Magnesium in PDB 3u56: Crystal Structure of Mutant Ribosomal Protein T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus

The structure of Crystal Structure of Mutant Ribosomal Protein T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus, PDB code: 3u56 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)	28.30 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.690, 75.410, 85.880, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.8

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>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Mutant Ribosomal Protein T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus (pdb code 3u56). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Crystal Structure of Mutant Ribosomal Protein T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus, PDB code: 3u56:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Crystal Structure of Mutant Ribosomal Protein T217V 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 T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:17.2 occ:1.00 O2' B:C2175 2.2 15.4 1.0 O A:THR216 2.4 11.3 1.0 OG1 A:THR215 2.5 6.1 1.0 O A:HOH404 2.5 9.5 1.0 O A:GLY219 2.6 17.0 1.0 O4' B:A2176 2.9 14.6 1.0 CG2 A:THR215 3.3 15.9 1.0 C4' B:A2176 3.4 16.1 1.0 C5' B:A2176 3.4 15.5 1.0 C2' B:C2175 3.4 14.4 1.0 CB A:THR215 3.4 14.4 1.0 C A:THR216 3.5 10.9 1.0 C A:GLY219 3.8 10.3 1.0 O A:VAL217 3.8 11.2 1.0 N A:THR216 3.8 12.0 1.0 N A:GLY219 3.9 10.5 1.0 C A:VAL217 4.0 13.8 1.0 C1' B:A2176 4.1 12.4 1.0 C1' B:C2175 4.1 14.8 1.0 O2 B:C2175 4.2 12.1 1.0 O5' B:A2176 4.2 12.5 1.0 CA A:THR216 4.4 11.9 1.0 CA A:GLY219 4.4 12.1 1.0 C A:THR215 4.4 11.7 1.0 N A:VAL217 4.5 9.6 1.0 O A:PRO220 4.5 13.8 1.0 OE2 A:GLU42 4.5 13.0 1.0 CA A:THR215 4.5 10.2 1.0 N A:MET218 4.5 13.8 1.0 CA A:VAL217 4.5 12.3 1.0 C3' B:C2175 4.5 14.3 1.0 O3' B:C2175 4.6 19.4 1.0 C A:MET218 4.7 13.3 1.0 C3' B:A2176 4.8 17.4 1.0 C A:PRO220 4.8 14.2 1.0 N A:PRO220 4.8 10.8 1.0 N9 B:A2176 4.9 14.4 1.0 CD A:GLU42 4.9 10.5 1.0 CA A:MET218 4.9 12.5 1.0 OG1 A:THR216 4.9 16.5 1.0 OE1 A:GLU42 5.0 9.8 1.0

Magnesium binding site 2 out of 11 in the Crystal Structure of Mutant Ribosomal Protein T217V 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 T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2202 b:24.8 occ:1.00 O B:HOH2307 2.4 18.9 1.0 O B:HOH2308 2.5 24.7 1.0 O B:HOH2311 2.5 14.6 1.0 O B:HOH2309 2.5 22.7 1.0 O B:HOH2313 2.7 34.1 1.0 O B:HOH2310 2.7 23.8 1.0 MG B:MG2203 3.6 29.2 1.0 O B:HOH2369 3.8 29.5 1.0 N6 B:A2169 4.1 19.9 1.0 N1 B:A2170 4.2 20.3 1.0 N1 B:A2169 4.3 19.2 1.0 O B:HOH2312 4.3 20.6 1.0 C2 B:A2170 4.3 18.2 1.0 O B:HOH2337 4.4 24.6 1.0 O B:HOH2316 4.5 23.7 1.0 O2' B:A2119 4.6 16.5 1.0 OP1 B:G2112 4.6 29.3 1.0 C6 B:A2169 4.7 19.7 1.0

Magnesium binding site 3 out of 11 in the Crystal Structure of Mutant Ribosomal Protein T217V 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 T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2203 b:29.2 occ:1.00 O B:HOH2312 2.3 20.6 1.0 OP1 B:C2111 2.3 32.2 1.0 O B:HOH2313 2.4 34.1 1.0 O B:HOH2310 2.5 23.8 1.0 O B:HOH2316 2.7 23.7 1.0 O B:HOH2314 2.7 30.2 1.0 P B:C2111 3.5 26.2 1.0 MG B:MG2202 3.6 24.8 1.0 O3' B:G2110 3.7 22.8 1.0 C5' B:C2111 3.9 26.2 1.0 O B:HOH2309 3.9 22.7 1.0 O5' B:C2111 4.2 25.1 1.0 OP2 B:G2112 4.2 34.1 1.0 O B:HOH2337 4.6 24.6 1.0 C4' B:C2111 4.6 28.7 1.0 O B:HOH2308 4.6 24.7 1.0 C3' B:C2111 4.8 31.2 1.0 OP2 B:C2111 4.8 25.3 1.0 O B:HOH2369 4.8 29.5 1.0 O2' B:G2110 4.9 20.6 1.0

Magnesium binding site 4 out of 11 in the Crystal Structure of Mutant Ribosomal Protein T217V 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 T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2204 b:24.0 occ:1.00 O B:HOH2351 2.5 22.1 1.0 O B:HOH2353 2.5 19.4 1.0 O B:HOH2371 2.5 22.1 1.0 O6 B:G2156 2.6 17.2 1.0 O B:HOH2352 2.6 21.4 1.0 C6 B:G2156 3.5 20.4 1.0 O B:HOH2345 3.5 24.6 1.0 MG B:MG2206 3.6 23.1 1.0 O B:HOH2389 3.8 27.6 1.0 N1 B:G2156 4.0 17.3 1.0 O2' B:G2133 4.1 19.1 1.0 O B:HOH2323 4.4 32.3 1.0 OP2 B:A2134 4.5 16.2 1.0 C5 B:G2156 4.5 20.2 1.0 N7 B:G2155 4.6 19.7 1.0 O B:HOH2373 4.7 25.6 1.0 O B:HOH2372 4.9 20.2 1.0 O B:HOH2384 4.9 27.0 1.0 O6 B:G2155 4.9 18.1 1.0

Magnesium binding site 5 out of 11 in the Crystal Structure of Mutant Ribosomal Protein T217V 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 5 of Crystal Structure of Mutant Ribosomal Protein T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2205 b:24.9 occ:1.00 OP1 B:C2139 2.5 22.5 1.0 O B:HOH2358 2.7 16.3 1.0 O B:HOH2359 2.7 24.0 1.0 O B:HOH2360 2.9 34.6 1.0 P B:C2139 3.6 21.1 1.0 O3' B:C2138 3.7 19.5 1.0 C5' B:C2139 3.9 20.8 1.0 O5' B:C2139 4.2 19.9 1.0 OP2 B:C2139 4.9 31.6 1.0

Magnesium binding site 6 out of 11 in the Crystal Structure of Mutant Ribosomal Protein T217V 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 6 of Crystal Structure of Mutant Ribosomal Protein T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2206 b:23.1 occ:1.00 O B:HOH2372 2.5 20.2 1.0 O6 B:G2156 2.5 17.2 1.0 O6 B:G2157 2.5 21.3 1.0 O B:HOH2371 2.5 22.1 1.0 O B:HOH2373 2.7 25.6 1.0 MG B:MG2209 3.0 25.8 1.0 C6 B:G2156 3.4 20.4 1.0 C6 B:G2157 3.5 23.4 1.0 N7 B:G2156 3.6 20.3 1.0 MG B:MG2204 3.6 24.0 1.0 N1 B:G2157 3.8 20.3 1.0 C5 B:G2156 3.9 20.2 1.0 O2' B:G2133 4.1 19.1 1.0 O B:HOH2353 4.3 19.4 1.0 O B:HOH2351 4.3 22.1 1.0 O B:HOH2389 4.4 27.6 1.0 OP2 B:G2155 4.6 20.2 1.0 N1 B:G2156 4.7 17.3 1.0 C5 B:G2157 4.7 23.4 1.0 C8 B:G2156 4.8 22.7 1.0

Magnesium binding site 7 out of 11 in the Crystal Structure of Mutant Ribosomal Protein T217V 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 7 of Crystal Structure of Mutant Ribosomal Protein T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2207 b:30.1 occ:1.00 O B:HOH2382 2.4 15.8 1.0 O B:HOH2381 2.5 18.4 1.0 O B:HOH2375 2.7 14.7 1.0 O6 B:G2123 2.7 10.8 1.0 O4 B:U2122 2.8 12.3 1.0 C4 B:U2122 3.6 11.6 1.0 C6 B:G2123 3.7 13.2 1.0 N4 B:C2175 4.0 13.8 1.0 C5 B:U2122 4.0 15.0 1.0 N7 B:G2123 4.1 14.5 1.0 C5 B:G2123 4.3 11.6 1.0 O6 B:G2124 4.3 15.3 1.0 N6 B:A2176 4.4 16.8 1.0 O B:HOH2383 4.5 14.9 1.0 N3 B:U2122 4.7 11.3 1.0 O B:HOH2334 4.8 16.4 1.0 N4 B:C2174 4.9 17.3 1.0 N1 B:G2123 5.0 9.6 1.0

Magnesium binding site 8 out of 11 in the Crystal Structure of Mutant Ribosomal Protein T217V 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 8 of Crystal Structure of Mutant Ribosomal Protein T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2208 b:29.4 occ:1.00 O6 B:G2125 2.4 25.3 1.0 O B:HOH2395 2.5 33.7 1.0 O B:HOH2394 2.6 25.2 1.0 O B:HOH2376 2.6 15.6 1.0 O B:HOH2383 2.7 14.9 1.0 C6 B:G2125 3.4 16.6 1.0 N7 B:G2125 3.9 13.6 1.0 C5 B:G2125 4.0 12.0 1.0 OP2 B:G2124 4.2 15.6 1.0 N1 B:G2125 4.6 21.4 1.0 N7 B:G2124 4.7 16.1 1.0 O B:HOH2381 4.9 18.4 1.0 OP1 B:U2172 5.0 30.9 1.0

Magnesium binding site 9 out of 11 in the Crystal Structure of Mutant Ribosomal Protein T217V 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 9 of Crystal Structure of Mutant Ribosomal Protein T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2209 b:25.8 occ:1.00 O B:HOH2387 2.5 26.3 1.0 O6 B:G2157 2.5 21.3 1.0 O B:HOH2385 2.6 19.9 1.0 O B:HOH2372 2.6 20.2 1.0 O B:HOH2386 2.8 26.9 1.0 MG B:MG2206 3.0 23.1 1.0 C6 B:G2157 3.7 23.4 1.0 O B:HOH2374 4.0 24.4 1.0 O B:HOH2388 4.1 29.6 1.0 N7 B:G2156 4.1 20.3 1.0 N7 B:G2157 4.1 22.9 1.0 C5 B:G2157 4.3 23.4 1.0 OP2 B:G2156 4.4 20.1 1.0 O B:HOH2373 4.5 25.6 1.0 N1 B:G2157 4.8 20.3 1.0 C8 B:G2156 4.9 22.7 1.0 O6 B:G2156 4.9 17.2 1.0 OP2 B:G2155 4.9 20.2 1.0

Magnesium binding site 10 out of 11 in the Crystal Structure of Mutant Ribosomal Protein T217V 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 10 of Crystal Structure of Mutant Ribosomal Protein T217V TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2210 b:35.6 occ:1.00 O B:HOH2378 2.4 25.7 1.0 O6 B:G2149 2.4 32.7 1.0 O4 B:U2150 2.6 27.2 1.0 O B:HOH2326 2.8 26.4 1.0 O B:HOH2342 3.1 34.6 1.0 C6 B:G2149 3.5 30.7 1.0 C4 B:U2150 3.5 28.6 1.0 O6 B:G2141 3.7 28.6 1.0 N4 B:C2142 3.9 22.5 1.0 MG B:MG2211 4.0 36.3 1.0 N3 B:U2150 4.0 29.7 1.0 N7 B:G2149 4.0 30.5 1.0 C5 B:G2149 4.1 30.6 1.0 O6 B:G2148 4.2 38.3 1.0 O6 B:G2151 4.5 22.7 1.0 C6 B:G2148 4.6 31.8 1.0 N1 B:G2149 4.6 28.0 1.0 C5 B:U2150 4.6 33.5 1.0 O B:HOH2328 4.8 17.6 1.0 N4 B:C2140 4.8 20.8 1.0 C6 B:G2141 4.9 26.9 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 Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus To Be Published.