Sodium in PDB 3u4m: Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus

The structure of Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus, PDB code: 3u4m was solved by A.G.Gabdulkhakov, N.A.Nevskaya, S.V.Nikonov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.68 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.550, 68.900, 117.560, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.8

The structure of Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus (pdb code 3u4m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus, PDB code: 3u4m:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus


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 Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:19.5 occ:1.00 O A:ARG6 2.9 13.0 1.0 O A:HOH408 2.9 21.1 1.0 OG1 A:THR34 3.0 13.3 1.0 O A:HOH409 3.0 26.7 1.0 CD1 A:LEU10 3.3 15.2 1.0 CG A:ARG6 3.4 12.6 1.0 C A:ARG6 3.6 10.2 1.0 CB A:THR34 3.7 11.2 1.0 CG2 A:THR34 3.7 14.4 1.0 CA A:ARG6 3.8 10.0 1.0 CB A:ALA9 3.9 17.8 1.0 CB A:ARG6 4.1 12.2 1.0 CG A:LEU10 4.2 21.9 1.0 N A:LEU10 4.3 13.2 1.0 CD2 A:LEU10 4.3 11.4 1.0 CD A:ARG6 4.7 11.2 1.0 CB A:LEU10 4.7 12.2 1.0 C A:ALA9 4.8 18.3 1.0 N A:TYR7 4.8 11.9 1.0 CA A:ALA9 4.8 15.7 1.0 CA A:LEU10 4.8 11.6 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:15.8 occ:1.00 NH2 A:ARG6 2.7 8.1 1.0 OE2 A:GLU39 2.8 9.8 1.0 O A:LEU32 3.0 10.8 1.0 C A:MET218 3.3 8.9 1.0 N A:THR34 3.3 10.8 1.0 N A:GLY219 3.4 7.0 1.0 OE1 A:GLU39 3.4 9.6 1.0 O A:MET218 3.4 10.7 1.0 CD2 A:LEU10 3.4 11.4 1.0 CD A:GLU39 3.5 12.0 1.0 CA A:ALA33 3.5 12.1 1.0 CA A:GLY219 3.6 7.9 1.0 CB A:MET218 3.7 9.7 1.0 C A:LEU32 3.7 12.2 1.0 C A:ALA33 3.8 11.4 1.0 N A:ALA35 3.8 10.4 1.0 OG1 A:THR216 3.8 8.9 1.0 CZ A:ARG6 3.9 11.5 1.0 CA A:MET218 3.9 10.5 1.0 N A:ALA33 4.0 8.0 1.0 N A:MET218 4.2 8.4 1.0 NH1 A:ARG6 4.2 8.8 1.0 OG1 A:THR34 4.2 13.3 1.0 CB A:ALA35 4.4 10.9 1.0 CA A:THR34 4.4 13.0 1.0 C A:THR34 4.5 10.6 1.0 CA A:ALA35 4.7 11.9 1.0 CB A:ALA33 4.7 10.2 1.0 CG A:LEU10 4.8 21.9 1.0 O A:ALA33 4.9 13.7 1.0 CB A:THR216 4.9 9.9 1.0 CG A:MET218 4.9 6.5 1.0 CB A:THR34 5.0 11.2 1.0 CG A:GLU39 5.0 9.2 1.0 NE A:ARG6 5.0 10.2 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:20.6 occ:1.00 OP2 B:U2130 2.6 13.0 1.0 OP1 B:C2129 2.9 11.0 1.0 O A:HOH466 3.0 26.3 1.0 N A:ARG6 3.1 11.0 1.0 CB A:ARG6 3.2 12.2 1.0 O B:HOH2314 3.5 14.0 1.0 P B:C2129 3.5 13.3 1.0 O5' B:C2129 3.6 11.3 1.0 P B:U2130 3.7 13.4 1.0 CA A:ARG6 3.7 10.0 1.0 CG A:LYS5 3.7 19.2 1.0 N A:LYS5 3.8 14.7 1.0 OP2 B:C2129 4.0 10.5 1.0 C5' B:C2129 4.0 13.4 1.0 OP1 B:U2130 4.1 12.5 1.0 C A:LYS5 4.1 12.0 1.0 O3' B:C2129 4.1 11.8 1.0 C A:GLY4 4.2 14.3 1.0 CA A:LYS5 4.3 14.5 1.0 O B:HOH2413 4.3 31.6 1.0 C3' B:C2129 4.4 11.2 1.0 CA A:GLY4 4.5 14.9 1.0 CG A:ARG6 4.5 12.6 1.0 CB A:LYS5 4.6 14.1 1.0 CD A:ARG6 4.8 11.2 1.0 C4' B:C2129 4.8 12.1 1.0 CE A:LYS5 4.8 24.7 1.0 N A:TYR7 4.9 11.9 1.0 C A:ARG6 4.9 10.2 1.0 O A:GLY4 4.9 12.1 1.0 NE A:ARG6 4.9 10.2 1.0 CD A:LYS5 4.9 22.6 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:16.3 occ:1.00 O A:THR216 2.8 8.6 1.0 O2 B:C2175 2.8 7.7 1.0 OE2 A:GLU42 2.9 7.3 1.0 O2' B:C2175 2.9 8.1 1.0 O4' B:A2176 3.0 7.9 1.0 OE1 A:GLU42 3.1 12.1 1.0 O A:THR217 3.3 8.3 1.0 CD A:GLU42 3.3 8.9 1.0 N2 B:G2123 3.5 7.3 1.0 C2' B:C2175 3.6 8.3 1.0 C A:THR216 3.7 7.4 1.0 CG2 A:THR215 3.7 9.7 1.0 C A:THR217 3.8 8.6 1.0 C1' B:A2176 3.9 9.3 1.0 OG1 A:THR215 3.9 6.9 1.0 C1' B:C2175 4.0 9.3 1.0 CA A:THR217 4.0 6.8 1.0 C2 B:C2175 4.0 10.3 1.0 C4' B:A2176 4.0 7.5 1.0 N A:THR217 4.3 8.3 1.0 C5' B:A2176 4.3 9.0 1.0 N9 B:A2176 4.4 9.1 1.0 CB A:THR215 4.5 9.2 1.0 N1 B:C2175 4.5 10.1 1.0 N A:THR216 4.5 9.2 1.0 O A:GLY219 4.6 10.9 1.0 CG A:GLU42 4.7 7.7 1.0 N3 B:G2124 4.7 10.1 1.0 N A:MET218 4.8 8.4 1.0 CA A:THR216 4.8 7.1 1.0 C8 B:A2176 4.8 8.3 1.0 C2 B:G2123 4.8 9.2 1.0 O5' B:A2176 4.8 10.4 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2210 b:16.6 occ:1.00 O2' B:G2123 2.7 9.7 1.0 OE1 A:GLU42 2.8 12.1 1.0 CE1 A:HIS44 3.0 7.1 1.0 N3 B:G2123 3.0 8.0 1.0 NE2 A:HIS44 3.1 7.9 1.0 C2' B:G2123 3.2 10.5 1.0 CD A:GLU42 3.3 8.9 1.0 O4' B:G2124 3.3 8.9 1.0 C1' B:G2123 3.4 11.4 1.0 CG A:GLU42 3.5 7.7 1.0 CB A:GLU42 3.7 8.7 1.0 N2 B:G2123 3.8 7.3 1.0 CB A:HIS172 3.8 5.4 1.0 C2 B:G2123 3.8 9.2 1.0 C4 B:G2123 3.9 7.4 1.0 ND1 A:HIS44 4.0 6.9 1.0 N9 B:G2123 4.1 9.9 1.0 CD2 A:HIS44 4.2 7.3 1.0 C1' B:G2124 4.2 9.0 1.0 OE2 A:GLU42 4.3 7.3 1.0 C4' B:G2124 4.3 9.6 1.0 O4' B:G2123 4.5 9.6 1.0 C5' B:G2124 4.6 11.2 1.0 N A:ALA173 4.6 8.8 1.0 CG A:HIS44 4.6 7.2 1.0 CG A:HIS172 4.7 6.9 1.0 C3' B:G2123 4.7 10.4 1.0 O A:ALA173 4.8 7.6 1.0 CA A:HIS172 4.8 9.3 1.0 N9 B:G2124 4.9 7.2 1.0 CA A:GLU42 4.9 9.9 1.0 C A:ALA173 4.9 10.8 1.0 C A:HIS172 4.9 10.3 1.0 N3 B:A2176 4.9 7.9 1.0

S.Tishchenko, A.Gabdulkhakov, N.Nevskaya, A.Sarskikh, O.Kostareva, E.Nikonova, A.Sycheva, S.Moshkovskii, M.Garber, S.Nikonov. High-Resolution Crystal Structure of the Isolated Ribosomal L1 Stalk. Acta Crystallogr.,Sect.D V. 68 1051 2012.
ISSN: ISSN 0907-4449
PubMed: 22868771
DOI: 10.1107/S0907444912020136