Magnesium in PDB 5i8q: S. Cerevisiae PRP43 in Complex with Rna and Adpnp

All present enzymatic activity of S. Cerevisiae PRP43 in Complex with Rna and Adpnp:
3.6.4.13;

The structure of S. Cerevisiae PRP43 in Complex with Rna and Adpnp, PDB code: 5i8q was solved by Y.He, K.H.Nielsen, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.45 / 4.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	168.063, 154.031, 78.988, 90.00, 90.00, 90.00
R / Rfree (%)	26 / 28.6

The binding sites of Magnesium atom in the S. Cerevisiae PRP43 in Complex with Rna and Adpnp (pdb code 5i8q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the S. Cerevisiae PRP43 in Complex with Rna and Adpnp, PDB code: 5i8q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the S. Cerevisiae PRP43 in Complex with Rna and Adpnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S. Cerevisiae PRP43 in Complex with Rna and Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:0.8 occ:1.00 O1B A:ANP802 2.0 0.0 1.0 O3G A:ANP802 2.0 0.1 1.0 OG1 A:THR123 2.1 0.5 1.0 OD2 A:ASP215 2.5 0.2 1.0 OG A:SER382 2.9 0.0 1.0 PG A:ANP802 3.1 0.8 1.0 PB A:ANP802 3.2 0.0 1.0 CB A:THR123 3.4 1.0 1.0 N3B A:ANP802 3.4 0.2 1.0 CG A:ASP215 3.5 0.9 1.0 O1G A:ANP802 3.5 0.3 1.0 OD1 A:ASP215 3.7 0.3 1.0 N A:THR123 3.7 0.5 1.0 O2B A:ANP802 3.9 0.5 1.0 CE A:LYS122 4.1 0.7 1.0 CA A:THR123 4.1 0.8 1.0 CB A:LYS122 4.2 0.5 1.0 CB A:SER382 4.2 0.6 1.0 NZ A:LYS122 4.4 0.4 1.0 O2G A:ANP802 4.4 0.3 1.0 O2A A:ANP802 4.4 0.5 1.0 CG2 A:THR123 4.4 0.0 1.0 O3A A:ANP802 4.5 0.6 1.0 CA A:SER382 4.7 0.1 1.0 C A:LYS122 4.7 0.3 1.0 CB A:ASP215 4.9 0.9 1.0 CA A:LYS122 4.9 0.9 1.0 PA A:ANP802 5.0 0.1 1.0

Magnesium binding site 2 out of 2 in the S. Cerevisiae PRP43 in Complex with Rna and Adpnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S. Cerevisiae PRP43 in Complex with Rna and Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:0.0 occ:1.00 OG1 B:THR123 2.0 0.4 1.0 O3G B:ANP802 2.0 0.7 1.0 O2B B:ANP802 2.0 0.1 1.0 OD2 B:ASP215 2.4 0.8 1.0 OG B:SER382 2.5 0.0 1.0 PG B:ANP802 3.1 0.9 1.0 PB B:ANP802 3.2 0.7 1.0 CB B:THR123 3.4 0.0 1.0 CG B:ASP215 3.4 0.7 1.0 N3B B:ANP802 3.4 0.0 1.0 O1G B:ANP802 3.5 0.5 1.0 CB B:SER382 3.7 0.1 1.0 OD1 B:ASP215 3.7 0.7 1.0 O1B B:ANP802 3.9 0.8 1.0 N B:THR123 4.0 0.4 1.0 CA B:SER382 4.2 0.9 1.0 CA B:THR123 4.3 0.6 1.0 CG2 B:THR123 4.3 0.2 1.0 O2G B:ANP802 4.4 0.7 1.0 O2A B:ANP802 4.4 0.5 1.0 CE B:LYS122 4.4 0.5 1.0 O3A B:ANP802 4.5 0.2 1.0 CB B:LYS122 4.6 0.2 1.0 NZ B:LYS122 4.7 0.3 1.0 OE1 B:GLU216 4.7 0.2 1.0 CB B:ASP215 4.8 0.5 1.0 NE2 B:GLN147 4.8 0.0 1.0 CG B:GLU216 4.9 0.5 1.0 PA B:ANP802 5.0 0.8 1.0 CD B:GLU216 5.0 0.8 1.0

Y.He, J.P.Staley, G.R.Andersen, K.H.Nielsen. Structure of the Deah/Rha Atpase PRP43P Bound to Rna Implicates A Pair of Hairpins and Motif Va in Translocation Along Rna. Rna V. 23 1110 2017.
ISSN: ESSN 1469-9001
PubMed: 28416566
DOI: 10.1261/RNA.060954.117