh1519, B: Hoh1663, conact list: Atom Atom Distance (A) Na O B:Asn199 2.47 Na CB B:Asn199 4.43 Na C B:Asn199 3.60 Na CA B:Asn199 4.52 Na N B:Asn200 4.45 Na ND2 B:Asn200 4.28 Na CA B:Asn200 4.47 Na CB B:Phe203 4.95 Na CD2 B:Phe203 4.58 Na O B:Ala220 4.75 Na O B:Ala221 4.58 Na O B:Cys223 4.73 Na O B:Hoh1007 2.58 Na O B:Hoh1008 2.33 Na O B:Hoh1009 4.25 Na O B:Hoh1010 2.39 Na O B:Hoh1011 4.67 Na O B:Hoh1517 3.72 Na O B:Hoh1518 2.36 Na O B:Hoh1519 2.45 Na O B:Hoh1663 4.39 interactive model: Sodium binding site 6 out of 7 in 1hx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1hx6. 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: B: Arg108, B: Glu111, B: Glu261, B: Asn262, B: Mpd511, B: Hoh1429, B: Hoh1433, B: Hoh1434, B: Hoh1435, B: Hoh1436, B: Hoh1437, B: Hoh1696, B: Hoh1731, conact list: Atom Atom Distance (A) Na CZ B:Arg108 4.55 Na NH2 B:Arg108 3.97 Na NH1 B:Arg108 4.86 Na O B:Glu111 4.63 Na OE1 B:Glu111 2.65 Na CB B:Glu111 4.94 Na OE2 B:Glu111 3.72 Na CD B:Glu111 3.47 Na CG B:Glu111 4.74 Na OE1 B:Glu261 2.33 Na CB B:Glu261 4.31 Na OE2 B:Glu261 4.47 Na CD B:Glu261 3.47 Na CG B:Glu261 4.06 Na O B:Asn262 4.09 Na N B:Asn262 4.99 Na CM B:Mpd511 4.19 Na C1 B:Mpd511 4.80 Na O B:Hoh1429 5.00 Na O B:Hoh1433 2.29 Na O B:Hoh1434 2.68 Na O B:Hoh1435 2.36 Na O B:Hoh1436 2.26 Na O B:Hoh1437 4.73 Na O B:Hoh1696 4.61 Na O B:Hoh1731 4.99 interactive model: Sodium binding site 7 out of 7 in 1hx6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 1hx6. 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: Ala50, C: Asn51, C: Arg52, C: Hoh1059, conact list: Atom Atom Distance (A) Na O C:Ala50 4.80 Na O C:Asn51 2.41 Na CB C:Asn51 4.97 Na C C:Asn51 3.54 Na CA C:Asn51 4.15 Na N C:Arg52 4.66 Na CA C:Arg52 4.94 Na O C:Hoh1059 2.54 interactive model: