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Sodium in the structure of Agao in Covalent Complex With the Inhibitor Noba ("4-(2-Naphthyloxy)- 2-Butyn-1-Amine") (pdb 1sii)

The binding sites of Sodium atom in the structure of Agao in Covalent Complex With the Inhibitor Noba ("4-(2-Naphthyloxy)- 2-Butyn-1-Amine") (pdb code 1sii). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 1sii structure was solved by J.M.GUSS, D.B.LANGLEY, A.P.DUFF, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)19.9-1.7
Space groupC121
a (A)158.060
b (A)62.619
c (A)91.990
alpha (°)90.00
beta (°)112.11
gamma (°)90.00
Rfactor (%)15.7
Rfree (%)18.3

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 1sii

Sodium binding site 1 out of 1 in 1sii
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 1sii
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1sii. 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: Arg49, A: Asn273, A: Asp440, A: Met441, A: Ala442, A: Phe446, A: Tyr546, A: Asp581, A: Ile582, A: Val583, A: Hoh1234,

conact list:

AtomAtomDistance (A)
NaHH22 A:Arg493.88
NaHH21 A:Arg493.35
NaNH2 A:Arg493.93
NaHB2 A:Asn2734.96
NaHB3 A:Asn2734.71
NaO A:Asp4404.39
NaCB A:Asp4404.59
NaHA A:Asp4403.86
NaOD2 A:Asp4404.48
NaOD1 A:Asp4402.47
NaC A:Asp4403.76
NaCG A:Asp4403.71
NaCA A:Asp4404.23
NaHB2 A:Met4413.88
NaN A:Met4413.33
NaCB A:Met4414.44
NaC A:Met4413.44
NaCA A:Met4413.87
NaO A:Met4412.40
NaHA A:Met4414.75
NaH A:Met4413.17
NaN A:Ala4424.62
NaHA A:Ala4424.61
NaHB1 A:Ala4424.64
NaHB3 A:Phe4464.91
NaCD1 A:Phe4463.89
NaHD1 A:Phe4463.08
NaO A:Phe4464.95
NaHA A:Phe4464.55
NaHE1 A:Phe4463.88
NaCE1 A:Phe4464.30
NaHB2 A:Tyr5464.08
NaCB A:Tyr5464.94
NaO A:Asp5814.71
NaCB A:Asp5814.54
NaHA A:Asp5813.56
NaOD2 A:Asp5814.62
NaOD1 A:Asp5812.52
NaC A:Asp5813.87
NaCG A:Asp5813.75
NaCA A:Asp5814.10
NaN A:Ile5823.32
NaHG13 A:Ile5824.70
NaHG12 A:Ile5824.72
NaC A:Ile5823.53
NaCA A:Ile5823.99
NaO A:Ile5822.56
NaHA A:Ile5824.56
NaH A:Ile5822.97
NaN A:Val5834.65
NaCG2 A:Val5834.81
NaHG21 A:Val5834.04
NaHA A:Val5834.61
NaHG23 A:Val5834.69
NaO A:Hoh12342.81

interactive model:

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