Magnesium in PDB 4d25: Crystal Structure of the Bombyx Mori Vasa Helicase (E339Q) in Complex with Rna and Amppnp

The structure of Crystal Structure of the Bombyx Mori Vasa Helicase (E339Q) in Complex with Rna and Amppnp, PDB code: 4d25 was solved by P.Spinelli, R.S.Pillai, J.Kadlec, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.91 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.480, 78.570, 104.580, 90.00, 90.00, 90.00
R / Rfree (%)	17.142 / 20.837

The binding sites of Magnesium atom in the Crystal Structure of the Bombyx Mori Vasa Helicase (E339Q) in Complex with Rna and Amppnp (pdb code 4d25). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Bombyx Mori Vasa Helicase (E339Q) in Complex with Rna and Amppnp, PDB code: 4d25:

Magnesium binding site 1 out of 1 in the Crystal Structure of the Bombyx Mori Vasa Helicase (E339Q) in Complex with Rna and Amppnp


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 the Bombyx Mori Vasa Helicase (E339Q) in Complex with Rna and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1565 b:9.1 occ:1.00 O1G A:ANP1564 2.0 8.3 1.0 O2B A:ANP1564 2.0 7.9 1.0 O A:HOH2186 2.1 7.0 1.0 O A:HOH2098 2.2 7.2 1.0 O A:HOH2099 2.2 6.4 1.0 O A:HOH2187 2.3 7.9 1.0 PG A:ANP1564 3.2 8.2 1.0 PB A:ANP1564 3.2 7.8 1.0 N3B A:ANP1564 3.4 7.9 1.0 OD2 A:ASP338 3.9 9.6 1.0 NE2 A:GLN339 3.9 8.4 1.0 OG1 A:THR231 3.9 7.7 1.0 OD1 A:ASP338 3.9 9.0 1.0 O2G A:ANP1564 4.0 8.1 1.0 O1A A:ANP1564 4.3 8.4 1.0 O3A A:ANP1564 4.3 7.9 1.0 CA A:GLY494 4.3 8.1 1.0 O1B A:ANP1564 4.3 7.6 1.0 CG A:ASP338 4.3 9.1 1.0 O3G A:ANP1564 4.4 8.2 1.0 CE A:LYS230 4.4 7.4 1.0 O A:GLY494 4.4 8.3 1.0 O A:HOH2189 4.4 6.0 1.0 O2A A:ANP1564 4.5 8.2 1.0 PA A:ANP1564 4.5 8.1 1.0 CB A:LYS230 4.6 7.6 1.0 N A:THR231 4.8 7.7 1.0 C A:GLY494 4.9 8.3 1.0 NZ A:LYS230 4.9 7.5 1.0

J.Xiol, P.Spinelli, M.A.Laussmann, D.Homolka, Z.Yang, E.Cora, Y.Coute, S.Conn, J.Kadlec, R.Sachidanandam, M.Kaksonen, S.Cusack, A.Ephrussi, R.S.Pillai. Rna Clamping By Vasa Assembles A Pirna Amplifier Complex on Transposon Transcripts. Cell(Cambridge,Mass.) V. 157 1698 2014.
ISSN: ISSN 0092-8674
PubMed: 24910301
DOI: 10.1016/J.CELL.2014.05.018