Magnesium in PDB 2bon: Structure of An Escherichia Coli Lipid Kinase (Yegs)

The structure of Structure of An Escherichia Coli Lipid Kinase (Yegs), PDB code: 2bon was solved by H.M.Bakali, K.A.Johnson, B.M.Hallberg, M.D.Herman, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.04 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.326, 166.164, 48.474, 90.00, 97.03, 90.00
R / Rfree (%)	22 / 26.7

The binding sites of Magnesium atom in the Structure of An Escherichia Coli Lipid Kinase (Yegs) (pdb code 2bon). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of An Escherichia Coli Lipid Kinase (Yegs), PDB code: 2bon:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of An Escherichia Coli Lipid Kinase (Yegs)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of An Escherichia Coli Lipid Kinase (Yegs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1302 b:66.6 occ:1.00 O A:LEU220 2.0 62.8 1.0 O A:LEU215 2.1 60.4 1.0 OD2 A:ASP218 2.1 65.8 1.0 O A:HOH2007 2.2 62.6 1.0 O A:HOH2018 2.2 65.1 1.0 O A:HOH2024 2.2 60.1 1.0 C A:LEU220 3.1 62.3 1.0 CG A:ASP218 3.1 63.7 1.0 C A:LEU215 3.3 61.2 1.0 OD1 A:ASP218 3.5 62.6 1.0 N A:LEU220 3.7 63.1 1.0 N A:LEU215 3.8 61.4 1.0 CA A:LEU220 3.8 61.3 1.0 CA A:LEU215 4.1 62.0 1.0 CB A:LEU220 4.2 60.5 1.0 N A:LEU221 4.2 64.0 1.0 O A:ASN200 4.3 65.2 1.0 N A:ILE216 4.3 61.7 1.0 OD1 A:ASN200 4.3 65.2 1.0 N A:ASP218 4.4 63.0 1.0 OD2 A:ASP125 4.4 61.9 1.0 OE1 A:GLN222 4.5 64.4 1.0 CB A:LEU215 4.5 61.2 1.0 CB A:ASP218 4.5 63.2 1.0 CA A:ILE216 4.5 62.4 1.0 CA A:LEU221 4.6 64.8 1.0 C A:ILE216 4.8 63.6 1.0 O A:GLY199 4.8 63.3 1.0 N A:GLY219 4.8 63.8 1.0 CA A:ASP218 4.8 64.3 1.0 N A:ASN217 4.9 63.6 1.0 C A:ALA214 4.9 61.9 1.0 C A:ASP218 5.0 63.9 1.0 C A:GLY219 5.0 62.8 1.0

Magnesium binding site 2 out of 2 in the Structure of An Escherichia Coli Lipid Kinase (Yegs)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of An Escherichia Coli Lipid Kinase (Yegs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1302 b:65.5 occ:1.00 O B:LEU215 2.1 61.3 1.0 O B:HOH2026 2.1 61.7 1.0 O B:HOH2030 2.1 60.4 1.0 O B:LEU220 2.1 62.7 1.0 OD1 B:ASP218 2.2 64.2 1.0 O B:HOH2025 2.2 61.4 1.0 CG B:ASP218 3.1 62.2 1.0 C B:LEU215 3.3 62.3 1.0 C B:LEU220 3.3 62.3 1.0 OD2 B:ASP218 3.4 61.2 1.0 N B:LEU215 3.7 62.5 1.0 N B:LEU220 3.9 62.2 1.0 CA B:LEU220 4.0 62.2 1.0 CA B:LEU215 4.1 61.5 1.0 O B:ASN200 4.2 65.0 1.0 N B:ILE216 4.3 62.3 1.0 OD1 B:ASN200 4.3 64.4 1.0 N B:LEU221 4.3 63.6 1.0 CB B:LEU220 4.4 61.8 1.0 CA B:ILE216 4.4 62.0 1.0 OE1 B:GLN222 4.5 64.8 1.0 N B:ASP218 4.5 62.3 1.0 CB B:LEU215 4.5 61.4 1.0 CB B:ASP218 4.5 61.9 1.0 CA B:LEU221 4.6 64.0 1.0 OD2 B:ASP125 4.7 63.5 1.0 O B:GLY199 4.7 64.0 1.0 C B:ILE216 4.7 62.9 1.0 N B:ASN217 4.8 62.8 1.0 N B:GLY219 4.8 62.5 1.0 C B:ALA214 4.8 63.2 1.0 CD1 B:ILE282 4.9 72.1 1.0 CA B:ASP218 4.9 62.5 1.0 CA B:ASN200 4.9 64.6 1.0

H.M.Bakali, M.D.Herman, K.A.Johnson, A.A.Kelly, A.Wieslander, B.M.Hallberg, P.Nordlund. Crystal Structure of Yegs, A Homologue to the Mammalian Diacylglycerol Kinases, Reveals A Novel Regulatory Metal Binding Site. J.Biol.Chem. V. 282 19644 2007.
ISSN: ISSN 0021-9258
PubMed: 17351295
DOI: 10.1074/JBC.M604852200