Magnesium in PDB 5jpt: Crystal Structure of the PRP43P Deah-Box Rna Helicase in Complex with Cdp

All present enzymatic activity of Crystal Structure of the PRP43P Deah-Box Rna Helicase in Complex with Cdp:
3.6.4.13;

The structure of Crystal Structure of the PRP43P Deah-Box Rna Helicase in Complex with Cdp, PDB code: 5jpt was solved by J.Robert-Paganin, S.Rety, N.Leulliot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.31 / 2.94
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.070, 118.070, 252.150, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 25.7

The structure of Crystal Structure of the PRP43P Deah-Box Rna Helicase in Complex with Cdp also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of the PRP43P Deah-Box Rna Helicase in Complex with Cdp (pdb code 5jpt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the PRP43P Deah-Box Rna Helicase in Complex with Cdp, PDB code: 5jpt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the PRP43P Deah-Box Rna Helicase in Complex with Cdp


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 PRP43P Deah-Box Rna Helicase in Complex with Cdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:32.8 occ:1.00 O A:HOH903 2.0 36.3 1.0 OG1 A:THR123 2.1 39.4 1.0 O A:HOH902 2.1 40.3 1.0 O A:HOH901 2.1 39.6 1.0 O3B A:CDP801 2.1 36.6 1.0 O A:HOH904 2.3 37.4 1.0 O1B A:CDP801 3.0 34.9 1.0 PB A:CDP801 3.1 34.5 1.0 CB A:THR123 3.2 38.2 1.0 O A:SER382 3.6 42.8 1.0 OE2 A:GLU216 3.7 45.1 1.0 O1A A:CDP801 4.0 40.5 1.0 OD2 A:ASP215 4.0 37.1 1.0 N A:THR123 4.0 39.0 1.0 O2B A:CDP801 4.1 38.1 1.0 CG2 A:THR123 4.2 34.4 1.0 CA A:THR123 4.2 37.5 1.0 O3A A:CDP801 4.3 31.3 1.0 C A:SER382 4.5 38.7 1.0 PA A:CDP801 4.5 39.5 1.0 CD A:GLU216 4.5 41.2 1.0 O2A A:CDP801 4.6 32.9 1.0 OD1 A:ASP215 4.6 36.0 1.0 O A:THR381 4.7 41.2 1.0 CG A:ASP215 4.7 38.0 1.0 CE A:LYS122 4.7 38.8 1.0 CB A:LYS122 4.9 38.3 1.0 OE1 A:GLN147 4.9 39.9 1.0 NZ A:LYS122 5.0 39.6 1.0 CG A:GLU216 5.0 39.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the PRP43P Deah-Box Rna Helicase in Complex with Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the PRP43P Deah-Box Rna Helicase in Complex with Cdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:34.5 occ:1.00 OG1 B:THR123 2.1 44.1 1.0 O B:HOH902 2.1 41.2 1.0 O B:HOH903 2.1 48.5 1.0 O1B B:CDP801 2.1 41.7 1.0 O B:HOH906 2.1 39.6 1.0 O B:HOH905 2.3 45.6 1.0 CB B:THR123 3.1 43.0 1.0 O3B B:CDP801 3.2 41.8 1.0 PB B:CDP801 3.2 39.6 1.0 O B:SER382 3.4 46.9 1.0 OE2 B:GLU216 3.7 55.4 1.0 O B:HOH901 3.9 43.4 1.0 CG2 B:THR123 4.0 39.4 1.0 O2A B:CDP801 4.0 48.2 1.0 N B:THR123 4.1 42.0 1.0 OD2 B:ASP215 4.1 38.4 1.0 CA B:THR123 4.2 42.1 1.0 O2B B:CDP801 4.2 38.1 1.0 C B:SER382 4.3 43.2 1.0 O3A B:CDP801 4.4 37.0 1.0 CD B:GLU216 4.4 44.1 1.0 O1A B:CDP801 4.5 43.8 1.0 PA B:CDP801 4.5 41.6 1.0 O B:THR381 4.7 45.0 1.0 OD1 B:ASP215 4.7 38.0 1.0 OE1 B:GLN147 4.7 39.8 1.0 CG B:ASP215 4.8 38.5 1.0 CG B:GLU216 4.8 38.9 1.0 CA B:SER382 4.8 41.6 1.0

J.Robert-Paganin, M.Halladjian, M.Blaud, S.Lebaron, L.Delbos, F.Chardon, R.Capeyrou, O.Humbert, Y.Henry, A.K.Henras, S.Rety, N.Leulliot. Functional Link Between Deah/Rha Helicase PRP43 Activation and Atp Base Binding. Nucleic Acids Res. V. 45 1539 2017.
ISSN: ESSN 1362-4962
PubMed: 28180308
DOI: 10.1093/NAR/GKW1233