Sodium in PDB 434d: 5'-R(*Up*Ap*Gp*Cp*Up*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3'

The structure of 5'-R(*Up*Ap*Gp*Cp*Up*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3', PDB code: 434d was solved by U.Mueller, H.Schuebel, M.Sprinzl, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.16
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	26.300, 28.900, 28.900, 110.50, 96.90, 96.90
R / Rfree (%)	12.3 / 18

The structure of 5'-R(*Up*Ap*Gp*Cp*Up*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3' also contains other interesting chemical elements:

Strontium

(Sr)

1 atom

The binding sites of Sodium atom in the 5'-R(*Up*Ap*Gp*Cp*Up*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3' (pdb code 434d). 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 5'-R(*Up*Ap*Gp*Cp*Up*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3', PDB code: 434d:

Sodium binding site 1 out of 1 in the 5'-R(*Up*Ap*Gp*Cp*Up*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3'


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 5'-R(*Up*Ap*Gp*Cp*Up*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3' within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8 b:20.0 occ:0.50 O B:HOH1002 2.2 12.0 0.5 O A:HOH1141 2.2 18.5 0.5 O B:HOH1006 2.6 27.9 1.0 O A:HOH1026 2.9 26.6 1.0 O B:HOH1001 3.0 18.0 0.5 O A:HOH1155 3.2 38.3 1.0 O B:HOH1102 3.4 34.5 1.0 O6 B:G11 4.0 21.4 1.0 N4 A:C4 4.1 18.5 1.0 O A:HOH1140 4.3 21.9 0.5 O A:HOH1086 4.6 42.1 1.0 O A:HOH1093 4.9 35.0 1.0 O A:HOH1067 5.0 22.6 1.0

U.Mueller, H.Schubel, M.Sprinzl, U.Heinemann. Crystal Structure of Acceptor Stem of Trna(Ala) From Escherichia Coli Shows Unique G.U Wobble Base Pair at 1.16 A Resolution. Rna V. 5 670 1999.
ISSN: ISSN 1355-8382
PubMed: 10334337
DOI: 10.1017/S1355838299982304