Chemical elements
  Sodium
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Sodium in the structure of Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109. (pdb 3dc7)






The binding sites of Sodium atom in the structure of Crystal Structure of the Protein Q88SR8 From Lactobacillus Plantarum. Northeast Structural Genomics Consortium Target LPR109. (pdb code 3dc7). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3dc7 structure was solved by A.P.KUZIN, M.ABASHIDZE, S.M.VOROBIEV, J.SEETHARAMAN, L.ZHAO, L.MAO, C.CICCOSANTI, R.XIAO, R.NAIR, M.C.BARAN, T.B.ACTON, B.ROST, G.T.MONTELIONE, J.F.HUNT, L.TONG, NORTHEAST STRUCTURAL GENOMICSCONSORTIUM (NESG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)19.7-2.1
Space groupP212121
a (A)48.610
b (A)101.440
c (A)125.550
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)18.4
Rfree (%)22.4


Sodium Binding Sites:

Sodium binding site 1 out of 2 in 3dc7


Sodium binding site 1 out of 2 in 3dc7
Click to enlarge
stereopicture of Sodium binding site 1 out of 2 in 3dc7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3dc7. 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: Gly28, B: Asp29, B: Ser30, B: Ile31, B: Thr32, B: Phe89, B: Gly90,

conact list:


AtomAtomDistance (A)
NaO B:Gly284.46
NaN B:Gly284.60
NaC B:Gly283.27
NaCA B:Gly283.25
NaO B:Asp293.97
NaN B:Asp292.39
NaCB B:Asp293.63
NaOD2 B:Asp293.52
NaC B:Asp293.78
NaOD1 B:Asp292.24
NaCG B:Asp292.85
NaCA B:Asp293.34
NaN B:Ser304.52
NaN B:Ile314.19
NaCB B:Ile314.20
NaC B:Ile314.48
NaCA B:Ile314.47
NaN B:Thr323.90
NaCB B:Thr323.93
NaOG1 B:Thr323.26
NaCA B:Thr324.57
NaO B:Phe892.28
NaN B:Phe895.00
NaCB B:Phe893.77
NaCD1 B:Phe894.05
NaCD2 B:Phe894.53
NaC B:Phe893.47
NaCE1 B:Phe894.82
NaCG B:Phe893.89
NaCA B:Phe894.23
NaN B:Gly904.50
NaCA B:Gly904.71

interactive model:


Sodium binding site 2 out of 2 in 3dc7


Sodium binding site 2 out of 2 in 3dc7
Click to enlarge
stereopicture of Sodium binding site 2 out of 2 in 3dc7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3dc7. 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: Arg182, A: Asp183, C: Val175, C: Pro176, C: His177, C: Phe219, A: Hoh289, C: Hoh250, C: Hoh289,

conact list:


AtomAtomDistance (A)
NaO A:Arg1824.52
NaCB A:Asp1834.73
NaOD2 A:Asp1833.88
NaOD1 A:Asp1832.28
NaCG A:Asp1833.42
NaO C:Val1754.28
NaC C:Val1754.73
NaO C:Pro1764.41
NaN C:Pro1764.34
NaCB C:Pro1763.88
NaC C:Pro1763.20
NaCG C:Pro1764.96
NaCA C:Pro1763.12
NaO C:His1773.58
NaN C:His1772.40
NaCB C:His1773.85
NaC C:His1773.91
NaCA C:His1773.47
NaCE2 C:Phe2194.99
NaCZ C:Phe2194.10
NaCE1 C:Phe2194.92
NaO A:Hoh2892.25
NaO C:Hoh2503.27
NaO C:Hoh2894.54

interactive model:




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