Magnesium in PDB 7pmm: Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3

All present enzymatic activity of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3:
3.6.4.13;

The structure of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3, PDB code: 7pmm was solved by J.P.Wurm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.39 / 3.00
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	169.69, 169.69, 111.99, 90, 90, 90
R / Rfree (%)	19.7 / 22.5

The structure of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 (pdb code 7pmm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3, PDB code: 7pmm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:63.1 occ:1.00 O A:HOH604 2.0 64.1 1.0 O A:HOH601 2.0 81.0 1.0 F2 A:BEF501 2.0 63.3 1.0 O3B A:ADP500 2.0 63.1 1.0 O A:HOH603 2.0 75.2 1.0 O A:HOH602 2.0 72.7 1.0 BE A:BEF501 3.4 63.1 1.0 PB A:ADP500 3.4 63.1 1.0 O1A A:ADP500 3.4 76.6 1.0 OD2 A:ASP153 3.5 72.6 1.0 O1B A:ADP500 3.6 63.1 1.0 OG1 A:THR54 3.8 70.3 1.0 OE2 A:GLU154 3.9 73.5 1.0 OD1 A:ASP153 3.9 74.2 1.0 CA A:GLY304 4.1 63.7 1.0 CG A:ASP153 4.1 72.7 1.0 F3 A:BEF501 4.2 65.6 1.0 O2B A:ADP500 4.2 63.1 1.0 O A:GLY304 4.4 66.5 1.0 PA A:ADP500 4.5 64.6 1.0 F1 A:BEF501 4.5 66.2 1.0 O3A A:ADP500 4.5 66.6 1.0 C A:GLY304 4.8 59.4 1.0 CB A:LYS53 4.8 59.2 1.0 O2A A:ADP500 4.8 63.1 1.0 NZ A:LYS53 4.9 60.2 1.0 N A:THR54 4.9 64.6 1.0 CD A:GLU154 5.0 71.2 1.0

Magnesium binding site 2 out of 2 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:90.5 occ:1.00 O B:HOH604 2.0 85.6 1.0 O B:HOH603 2.0 97.8 1.0 F2 B:BEF501 2.0 95.3 1.0 O3B B:ADP500 2.0 90.8 1.0 O B:HOH602 2.0 96.7 1.0 O B:HOH601 2.0 101.0 1.0 PB B:ADP500 3.4 87.7 1.0 BE B:BEF501 3.4 92.7 1.0 OD2 B:ASP153 3.4 106.6 1.0 O2A B:ADP500 3.4 101.3 1.0 OG1 B:THR54 3.6 90.5 1.0 O2B B:ADP500 3.7 88.6 1.0 OD1 B:ASP153 3.9 91.0 1.0 CG B:ASP153 4.0 95.0 1.0 CA B:GLY304 4.1 92.7 1.0 OE2 B:GLU154 4.1 92.2 1.0 O B:GLY304 4.3 102.0 1.0 O1B B:ADP500 4.3 85.3 1.0 F1 B:BEF501 4.3 92.2 1.0 O3A B:ADP500 4.4 101.2 1.0 F3 B:BEF501 4.4 93.6 1.0 PA B:ADP500 4.5 85.1 1.0 CE B:LYS53 4.6 84.7 1.0 C B:GLY304 4.7 97.8 1.0 N B:THR54 4.8 85.2 1.0 CB B:LYS53 4.8 82.1 1.0 CB B:THR54 5.0 85.2 1.0

J.P.Wurm, J.P.Wurm. N/A N/A.