Magnesium in PDB 1mji: Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex

The structure of Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex, PDB code: 1mji was solved by A.Perederina, N.Nevskaya, O.Nikonov, A.Nikulin, P.Dumas, M.Yao, I.Tanaka, M.Garber, G.Gongadze, S.Nikonov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.91 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.890, 99.600, 65.730, 90.00, 100.05, 90.00
R / Rfree (%)	21 / 28.8

The structure of Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex (pdb code 1mji). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex, PDB code: 1mji:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:25.1 occ:1.00 O2 C:C47 2.4 17.7 1.0 O4' C:U48 2.8 24.6 1.0 O2' C:C38 2.9 36.6 1.0 O4' C:A39 3.2 28.0 1.0 O2' C:C47 3.5 21.0 1.0 C2 C:C47 3.5 16.0 1.0 C1' C:U48 3.6 24.2 1.0 C2' C:C47 3.7 20.6 1.0 C4' C:U48 3.8 25.9 1.0 O2 C:C38 3.8 35.7 1.0 C2' C:C38 3.8 37.1 1.0 C4' C:A39 3.9 30.0 1.0 C1' C:C47 4.0 17.6 1.0 C1' C:A39 4.0 25.1 1.0 N1 C:C47 4.2 16.7 1.0 C5' C:U48 4.3 24.2 1.0 N1 C:U48 4.3 23.7 1.0 N3 C:C47 4.4 14.7 1.0 C5' C:A39 4.4 32.7 1.0 C1' C:C38 4.5 36.3 1.0 C6 C:U48 4.7 22.8 1.0 C2' C:U48 4.7 26.0 1.0 N2 C:G44 4.8 20.3 1.0 O2' C:U48 4.9 25.3 1.0 O2' C:A39 4.9 29.1 1.0 C2 C:C38 4.9 34.1 1.0 N9 C:A39 4.9 23.9 1.0 O5' C:U48 4.9 24.4 1.0

Magnesium binding site 2 out of 4 in the Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg204 b:32.2 occ:1.00 O2' D:C38 2.5 36.3 1.0 O2 D:C47 2.8 18.3 1.0 O4' D:U48 3.0 24.9 1.0 O4' D:A39 3.1 23.6 1.0 O2' D:C47 3.4 24.4 1.0 C2' D:C38 3.4 35.9 1.0 C4' D:A39 3.6 24.8 1.0 C2' D:C47 3.7 21.3 1.0 O2 D:C38 3.8 31.4 1.0 C1' D:U48 3.8 24.4 1.0 C4' D:U48 3.9 25.6 1.0 C2 D:C47 3.9 17.1 1.0 C5' D:A39 4.0 26.5 1.0 C1' D:A39 4.1 21.9 1.0 C1' D:C47 4.2 19.2 1.0 C1' D:C38 4.2 34.5 1.0 C5' D:U48 4.4 24.8 1.0 N1 D:C47 4.6 17.0 1.0 N1 D:U48 4.6 21.2 1.0 O D:HOH223 4.6 26.6 1.0 C3' D:C38 4.8 36.6 1.0 C2 D:C38 4.8 29.6 1.0 O2' D:A39 4.8 24.1 1.0 N3 D:C47 4.9 17.9 1.0 O5' D:A39 4.9 32.2 1.0 C2' D:U48 4.9 27.1 1.0 O3' D:C38 5.0 33.2 1.0 O2' D:U48 5.0 27.2 1.0 C2' D:A39 5.0 22.9 1.0 C6 D:U48 5.0 19.6 1.0

Magnesium binding site 3 out of 4 in the Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:13.0 occ:1.00 O A:THR161 2.6 21.5 1.0 O A:ARG128 2.7 26.5 1.0 O A:ALA163 2.8 24.8 1.0 OD1 A:ASN130 2.9 21.3 1.0 O C:HOH211 3.0 28.3 1.0 C A:THR161 3.5 19.8 1.0 CG A:ASN130 3.6 22.0 1.0 O A:GLY129 3.8 24.3 1.0 O A:HOH215 3.8 29.7 1.0 C A:GLY129 3.8 23.6 1.0 ND2 A:ASN130 3.8 22.1 1.0 C A:ARG128 3.9 25.1 1.0 CA A:GLY129 3.9 23.2 1.0 C A:ALA163 4.0 24.7 1.0 OG1 A:THR161 4.1 21.7 1.0 N A:ALA163 4.2 22.9 1.0 N A:THR161 4.2 19.3 1.0 C A:THR162 4.2 22.4 1.0 N A:THR162 4.3 19.4 1.0 CA A:THR162 4.3 20.8 1.0 N A:GLY129 4.4 23.8 1.0 N A:ASN130 4.4 23.0 1.0 CA A:THR161 4.4 19.6 1.0 CA A:ALA163 4.7 23.8 1.0 O A:THR162 4.8 24.4 1.0 CB A:ASN130 4.9 21.6 1.0 CB A:THR161 4.9 20.3 1.0 CA A:ASN130 5.0 23.6 1.0 CG1 A:VAL160 5.0 14.1 1.0

Magnesium binding site 4 out of 4 in the Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:7.1 occ:1.00 O B:HOH219 2.4 31.7 1.0 O B:THR161 2.5 19.4 1.0 O B:ARG128 2.7 29.2 1.0 O B:ALA163 2.7 25.7 1.0 OD1 B:ASN130 3.0 19.6 1.0 C B:THR161 3.5 18.9 1.0 CG B:ASN130 3.7 18.3 1.0 C B:ARG128 3.7 26.6 1.0 C B:ALA163 3.8 23.8 1.0 O B:GLY129 3.8 24.3 1.0 C B:GLY129 3.9 23.2 1.0 ND2 B:ASN130 3.9 17.1 1.0 CA B:GLY129 4.0 23.8 1.0 O B:HOH252 4.0 41.8 1.0 N B:ALA163 4.1 21.3 1.0 OG1 B:THR161 4.2 19.3 1.0 N B:THR161 4.3 17.3 1.0 N B:GLY129 4.3 24.8 1.0 C B:THR162 4.3 20.6 1.0 N B:THR162 4.4 19.1 1.0 CA B:THR161 4.4 18.3 1.0 N B:ASN130 4.5 21.4 1.0 CA B:THR162 4.5 19.4 1.0 CA B:ALA163 4.6 22.3 1.0 CB B:ARG128 4.8 28.3 1.0 N B:GLU164 4.8 25.2 1.0 CA B:ARG128 4.9 27.0 1.0 O B:THR162 4.9 22.6 1.0 CB B:THR161 4.9 18.6 1.0 CA B:GLU164 5.0 27.1 1.0 CB B:ASN130 5.0 19.8 1.0

A.Perederina, N.Nevskaya, O.Nikonov, A.Nikulin, P.Dumas, M.Yao, I.Tanaka, M.Garber, G.Gongadze, S.Nikonov. Detailed Analysis of Rna-Protein Interactions Within the Bacterial Ribosomal Protein L5/5S Rrna Complex Rna V. 8 1548 2002.
ISSN: ISSN 1355-8382
PubMed: 12515387