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Sodium in the structure of Complex of YPD1 And SLN1-R1 With Bound MG2+ and BEF3- (pdb 2r25)

The binding sites of Sodium atom in the structure of Complex of YPD1 And SLN1-R1 With Bound MG2+ and BEF3- (pdb code 2r25). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2r25 structure was solved by D.M.COPELAND, X.ZHAO, A.S.SOARES, A.H.WEST, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)17.8-1.7
Space groupP212121
a (A)52.013
b (A)75.544
c (A)98.392
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)19.6
Rfree (%)24

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 2r25

Sodium binding site 1 out of 1 in 2r25
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 2r25
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2r25. 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: Tyr1138, B: Asn1139, B: Met1140, B: Ile1141, B: Tyr1165, B: Ser1167, B: Pro1168, B: Ile1169,

conact list:

AtomAtomDistance (A)
NaO B:Tyr11382.50
NaN B:Tyr11384.55
NaCB B:Tyr11384.07
NaC B:Tyr11383.59
NaCA B:Tyr11384.39
NaO B:Asn11393.17
NaN B:Asn11394.41
NaC B:Asn11393.38
NaCA B:Asn11394.43
NaO B:Met11404.02
NaN B:Met11403.28
NaCB B:Met11404.56
NaC B:Met11403.31
NaCA B:Met11403.12
NaN B:Ile11413.38
NaCB B:Ile11414.42
NaCD1 B:Ile11414.34
NaCG1 B:Ile11413.76
NaCA B:Ile11414.46
NaCE2 B:Tyr11654.51
NaCD1 B:Tyr11654.66
NaCZ B:Tyr11653.19
NaCE1 B:Tyr11653.31
NaOH B:Tyr11652.23
NaO B:Ser11674.11
NaCB B:Ser11673.31
NaOG B:Ser11674.47
NaC B:Ser11673.70
NaCA B:Ser11674.11
NaO B:Pro11682.59
NaN B:Pro11683.65
NaCB B:Pro11684.85
NaCD B:Pro11684.01
NaC B:Pro11683.66
NaCA B:Pro11684.19
NaN B:Ile11694.83

interactive model:

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