Sodium in the structure of Crystal Structure of CA2+-Free S100A2 At 1.6 A Resolution (pdb 2rgi)

The binding sites of Sodium atom in the structure of Crystal Structure of CA2+-Free S100A2 At 1.6 A Resolution (pdb code 2rgi). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2rgi structure was solved by M.KOCH, J.DIEZ, G.FRITZ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.3-1.6 Space group P212121 a (A) 43.516 b (A) 57.820 c (A) 59.794 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 22.7 Sodium Binding Sites: Sodium binding site 1 out of 3 in 2rgi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2rgi. 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: Tyr19, A: Ser20, A: Ser21, A: Gln22, A: Glu23, A: Gly24, A: Asp25, A: Lys26, A: Lys28, A: Leu29, A: Glu33, A: Gln69, A: Hoh105, A: Hoh106, A: Hoh110, A: Hoh112, conact list: Atom Atom Distance (A) Na O A:Tyr19 4.76 Na O A:Ser20 2.53 Na N A:Ser20 4.96 Na CB A:Ser20 4.21 Na C A:Ser20 3.44 Na CA A:Ser20 3.69 Na N A:Ser21 4.67 Na N A:Gln22 4.90 Na O A:Glu23 2.24 Na N A:Glu23 4.11 Na CB A:Glu23 4.65 Na C A:Glu23 3.45 Na CA A:Glu23 4.30 Na O A:Gly24 4.56 Na N A:Gly24 4.40 Na C A:Gly24 4.13 Na CA A:Gly24 4.49 Na O A:Asp25 2.42 Na N A:Asp25 3.96 Na CB A:Asp25 4.95 Na C A:Asp25 3.49 Na CA A:Asp25 4.34 Na N A:Lys26 4.35 Na C A:Lys26 4.82 Na CA A:Lys26 4.42 Na O A:Lys28 2.29 Na N A:Lys28 4.30 Na CB A:Lys28 4.41 Na C A:Lys28 3.38 Na CA A:Lys28 4.27 Na N A:Leu29 4.23 Na CB A:Leu29 4.81 Na CA A:Leu29 4.19 Na OE1 A:Glu33 4.66 Na OE1 A:Gln69 4.71 Na O A:Hoh105 2.32 Na O A:Hoh106 2.34 Na O A:Hoh110 3.91 Na O A:Hoh112 4.39 interactive model: Sodium binding site 2 out of 3 in 2rgi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2rgi. 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: Leu38, A: His39, A: Lys40, A: Leu42, A: Pro43, A: Ser44, A: Hoh115, A: Hoh125, A: Hoh179, A: Hoh189, A: Hoh190, conact list: Atom Atom Distance (A) Na O A:Leu38 3.26 Na C A:Leu38 4.22 Na O A:His39 2.34 Na N A:His39 4.42 Na CB A:His39 4.83 Na C A:His39 3.24 Na CA A:His39 3.64 Na N A:Lys40 4.41 Na C A:Lys40 4.95 Na CA A:Lys40 4.97 Na O A:Leu42 2.26 Na N A:Leu42 4.19 Na CB A:Leu42 4.59 Na C A:Leu42 3.31 Na CA A:Leu42 4.22 Na O A:Pro43 3.39 Na N A:Pro43 4.14 Na C A:Pro43 3.64 Na CA A:Pro43 4.11 Na N A:Ser44 4.22 Na CA A:Ser44 4.53 Na O A:Hoh115 4.34 Na O A:Hoh125 3.70 Na O A:Hoh179 4.19 Na O A:Hoh189 2.17 Na O A:Hoh190 3.98 interactive model: Sodium binding site 3 out of 3 in 2rgi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2rgi. 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: Tyr19, B: Ser20, B: Ser21, B: Gln22, B: Glu23, B: Gly24, B: Asp25, B: Lys26, B: Lys28, B: Leu29, B: Gln69, B: Hoh104, B: Hoh107, B: Hoh109, B: Hoh114, conact list: Atom Atom Distance (A) Na O B:Tyr19 4.86 Na O B:Ser20 2.46 Na CB B:Ser20 4.19 Na C B:Ser20 3.44 Na CA B:Ser20 3.74 Na N B:Ser21 4.67 Na N B:Gln22 5.00 Na O B:Glu23 2.33 Na N B:Glu23 4.22 Na CB B:Glu23 4.89 Na C B:Glu23 3.48 Na CG B:Glu23 4.90 Na CA B:Glu23 4.36 Na O B:Gly24 4.58 Na N B:Gly24 4.39 Na C B:Gly24 4.13 Na CA B:Gly24 4.45 Na O B:Asp25 2.50 Na N B:Asp25 3.96 Na C B:Asp25 3.55 Na CA B:Asp25 4.39 Na N B:Lys26 4.41 Na C B:Lys26 4.95 Na CA B:Lys26 4.54 Na O B:Lys28 2.30 Na N B:Lys28 4.34 Na CB B:Lys28 4.61 Na C B:Lys28 3.43 Na CA B:Lys28 4.34 Na N B:Leu29 4.28 Na CB B:Leu29 4.87 Na CA B:Leu29 4.22 Na OE1 B:Gln69 4.66 Na O B:Hoh104 3.87 Na O B:Hoh107 2.52 Na O B:Hoh109 2.28 Na O B:Hoh114 4.18 interactive model: