Magnesium in PDB 2db3: Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa

All present enzymatic activity of Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa:
3.6.1.3;

The structure of Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa, PDB code: 2db3 was solved by T.Sengoku, O.Nureki, A.Nakamura, S.Kobayashi, S.Yokoyama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.46 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.050, 142.331, 130.465, 90.00, 90.86, 90.00
R / Rfree (%)	19.7 / 25

The binding sites of Magnesium atom in the Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa (pdb code 2db3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa, PDB code: 2db3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2801 b:37.4 occ:1.00 O A:HOH3105 2.1 24.7 1.0 O A:HOH3054 2.2 25.6 1.0 O3G A:ANP2901 2.2 24.0 1.0 O A:HOH2903 2.3 21.6 1.0 O1B A:ANP2901 2.4 24.1 1.0 O A:HOH3008 2.4 27.6 1.0 OD2 A:ASP399 3.4 32.0 1.0 PG A:ANP2901 3.5 25.8 1.0 PB A:ANP2901 3.6 26.5 1.0 OD1 A:ASP399 3.7 32.1 1.0 N3B A:ANP2901 3.7 27.1 1.0 OE2 A:GLU400 3.9 24.2 1.0 CG A:ASP399 4.0 30.5 1.0 OG1 A:THR296 4.0 26.8 1.0 CA A:GLY552 4.2 30.2 1.0 O1G A:ANP2901 4.3 28.1 1.0 O2A A:ANP2901 4.5 30.0 1.0 O3A A:ANP2901 4.5 28.5 1.0 O A:HOH2912 4.6 32.9 1.0 O2B A:ANP2901 4.6 27.5 1.0 O A:GLY552 4.7 31.5 1.0 O1A A:ANP2901 4.7 28.9 1.0 O2G A:ANP2901 4.7 27.4 1.0 CB A:LYS295 4.8 26.4 1.0 CE A:LYS295 4.8 25.8 1.0 PA A:ANP2901 4.8 30.0 1.0 N A:THR296 4.8 26.4 1.0 CD A:GLU400 4.9 28.0 1.0 C A:GLY552 5.0 30.7 1.0

Magnesium binding site 2 out of 4 in the Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2802 b:21.4 occ:1.00 O B:HOH3046 2.1 22.6 1.0 O3G B:ANP2902 2.1 21.3 1.0 O B:HOH2903 2.2 14.2 1.0 O B:HOH3118 2.2 21.4 1.0 O B:HOH3044 2.3 17.0 1.0 O1B B:ANP2902 2.3 19.1 1.0 PG B:ANP2902 3.5 22.1 1.0 PB B:ANP2902 3.6 22.6 1.0 OD2 B:ASP399 3.6 24.0 1.0 N3B B:ANP2902 3.7 21.3 1.0 OE2 B:GLU400 3.7 26.1 1.0 OD1 B:ASP399 3.8 23.9 1.0 OG1 B:THR296 3.9 20.8 1.0 CA B:GLY552 4.0 25.0 1.0 CG B:ASP399 4.1 23.8 1.0 O1G B:ANP2902 4.3 21.9 1.0 O B:HOH2935 4.4 28.1 1.0 O2A B:ANP2902 4.4 24.7 1.0 O3A B:ANP2902 4.5 21.4 1.0 O B:GLY552 4.5 25.4 1.0 CE B:LYS295 4.5 21.3 1.0 O2B B:ANP2902 4.5 21.5 1.0 O2G B:ANP2902 4.6 23.7 1.0 O1A B:ANP2902 4.8 21.7 1.0 PA B:ANP2902 4.8 23.2 1.0 CD B:GLU400 4.8 24.0 1.0 C B:GLY552 4.8 25.5 1.0 CB B:LYS295 4.8 21.5 1.0 N B:THR296 4.9 20.6 1.0 N B:GLY552 5.0 24.9 1.0 O B:HOH2909 5.0 20.5 1.0

Magnesium binding site 3 out of 4 in the Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2803 b:22.8 occ:1.00 O3G C:ANP2903 2.1 20.0 1.0 O C:HOH2905 2.2 15.8 1.0 O C:HOH3178 2.2 24.2 1.0 O C:HOH2904 2.2 19.1 1.0 O C:HOH3177 2.3 17.1 1.0 O1B C:ANP2903 2.3 17.8 1.0 PG C:ANP2903 3.5 22.2 1.0 OD2 C:ASP399 3.6 30.0 1.0 PB C:ANP2903 3.6 19.6 1.0 N3B C:ANP2903 3.8 20.5 1.0 OG1 C:THR296 3.8 23.9 1.0 OE2 C:GLU400 3.8 25.5 1.0 OD1 C:ASP399 3.8 29.1 1.0 CG C:ASP399 4.2 29.1 1.0 CA C:GLY552 4.2 21.4 1.0 O1G C:ANP2903 4.4 21.3 1.0 O2A C:ANP2903 4.4 19.7 1.0 O3A C:ANP2903 4.5 20.3 1.0 O C:GLY552 4.5 22.5 1.0 O2G C:ANP2903 4.6 22.2 1.0 O2B C:ANP2903 4.6 19.1 1.0 CE C:LYS295 4.6 24.0 1.0 O C:HOH2934 4.7 26.7 1.0 O1A C:ANP2903 4.7 18.8 1.0 PA C:ANP2903 4.8 20.3 1.0 CB C:LYS295 4.8 21.3 1.0 N C:THR296 4.8 20.5 1.0 CD C:GLU400 4.9 23.5 1.0 C C:GLY552 4.9 21.8 1.0 O C:HOH2920 5.0 25.3 1.0

Magnesium binding site 4 out of 4 in the Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2804 b:25.8 occ:1.00 O D:HOH2905 2.1 16.1 1.0 O D:HOH3095 2.2 27.9 1.0 O3G D:ANP2904 2.2 22.7 1.0 O D:HOH3096 2.2 29.7 1.0 O D:HOH3034 2.3 24.6 1.0 O1B D:ANP2904 2.3 22.1 1.0 PG D:ANP2904 3.5 22.1 1.0 PB D:ANP2904 3.6 24.0 1.0 OD2 D:ASP399 3.6 32.5 1.0 OD1 D:ASP399 3.6 32.5 1.0 N3B D:ANP2904 3.7 24.9 1.0 OE2 D:GLU400 3.9 24.0 1.0 OG1 D:THR296 3.9 27.8 1.0 CG D:ASP399 4.0 31.5 1.0 O1G D:ANP2904 4.2 23.8 1.0 CA D:GLY552 4.2 25.1 1.0 O D:HOH2916 4.5 26.8 1.0 O3A D:ANP2904 4.5 28.1 1.0 O2B D:ANP2904 4.6 23.9 1.0 CE D:LYS295 4.6 25.9 1.0 O2A D:ANP2904 4.6 30.7 1.0 O D:GLY552 4.7 25.2 1.0 O2G D:ANP2904 4.7 24.3 1.0 O1A D:ANP2904 4.8 31.7 1.0 CB D:LYS295 4.8 28.1 1.0 N D:THR296 4.8 29.4 1.0 PA D:ANP2904 4.9 31.0 1.0 CD D:GLU400 5.0 25.0 1.0 C D:GLY552 5.0 25.4 1.0

T.Sengoku, O.Nureki, A.Nakamura, S.Kobayashi, S.Yokoyama. Structural Basis For Rna Unwinding By the Dead-Box Protein Drosophila Vasa. Cell(Cambridge,Mass.) V. 125 287 2006.
ISSN: ISSN 0092-8674
PubMed: 16630817
DOI: 10.1016/J.CELL.2006.01.054