Magnesium in PDB 8arp: Crystal Structure of Dead-Box Protein DBP2 in Complex with Adp

All present enzymatic activity of Crystal Structure of Dead-Box Protein DBP2 in Complex with Adp:
3.6.4.13;

The structure of Crystal Structure of Dead-Box Protein DBP2 in Complex with Adp, PDB code: 8arp was solved by Q.X.Song, S.Rety, X.G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	119.40 / 3.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	145.939, 168.843, 168.87, 90, 90, 90
R / Rfree (%)	22.3 / 27

The binding sites of Magnesium atom in the Crystal Structure of Dead-Box Protein DBP2 in Complex with Adp (pdb code 8arp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Dead-Box Protein DBP2 in Complex with Adp, PDB code: 8arp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Dead-Box Protein DBP2 in Complex with Adp


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 Dead-Box Protein DBP2 in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2003 b:47.5 occ:1.00 O2B A:ADP2001 2.1 72.3 1.0 OD2 A:ASP267 2.8 50.0 1.0 OG1 A:THR164 3.0 79.2 1.0 PB A:ADP2001 3.2 58.3 1.0 OE2 A:GLU268 3.4 69.8 1.0 O3A A:ADP2001 3.4 60.0 1.0 CG A:ASP267 3.6 52.5 1.0 OD1 A:ASP267 3.6 68.1 1.0 O3B A:ADP2001 3.8 56.4 1.0 N A:THR164 4.0 75.9 1.0 CB A:LYS163 4.1 75.7 1.0 CB A:THR164 4.1 63.6 1.0 CA A:THR164 4.2 78.5 1.0 CE A:LYS163 4.3 73.0 1.0 O1B A:ADP2001 4.5 85.8 1.0 OH A:TYR167 4.5 64.6 1.0 C A:LYS163 4.5 62.1 1.0 CD A:GLU268 4.6 76.2 1.0 CA A:LYS163 4.9 65.0 1.0 PA A:ADP2001 4.9 60.0 1.0 CG2 A:THR164 5.0 49.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Dead-Box Protein DBP2 in Complex with Adp


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 Dead-Box Protein DBP2 in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2003 b:141.1 occ:1.00 OE2 C:GLU268 2.1 145.6 1.0 O1B C:ADP2001 2.1 111.7 1.0 O2B C:ADP2001 2.3 108.4 1.0 PB C:ADP2001 2.6 91.4 1.0 NZ C:LYS163 3.0 161.3 1.0 CE C:LYS163 3.0 160.8 1.0 OD2 C:ASP267 3.2 215.9 1.0 CD C:GLU268 3.2 148.2 1.0 O3B C:ADP2001 3.6 86.4 1.0 CG C:GLU268 3.7 151.4 1.0 OD1 C:ASP267 3.8 191.4 1.0 CG C:ASP267 3.9 203.8 1.0 O3A C:ADP2001 3.9 99.4 1.0 CG2 C:THR159 4.2 87.0 1.0 OE1 C:GLU268 4.2 152.2 1.0 CD C:LYS163 4.3 159.8 1.0 CB C:LYS163 4.6 159.0 1.0 CG2 C:THR164 4.6 88.4 1.0 CB C:THR159 4.8 94.0 1.0 CG C:LYS163 4.9 158.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Dead-Box Protein DBP2 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Dead-Box Protein DBP2 in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg2005 b:88.6 occ:1.00 O1B E:ADP2001 1.7 93.1 1.0 PB E:ADP2001 2.7 99.8 1.0 OD2 E:ASP267 2.8 96.0 1.0 O3A E:ADP2001 3.0 97.0 1.0 O2B E:ADP2001 3.1 98.8 1.0 CG2 E:THR164 3.1 138.8 1.0 OD1 E:ASP267 3.4 83.9 1.0 CG E:ASP267 3.5 84.9 1.0 CE E:LYS163 3.6 104.0 1.0 NZ E:LYS163 3.9 101.5 1.0 O3B E:ADP2001 4.0 101.0 1.0 OE2 E:GLU268 4.1 95.5 1.0 CB E:LYS163 4.4 100.7 1.0 N E:THR164 4.4 151.8 1.0 CD E:GLU268 4.5 101.5 1.0 CB E:THR164 4.5 147.3 1.0 PA E:ADP2001 4.5 81.7 1.0 O2A E:ADP2001 4.7 96.6 1.0 CA E:THR164 4.7 150.6 1.0 CD E:LYS163 4.7 94.0 1.0 OH E:TYR167 4.9 91.0 1.0 CG E:GLU268 4.9 89.8 1.0 C E:LYS163 4.9 115.7 1.0 CB E:ASP267 4.9 79.3 1.0

Q.X.Song, N.N.Liu, Z.X.Liu, Y.Z.Zhang, S.Rety, X.M.Hou, X.G.Xi. Nonstructural N- and C-Tails of DBP2 Confer the Protein Full Helicase Activities. J.Biol.Chem. 04592 2023.
ISSN: ESSN 1083-351X
PubMed: 36894019
DOI: 10.1016/J.JBC.2023.104592