Sodium in PDB 435d: 5'-R(*Up*Ap*Gp*Cp*Cp*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3'

The structure of 5'-R(*Up*Ap*Gp*Cp*Cp*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3', PDB code: 435d 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 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	26.680, 26.697, 30.459, 104.29, 104.22, 91.66
R / Rfree (%)	15.8 / 21.7

The binding sites of Sodium atom in the 5'-R(*Up*Ap*Gp*Cp*Cp*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3' (pdb code 435d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 5'-R(*Up*Ap*Gp*Cp*Cp*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3', PDB code: 435d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 5'-R(*Up*Ap*Gp*Cp*Cp*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*Cp*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:16.2 occ:1.00 O A:HOH1137 2.1 18.4 1.0 O A:HOH1113 2.2 21.8 1.0 O B:HOH1098 3.9 24.4 1.0 O B:HOH1114 4.0 7.9 1.0 N4 A:C4 4.0 15.1 1.0 N7 A:A2 4.1 19.6 1.0 O6 A:G3 4.1 10.9 1.0 N7 A:G3 4.3 9.6 1.0 C8 A:A2 4.6 19.2 1.0 O6 B:G11 4.6 13.8 1.0 C5 A:A2 4.6 19.0 1.0 N6 A:A2 4.9 21.8 1.0 C6 A:G3 4.9 9.2 1.0 C5 A:G3 5.0 9.3 1.0

Sodium binding site 2 out of 2 in the 5'-R(*Up*Ap*Gp*Cp*Cp*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 2 of 5'-R(*Up*Ap*Gp*Cp*Cp*Cp*C)-3', 5'-R(*Gp*Gp*Gp*Gp*Cp*Up*A)-3' within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1 b:19.8 occ:1.00 O D:HOH1053 2.1 25.3 1.0 O D:HOH1048 2.2 34.0 1.0 O D:HOH1115 2.4 18.7 1.0 O C:HOH1076 2.4 35.6 1.0 O6 D:G10 4.0 10.3 1.0 N7 D:G10 4.1 8.2 1.0 O D:HOH1059 4.3 28.9 1.0 O6 D:G11 4.4 16.0 1.0 C6 D:G10 4.8 8.3 1.0 O D:HOH1080 4.8 32.2 1.0 C5 D:G10 4.8 8.8 1.0 N7 D:G9 4.9 13.8 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