Magnesium in PDB 3umy: Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus

The structure of Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus, PDB code: 3umy 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)	27.20 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.110, 68.820, 88.830, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.6

The structure of Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus (pdb code 3umy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus, PDB code: 3umy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2201 b:15.2 occ:1.00 O B:HOH2320 2.5 9.6 1.0 O6 B:G2123 2.6 12.2 1.0 O4 B:U2122 2.6 11.9 1.0 O B:HOH2328 2.6 16.9 1.0 O B:HOH2324 2.7 19.4 1.0 O B:HOH2323 2.7 24.8 1.0 C4 B:U2122 3.4 12.4 1.0 C6 B:G2123 3.6 9.0 1.0 O B:HOH2364 3.8 22.8 1.0 O B:HOH2356 3.8 17.9 1.0 C5 B:U2122 3.9 8.1 1.0 N7 B:G2123 4.0 8.3 1.0 N4 B:C2175 4.0 7.4 1.0 N6 B:A2176 4.1 8.1 1.0 C5 B:G2123 4.1 12.6 1.0 N3 B:U2122 4.3 7.8 1.0 O B:HOH2311 4.4 18.9 1.0 O6 B:G2124 4.4 9.6 1.0 O B:HOH2331 4.4 13.0 1.0 O B:HOH2365 4.7 16.3 1.0 O B:HOH2305 4.8 23.2 1.0 N1 B:G2123 4.8 8.9 1.0 C6 B:A2176 4.9 14.5 1.0 O B:HOH2363 4.9 17.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2202 b:24.6 occ:1.00 O2 B:C2128 2.7 15.8 1.0 O2' B:A2173 2.7 15.3 1.0 O B:HOH2327 2.8 21.2 1.0 O2' B:C2128 2.8 10.3 1.0 O4' B:C2129 3.3 12.0 1.0 C2' B:C2128 3.4 17.4 1.0 C2' B:A2173 3.5 12.9 1.0 C5' B:C2174 3.5 11.1 1.0 C1' B:C2128 3.6 9.7 1.0 C2 B:C2128 3.9 15.6 1.0 N2 B:G2160 3.9 13.7 1.0 O B:HOH2378 3.9 21.9 1.0 O3' B:A2173 4.0 12.5 1.0 C1' B:C2129 4.0 11.3 1.0 C4' B:C2174 4.1 10.7 1.0 N1 B:C2128 4.3 16.6 1.0 C3' B:A2173 4.3 13.7 1.0 O4' B:C2174 4.3 14.8 1.0 C4' B:C2129 4.4 15.6 1.0 O2 B:C2161 4.5 13.6 1.0 O5' B:C2174 4.5 16.0 1.0 N1 B:C2129 4.6 12.3 1.0 O4' B:C2128 4.7 14.2 1.0 O B:HOH2325 4.7 21.0 1.0 C1' B:A2173 4.8 14.1 1.0 C5' B:C2129 4.8 16.1 1.0 C6 B:C2129 4.8 14.1 1.0 C3' B:C2128 4.8 16.5 1.0 P B:C2174 4.8 15.2 1.0 N2 B:G2127 4.8 12.7 1.0 OP1 B:C2174 4.9 14.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2203 b:32.9 occ:1.00 O B:HOH2357 2.7 22.4 1.0 OP2 B:G2155 2.8 18.1 1.0 O B:HOH2353 2.8 21.7 1.0 N7 B:G2156 2.8 17.1 1.0 O6 B:G2157 3.0 23.1 1.0 O B:HOH2368 3.4 25.5 1.0 O6 B:G2156 3.4 17.4 1.0 O B:HOH2410 3.6 16.2 1.0 P B:G2155 3.7 17.4 1.0 C5 B:G2156 3.7 16.2 1.0 O5' B:G2155 3.7 13.9 1.0 C8 B:G2156 3.8 12.7 1.0 C6 B:G2157 3.9 18.0 1.0 C6 B:G2156 3.9 16.1 1.0 O B:HOH2350 4.2 21.2 1.0 C8 B:G2155 4.2 16.3 1.0 N7 B:G2155 4.2 17.3 1.0 OP1 B:G2155 4.3 10.5 1.0 OP2 B:G2156 4.4 11.8 1.0 N1 B:G2157 4.7 14.6 1.0 C5 B:G2157 4.7 21.3 1.0 O B:HOH2402 4.9 23.9 1.0 N7 B:G2157 4.9 20.6 1.0 C4 B:G2156 4.9 14.2 1.0 C5' B:G2155 5.0 13.7 1.0 N9 B:G2156 5.0 12.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2204 b:40.6 occ:1.00 O B:HOH2375 2.7 25.7 1.0 O B:HOH2371 2.8 11.9 1.0 O B:HOH2374 2.8 22.7 1.0 O6 B:G2125 2.8 13.7 1.0 C6 B:G2125 3.7 12.8 1.0 N7 B:G2125 4.1 9.7 1.0 C5 B:G2125 4.2 8.7 1.0 O B:HOH2331 4.6 13.0 1.0 N1 B:G2125 4.7 11.2 1.0 O B:HOH2314 4.8 25.4 1.0 O B:HOH2317 4.8 12.8 1.0

S.V.Tishchenko, E.Y.Nikonova, O.S.Kostareva, A.G.Gabdulkhakov, A.V.Sarskikh, W.Piendl, S.V.Nikonov, M.B.Garber, N.A.Nevskaya. Crystal Structure of Mutant Ribosomal Protein T217A TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus To Be Published.