Magnesium in PDB 5aox: Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation

The structure of Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation, PDB code: 5aox was solved by V.Ahl, O.Weichenrieder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.75 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.480, 56.730, 170.590, 90.00, 93.69, 90.00
R / Rfree (%)	18.6 / 22.2

The binding sites of Magnesium atom in the Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation (pdb code 5aox). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation, PDB code: 5aox:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:24.5 occ:1.00 O C:HOH2113 2.1 19.3 1.0 O C:HOH2111 2.1 23.1 1.0 O C:HOH2112 2.1 21.0 1.0 OP2 C:A57 2.1 29.0 1.0 O C:HOH2110 2.1 17.9 1.0 O6 C:G59 2.1 17.5 1.0 C6 C:G59 3.2 16.8 1.0 P C:A57 3.6 32.0 1.0 H5'' C:A57 3.7 36.1 1.0 N7 C:G59 3.8 17.3 1.0 C5 C:G59 3.8 16.6 1.0 O6 C:G106 3.9 19.0 1.0 H2' C:G56 4.1 29.5 1.0 OP1 C:G58 4.1 24.6 1.0 H3' C:G56 4.1 31.4 1.0 N7 C:G58 4.2 17.2 1.0 O C:HOH2108 4.2 13.7 1.0 OP1 C:A57 4.3 33.0 1.0 N1 C:G59 4.3 16.0 1.0 H1 C:G59 4.4 19.2 1.0 O5' C:A57 4.4 29.6 1.0 C5' C:A57 4.4 30.1 1.0 O3' C:G56 4.4 29.7 1.0 C6 C:G106 4.5 18.1 1.0 H1 C:G106 4.6 21.2 1.0 C3' C:G56 4.6 26.1 1.0 H5' C:A57 4.7 36.1 1.0 H8 C:G58 4.8 21.3 1.0 N1 C:G106 4.8 17.7 1.0 C2' C:G56 4.8 24.6 1.0 C8 C:G58 4.9 17.8 1.0 O C:HOH2138 5.0 24.5 1.0

Magnesium binding site 2 out of 4 in the Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1111 b:42.5 occ:1.00 O C:HOH2047 2.1 37.5 1.0 O C:HOH2046 2.1 37.1 1.0 O C:HOH2086 2.1 25.6 1.0 O6 C:G41 2.2 28.7 1.0 O2' C:U17 2.6 19.2 1.0 HO2' C:U17 2.9 23.0 1.0 H61 C:A33 3.2 29.4 1.0 C6 C:G41 3.2 28.5 1.0 O3' C:U17 3.5 20.9 1.0 H41 C:C32 3.5 34.6 1.0 N7 C:G41 3.6 25.9 1.0 C5 C:G41 3.7 28.1 1.0 H4' C:U17 3.8 27.7 1.0 N6 C:A33 3.8 24.5 1.0 C2' C:U17 3.8 21.7 1.0 N1 C:A33 3.9 26.5 1.0 O C:HOH2087 4.0 48.1 1.0 C3' C:U17 4.1 20.5 1.0 H5' C:C18 4.1 28.1 1.0 C6 C:A33 4.3 26.2 1.0 N4 C:C32 4.3 28.8 1.0 H2' C:U17 4.3 26.1 1.0 H62 C:A33 4.4 29.4 1.0 OP1 C:C18 4.4 25.5 1.0 H42 C:C32 4.4 34.6 1.0 N1 C:G41 4.5 28.6 1.0 C4' C:U17 4.5 23.1 1.0 H1 C:G41 4.6 34.3 1.0 O6 C:G42 4.6 32.8 1.0 P C:C18 4.7 26.7 1.0 C8 C:G41 4.8 29.0 1.0 H1' C:U17 4.9 24.8 1.0 C1' C:U17 4.9 20.7 1.0 C2 C:A33 4.9 28.3 1.0 H5'' C:C18 4.9 28.1 1.0 C5' C:C18 4.9 23.5 1.0 H2 C:A33 5.0 34.0 1.0

Magnesium binding site 3 out of 4 in the Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1131 b:36.7 occ:1.00 O C:HOH2142 2.1 30.5 1.0 O C:HOH2011 2.1 18.5 1.0 OP1 C:C108 2.1 13.1 1.0 O C:HOH2012 2.1 28.0 1.0 O C:HOH2015 2.1 18.7 1.0 O C:HOH2141 2.1 35.4 1.0 P C:C108 3.4 13.1 1.0 H5'' C:C108 3.6 15.3 1.0 H22 C:G5 3.7 14.0 1.0 O5' C:C108 4.0 12.9 1.0 O C:HOH2006 4.0 24.5 1.0 OP2 C:C108 4.0 13.4 1.0 O2' C:G5 4.1 13.7 1.0 O C:HOH2055 4.2 26.4 1.0 C5' C:C108 4.2 12.7 1.0 N3 C:G5 4.4 12.2 1.0 HO2' C:G5 4.5 16.4 1.0 H1' C:G5 4.5 15.9 1.0 N2 C:G5 4.5 11.6 1.0 H5' C:C108 4.5 15.3 1.0 H2' C:G5 4.6 16.1 1.0 O4' C:G6 4.6 14.9 1.0 O3' C:A107 4.6 12.8 1.0 O C:HOH2057 4.6 19.7 1.0 H1' C:G6 4.7 15.6 1.0 H4' C:G6 4.7 19.9 1.0 C2' C:G5 4.8 13.4 1.0 O C:HOH2143 4.9 21.0 1.0 HO2' C:G6 4.9 15.4 1.0 C2 C:G5 5.0 11.8 1.0 H1' C:G25 5.0 13.6 1.0

Magnesium binding site 4 out of 4 in the Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Alu Rna Retrotransposition Complex in the Ribosome-Stalling Conformation within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1131 b:43.9 occ:1.00 O F:HOH2007 2.1 25.4 1.0 O F:HOH2062 2.1 39.9 1.0 OP1 F:C108 2.1 31.3 1.0 O F:HOH2066 2.1 35.1 1.0 O F:HOH2061 2.1 38.0 1.0 O F:HOH2010 2.1 40.8 1.0 P F:C108 3.4 31.3 1.0 H5'' F:C108 3.7 37.9 1.0 H22 F:G5 3.8 30.3 1.0 OP2 F:C108 3.9 31.8 1.0 O5' F:C108 4.1 32.0 1.0 O F:HOH2002 4.2 30.6 1.0 O2' F:G5 4.3 25.4 1.0 C5' F:C108 4.3 31.6 1.0 O4' F:G6 4.5 28.8 1.0 O F:HOH2032 4.5 32.6 1.0 N3 F:G5 4.5 24.9 1.0 HO2' F:G5 4.6 30.5 1.0 O3' F:A107 4.6 30.8 1.0 H1' F:G5 4.6 32.8 1.0 N2 F:G5 4.6 25.2 1.0 H5' F:C108 4.6 37.9 1.0 H1' F:G6 4.7 31.6 1.0 H2' F:G5 4.7 31.8 1.0 O F:HOH2063 4.7 34.8 1.0 H4' F:G6 4.7 35.3 1.0 O F:HOH2034 4.7 26.7 1.0 HO2' F:G6 4.9 33.9 1.0 C2' F:G5 4.9 26.5 1.0 OP2 F:C109 5.0 43.3 1.0

V.Ahl, H.Keller, S.Schmidt, O.Weichenrieder. Retrotransposition and Crystal Structure of An Alu Rnp in the Ribosome-Stalling Conformation. Mol.Cell V. 60 715 2015.
ISSN: ISSN 1097-2765
PubMed: 26585389
DOI: 10.1016/J.MOLCEL.2015.10.003