Magnesium in PDB 2qv7: Crystal Structure of Diacylglycerol Kinase Dgkb in Complex with Adp and Mg

All present enzymatic activity of Crystal Structure of Diacylglycerol Kinase Dgkb in Complex with Adp and Mg:
2.7.1.107;

The structure of Crystal Structure of Diacylglycerol Kinase Dgkb in Complex with Adp and Mg, PDB code: 2qv7 was solved by D.J.Miller, A.Jerga, C.O.Rock, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.17 / 2.30
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	123.760, 123.760, 47.680, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.6

The binding sites of Magnesium atom in the Crystal Structure of Diacylglycerol Kinase Dgkb in Complex with Adp and Mg (pdb code 2qv7). 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 Diacylglycerol Kinase Dgkb in Complex with Adp and Mg, PDB code: 2qv7:

Magnesium binding site 1 out of 1 in the Crystal Structure of Diacylglycerol Kinase Dgkb in Complex with Adp and Mg


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 Diacylglycerol Kinase Dgkb in Complex with Adp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:11.6 occ:1.00 O A:LYS213 2.2 31.0 1.0 O A:HOH582 2.2 25.5 1.0 O A:TYR218 2.2 28.5 1.0 O A:HOH511 2.3 20.7 1.0 OD2 A:ASP216 2.3 27.8 1.0 O A:HOH531 2.4 19.3 1.0 CG A:ASP216 3.3 28.5 1.0 C A:LYS213 3.4 31.1 1.0 C A:TYR218 3.4 28.7 1.0 OD1 A:ASP216 3.6 28.0 1.0 N A:LYS213 4.0 31.9 1.0 OD2 A:ASP124 4.1 27.6 1.0 N A:TYR218 4.1 28.6 1.0 CA A:LYS213 4.2 31.4 1.0 CA A:TYR218 4.2 28.8 1.0 O A:LEU198 4.3 34.2 1.0 N A:LEU214 4.4 30.6 1.0 O A:HOH554 4.4 28.9 1.0 N A:PHE219 4.5 28.7 1.0 CB A:TYR218 4.5 29.2 1.0 CA A:LEU214 4.6 30.1 1.0 N A:ASP216 4.6 28.6 1.0 CB A:ASP216 4.7 28.4 1.0 CB A:LYS213 4.7 31.5 1.0 CA A:PHE219 4.7 28.7 1.0 C A:LEU214 4.7 29.7 1.0 C A:PHE219 4.7 28.8 1.0 O A:HOH517 4.8 28.2 1.0 OG1 A:THR220 4.8 30.4 1.0 N A:THR220 4.9 29.2 1.0 N A:GLY217 4.9 28.4 1.0 OD1 A:ASN284 4.9 35.1 1.0 O A:GLY197 5.0 32.8 1.0 N A:ASP215 5.0 29.4 1.0

D.J.Miller, A.Jerga, C.O.Rock, S.W.White. Analysis of the Staphylococcus Aureus Dgkb Structure Reveals A Common Catalytic Mechanism For the Soluble Diacylglycerol Kinases. Structure V. 16 1036 2008.
ISSN: ISSN 0969-2126
PubMed: 18611377
DOI: 10.1016/J.STR.2008.03.019