Sodium in the structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex With Sulfite) (pdb 3lg1)

The binding sites of Sodium atom in the structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex With Sulfite) (pdb code 3lg1). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3lg1 structure was solved by A.A.TROFIMOV, K.M.POLYAKOV, K.M.BOYKO, A.A.FILIMONENKOV, P.V.DOROVATOVSKY, T.V.TIKHONOVA, V.O.POPOV, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-1.9 Space group P213 a (A) 192.620 b (A) 192.620 c (A) 192.620 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.1 Rfree (%) 18.3 Sodium Binding Sites: Sodium binding site 1 out of 8 in 3lg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3lg1. 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: Leu389, A: Glu390, A: Asn391, B: Asp147, A: Hoh550, A: Hoh627, A: Hoh1049, A: Hoh1055, B: Hoh568, B: Hoh588, B: Hoh842, conact list: Atom Atom Distance (A) Na O A:Leu389 4.23 Na O A:Glu390 2.35 Na C A:Glu390 3.47 Na CA A:Glu390 4.30 Na N A:Asn391 4.39 Na OD1 A:Asn391 4.34 Na CG A:Asn391 4.75 Na CA A:Asn391 4.51 Na OD1 B:Asp147 4.50 Na O A:Hoh550 2.33 Na O A:Hoh627 4.46 Na O A:Hoh1049 2.45 Na O A:Hoh1055 3.25 Na O B:Hoh568 3.78 Na O B:Hoh588 4.17 Na O B:Hoh842 4.45 interactive model: Sodium binding site 2 out of 8 in 3lg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3lg1. 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: Thr94, A: Ser95, A: Pg6532, A: Hoh880, A: Hoh928, A: Hoh931, A: Hoh936, A: Hoh1018, conact list: Atom Atom Distance (A) Na O A:Thr94 2.41 Na CB A:Thr94 4.60 Na C A:Thr94 3.63 Na CA A:Thr94 4.56 Na N A:Ser95 4.51 Na CA A:Ser95 4.43 Na C9 A:Pg6532 3.30 Na O5 A:Pg6532 2.64 Na C11 A:Pg6532 3.14 Na O3 A:Pg6532 2.95 Na C8 A:Pg6532 3.31 Na C6 A:Pg6532 3.10 Na C5 A:Pg6532 3.10 Na C7 A:Pg6532 3.15 Na C4 A:Pg6532 4.57 Na C10 A:Pg6532 2.91 Na O4 A:Pg6532 2.30 Na O6 A:Pg6532 2.69 Na O A:Hoh880 4.44 Na O A:Hoh928 4.09 Na O A:Hoh931 4.27 Na O A:Hoh936 2.38 Na O A:Hoh1018 4.32 interactive model: Sodium binding site 3 out of 8 in 3lg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3lg1. 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: Lys102, A: Asp450, A: So3537, A: Hoh831, A: Hoh858, A: Hoh879, A: Hoh906, conact list: Atom Atom Distance (A) Na NZ A:Lys102 4.70 Na OD2 A:Asp450 4.01 Na CG A:Asp450 4.93 Na S A:So3537 4.27 Na O1 A:So3537 4.87 Na O2 A:So3537 4.86 Na O A:Hoh831 4.69 Na O A:Hoh858 4.62 Na O A:Hoh879 2.26 Na O A:Hoh906 2.89 interactive model: Sodium binding site 4 out of 8 in 3lg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3lg1. 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: Arg81, A: Glu83, A: Ser84, A: His85, A: Glu115, A: Hec1007, A: Ca528, A: Hoh552, A: Hoh583, A: Hoh589, A: Hoh603, A: Hoh687, A: Hoh688, A: Hoh842, A: Hoh861, A: Hoh883, A: Hoh942, A: Hoh1018, A: Hoh1025, conact list: Atom Atom Distance (A) Na NH1 A:Arg81 4.34 Na O A:Glu83 4.55 Na CB A:Ser84 4.86 Na OG A:Ser84 4.55 Na CA A:Ser84 4.45 Na NE2 A:His85 4.90 Na N A:His85 4.82 Na CD2 A:His85 4.23 Na OE1 A:Glu115 4.21 Na CGA A:Hec1007 4.70 Na O2A A:Hec1007 4.32 Na O1A A:Hec1007 4.17 Na CA A:Ca528 3.89 Na O A:Hoh552 4.69 Na O A:Hoh583 3.87 Na O A:Hoh589 3.54 Na O A:Hoh603 2.37 Na O A:Hoh687 4.34 Na O A:Hoh688 2.49 Na O A:Hoh842 2.18 Na O A:Hoh861 4.68 Na O A:Hoh883 2.32 Na O A:Hoh942 4.95 Na O A:Hoh1018 3.87 Na O A:Hoh1025 3.43 interactive model: Sodium binding site 5 out of 8 in 3lg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3lg1. 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: Ser264, A: Glu265, A: Gln266, A: Gly268, A: Asp288, A: Hoh817, A: Hoh875, A: Hoh899, A: Hoh1027, conact list: Atom Atom Distance (A) Na O A:Ser264 4.64 Na O A:Glu265 2.38 Na OE2 A:Glu265 3.81 Na CD A:Glu265 4.40 Na C A:Glu265 3.51 Na CG A:Glu265 4.63 Na CA A:Glu265 4.14 Na N A:Gln266 4.59 Na C A:Gln266 4.77 Na CA A:Gln266 4.82 Na N A:Gly268 4.12 Na C A:Gly268 4.89 Na CA A:Gly268 4.15 Na CB A:Asp288 4.84 Na OD2 A:Asp288 2.54 Na OD1 A:Asp288 3.90 Na CG A:Asp288 3.55 Na O A:Hoh817 2.60 Na O A:Hoh875 4.00 Na O A:Hoh899 2.50 Na O A:Hoh1027 2.51 interactive model: Sodium binding site 6 out of 8 in 3lg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3lg1. 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: Thr94, B: Ser95, B: Pg6531, B: Hoh896, B: Hoh944, B: Hoh947, B: Hoh952, conact list: Atom Atom Distance (A) Na O B:Thr94 2.38 Na CB B:Thr94 4.61 Na C B:Thr94 3.59 Na CA B:Thr94 4.52 Na N B:Ser95 4.48 Na CA B:Ser95 4.47 Na C9 B:Pg6531 3.24 Na O5 B:Pg6531 2.83 Na C11 B:Pg6531 3.25 Na O3 B:Pg6531 3.10 Na C8 B:Pg6531 3.20 Na C6 B:Pg6531 3.05 Na C5 B:Pg6531 3.09 Na C7 B:Pg6531 3.16 Na C4 B:Pg6531 4.56 Na C10 B:Pg6531 2.98 Na O4 B:Pg6531 2.31 Na O6 B:Pg6531 2.85 Na O B:Hoh896 4.52 Na O B:Hoh944 4.05 Na O B:Hoh947 4.22 Na O B:Hoh952 2.42 interactive model: Sodium binding site 7 out of 8 in 3lg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3lg1. 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: Lys102, B: Asp450, B: So3536, B: Hoh848, B: Hoh875, B: Hoh895, B: Hoh912, B: Hoh922, B: Hoh1000, conact list: Atom Atom Distance (A) Na NZ B:Lys102 4.57 Na OD2 B:Asp450 4.02 Na CG B:Asp450 4.98 Na S B:So3536 3.96 Na O1 B:So3536 4.63 Na O2 B:So3536 4.65 Na O3 B:So3536 4.69 Na O B:Hoh848 4.86 Na O B:Hoh875 4.47 Na O B:Hoh895 2.17 Na O B:Hoh912 4.91 Na O B:Hoh922 2.63 Na O B:Hoh1000 4.97 interactive model: Sodium binding site 8 out of 8 in 3lg1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3lg1. 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: Arg81, B: Glu83, B: Ser84, B: His85, B: Glu115, B: Hec1007, B: Ca528, B: Pg4532, B: Hoh600, B: Hoh606, B: Hoh620, B: Hoh704, B: Hoh705, B: Hoh859, B: Hoh877, B: Hoh899, conact list: Atom Atom Distance (A) Na NH1 B:Arg81 4.33 Na O B:Glu83 4.69 Na CB B:Ser84 4.82 Na OG B:Ser84 4.54 Na CA B:Ser84 4.45 Na N B:His85 4.82 Na CD2 B:His85 4.35 Na OE1 B:Glu115 4.09 Na CGA B:Hec1007 4.64 Na O2A B:Hec1007 4.24 Na O1A B:Hec1007 4.14 Na CA B:Ca528 3.80 Na O3 B:Pg4532 4.82 Na O B:Hoh600 3.91 Na O B:Hoh606 3.34 Na O B:Hoh620 2.51 Na O B:Hoh704 4.60 Na O B:Hoh705 2.39 Na O B:Hoh859 2.48 Na O B:Hoh877 4.44 Na O B:Hoh899 2.26 interactive model: