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Sodium in PDB 2yme: Crystal Structure of A Mutant Binding Protein (5HTBP-Achbp) in Complex with Granisetron

Protein crystallography data

The structure of Crystal Structure of A Mutant Binding Protein (5HTBP-Achbp) in Complex with Granisetron, PDB code: 2yme was solved by D.Kesters, A.J.Thompson, M.Brams, R.V.Elk, R.Spurny, M.Geitmann, J.M.Villalgordo, A.Guskov, U.H.Danielson, S.C.R.Lummis, A.B.Smit, C.Ulens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.908 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.090, 138.900, 119.890, 90.00, 91.07, 90.00
R / Rfree (%) 16.95 / 22.63

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Mutant Binding Protein (5HTBP-Achbp) in Complex with Granisetron (pdb code 2yme). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of A Mutant Binding Protein (5HTBP-Achbp) in Complex with Granisetron, PDB code: 2yme:

Sodium binding site 1 out of 1 in 2yme

Go back to Sodium Binding Sites List in 2yme
Sodium binding site 1 out of 1 in the Crystal Structure of A Mutant Binding Protein (5HTBP-Achbp) in Complex with Granisetron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Mutant Binding Protein (5HTBP-Achbp) in Complex with Granisetron within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na1208

b:83.7
occ:1.00
O I:HOH2103 3.3 25.9 1.0
OD2 I:ASP195 3.4 36.5 1.0
OH I:TYR186 3.5 38.0 1.0
CB I:TYR193 3.8 27.8 1.0
CB I:ASP195 3.8 39.5 1.0
CG I:ASP195 4.1 45.5 1.0
O I:SER144 4.1 40.7 1.0
O I:ILE194 4.1 23.4 1.0
O I:HOH2070 4.2 43.6 1.0
C01 I:CWB1207 4.3 38.4 1.0
C I:ILE194 4.4 31.6 1.0
CZ I:TYR186 4.5 41.0 1.0
CE1 I:TYR186 4.5 38.5 1.0
CA I:GLY143 4.5 22.6 1.0
C I:TYR193 4.5 36.4 1.0
N I:ASP195 4.6 19.3 1.0
N I:ILE194 4.6 33.2 1.0
CB I:GLN184 4.6 42.6 1.0
CG I:TYR193 4.7 34.8 1.0
CA I:ASP195 4.7 26.1 1.0
CE I:LYS141 4.8 25.9 1.0
CA I:TYR193 4.8 23.0 1.0
O I:TYR193 4.8 39.5 1.0
CD2 I:TYR193 4.9 34.3 1.0
C I:GLY143 4.9 25.5 1.0

Reference:

D.Kesters, A.J.Thompson, M.Brams, R.Van Elk, R.Spurny, M.Geitmann, J.M.Villalgordo, A.Guskov, U.Helena Danielson, S.C.R.Lummis, A.B.Smit, C.Ulens. Structural Basis of Ligand Recognition in 5-HT3 Receptors. Embo Rep. V. 14 49 2013.
ISSN: ISSN 1469-221X
PubMed: 23196367
DOI: 10.1038/EMBOR.2012.189
Page generated: Tue Dec 15 06:00:44 2020

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