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

Protein crystallography data

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

Other elements in 3u4m:

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

Chlorine (Cl) 2 atoms
Sodium (Na) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Ribosomal Protein TTHL1 in Complex with 80NT 23S Rna From Thermus Thermophilus, PDB code: 3u4m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3u4m

Go back to Magnesium Binding Sites List in 3u4m
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg305

b:16.0
occ:1.00
O7 A:MLI302 2.4 15.8 1.0
O A:ALA35 2.4 11.0 1.0
O A:PHE37 2.4 11.4 1.0
O8 A:MLI302 2.5 13.1 1.0
O A:ALA33 2.5 13.7 1.0
OE1 A:GLU39 2.6 9.6 1.0
C2 A:MLI302 3.2 16.5 1.0
C3 A:MLI302 3.3 14.0 1.0
C A:ALA33 3.3 11.4 1.0
C A:ALA35 3.4 13.4 1.0
CD A:GLU39 3.5 12.0 1.0
N A:ALA35 3.5 10.4 1.0
C1 A:MLI302 3.5 14.6 1.0
C A:PHE37 3.6 12.4 1.0
CG A:GLU39 3.7 9.2 1.0
N A:PHE37 3.9 13.0 1.0
CA A:ALA35 4.0 11.9 1.0
C A:THR34 4.0 10.6 1.0
N A:THR34 4.0 10.8 1.0
CB A:ALA33 4.0 10.2 1.0
N A:GLU39 4.1 9.8 1.0
O6 A:MLI302 4.1 17.0 1.0
CA A:ALA33 4.2 12.1 1.0
CA A:THR34 4.2 13.0 1.0
CB A:GLU39 4.3 8.6 1.0
CB A:ALA35 4.4 10.9 1.0
O9 A:MLI302 4.4 18.5 1.0
CA A:PHE37 4.4 10.1 1.0
N A:LYS36 4.5 11.8 1.0
N A:ASP38 4.5 10.0 1.0
CA A:ASP38 4.5 10.7 1.0
OE2 A:GLU39 4.7 9.8 1.0
O A:THR34 4.8 12.3 1.0
C A:ASP38 4.8 10.7 1.0
CA A:GLU39 4.8 10.1 1.0
C A:LYS36 4.9 11.9 1.0
O A:HOH425 5.0 15.3 1.0
CA A:LYS36 5.0 13.2 1.0

Magnesium binding site 2 out of 5 in 3u4m

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Magnesium 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 Magnesium with other atoms in the Mg 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
B:Mg2206

b:14.3
occ:1.00
O4 B:U2122 2.4 10.7 1.0
O B:HOH2321 2.4 14.7 1.0
O B:HOH2302 2.4 9.5 1.0
O B:HOH2326 2.5 11.8 1.0
O B:HOH2325 2.5 14.3 1.0
O6 B:G2123 2.6 9.1 1.0
C4 B:U2122 3.1 9.4 1.0
C6 B:G2123 3.6 10.4 1.0
C5 B:U2122 3.7 8.3 1.0
O B:HOH2315 3.7 14.7 1.0
MG B:MG2207 3.7 29.8 1.0
N7 B:G2123 3.8 11.3 1.0
C5 B:G2123 4.0 9.7 1.0
N3 B:U2122 4.1 10.1 1.0
N6 B:A2176 4.3 7.9 1.0
O B:HOH2301 4.3 13.7 1.0
N4 B:C2175 4.3 10.9 1.0
O B:HOH2410 4.3 25.4 1.0
O8 B:MLI2205 4.4 27.2 1.0
O6 B:G2124 4.5 10.1 1.0
O1 B:SO42201 4.6 24.3 1.0
O B:HOH2366 4.6 19.3 1.0
O B:HOH2414 4.7 20.8 1.0
N1 B:G2123 4.8 7.6 1.0
O B:HOH2399 4.8 28.5 1.0
C6 B:U2122 4.9 8.6 1.0
O B:HOH2400 4.9 17.6 1.0

Magnesium binding site 3 out of 5 in 3u4m

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Magnesium 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 Magnesium with other atoms in the Mg 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
B:Mg2207

b:29.8
occ:1.00
O B:HOH2315 2.4 14.7 1.0
O B:HOH2304 2.5 13.0 1.0
O B:HOH2399 2.5 28.5 1.0
O B:HOH2325 2.6 14.3 1.0
O B:HOH2363 2.6 16.1 1.0
O B:HOH2321 2.8 14.7 1.0
MG B:MG2206 3.7 14.3 1.0
O B:HOH2424 3.9 17.4 1.0
O1 B:SO42201 4.1 24.3 1.0
O4 B:U2122 4.1 10.7 1.0
O B:HOH2400 4.2 17.6 1.0
MG B:MG2208 4.3 31.4 1.0
OP2 B:G2121 4.5 12.8 1.0
OP1 B:G2120 4.6 14.7 1.0
O B:HOH2372 4.7 21.5 1.0
O2 B:SO42201 4.7 27.3 1.0
S B:SO42201 4.9 26.6 1.0
O8 B:MLI2205 4.9 27.2 1.0
O B:HOH2334 4.9 17.7 1.0
N7 B:G2121 5.0 11.0 1.0
O B:HOH2326 5.0 11.8 1.0

Magnesium binding site 4 out of 5 in 3u4m

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Magnesium 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 Magnesium with other atoms in the Mg 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
B:Mg2208

b:31.4
occ:1.00
OP1 B:G2120 2.4 14.7 1.0
O B:HOH2304 2.5 13.0 1.0
O B:HOH2424 2.5 17.4 1.0
O B:HOH2376 2.6 20.5 1.0
O B:HOH2377 2.6 21.1 1.0
O B:HOH2378 2.8 33.0 1.0
O B:HOH2363 3.7 16.1 1.0
P B:G2120 3.7 12.5 1.0
O2 B:SO42201 3.9 27.3 1.0
O B:HOH2406 4.1 28.3 1.0
N7 B:G2120 4.2 16.1 1.0
MG B:MG2207 4.3 29.8 1.0
O5' B:G2120 4.4 11.9 1.0
OP2 B:G2120 4.4 11.2 1.0
C8 B:G2120 4.6 13.2 1.0
O B:HOH2372 4.6 21.5 1.0
O B:HOH2383 4.7 24.6 1.0
O B:HOH2315 4.8 14.7 1.0
O3' B:A2119 4.8 12.6 1.0
O2' B:G2110 4.9 13.3 1.0

Magnesium binding site 5 out of 5 in 3u4m

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2209

b:25.3
occ:1.00
O B:HOH2341 2.4 18.2 1.0
O B:HOH2379 2.5 23.4 1.0
O B:HOH2381 2.5 34.7 1.0
O B:HOH2380 2.6 27.6 1.0
O2 B:U2172 2.7 14.0 1.0
C2 B:U2172 3.9 15.6 1.0
C2 B:A2117 4.2 15.0 1.0
O4' B:A2119 4.3 12.7 1.0
O B:HOH2331 4.3 12.8 1.0
O B:HOH2339 4.3 19.7 1.0
C2 B:A2171 4.4 14.7 1.0
C1' B:U2172 4.5 18.8 1.0
O2' B:U2172 4.5 13.7 1.0
N1 B:U2172 4.7 14.9 1.0
O3' B:U2172 4.8 13.0 1.0
N3 B:U2172 4.8 14.4 1.0
N3 B:A2171 4.8 12.3 1.0
C4' B:A2119 4.9 11.4 1.0
N3 B:A2117 4.9 11.3 1.0
N1 B:A2117 4.9 13.2 1.0

Reference:

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
Page generated: Mon Dec 14 08:55:48 2020

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