Magnesium in PDB 3hww: Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate

All present enzymatic activity of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate:
2.2.1.9;

The structure of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate, PDB code: 3hww was solved by A.Priyadarshi, K.Y.Hwang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.32 / 1.95
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.910, 117.910, 175.276, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.5

The structure of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	37 atoms

The binding sites of Magnesium atom in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate (pdb code 3hww). 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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate, PDB code: 3hww:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg558 b:45.8 occ:1.00 O5 A:AKG557 1.8 75.2 1.0 O A:HOH738 2.3 51.5 1.0 OD1 A:ASP442 2.4 39.2 1.0 C2 A:AKG557 2.7 72.8 1.0 OD1 A:ASN469 2.9 53.9 1.0 O A:GLY471 3.0 68.7 1.0 O2 A:AKG557 3.1 73.4 1.0 C3 A:AKG557 3.3 72.2 1.0 CG A:ASP442 3.3 34.1 1.0 C1 A:AKG557 3.4 72.1 1.0 C4 A:AKG557 3.4 70.7 1.0 CG A:ASN469 3.5 53.6 1.0 ND2 A:ASN469 3.6 51.7 1.0 O A:VAL467 3.7 34.6 1.0 C A:GLY471 3.8 67.7 1.0 OD2 A:ASP442 3.8 38.5 1.0 N A:ASP442 3.8 28.2 1.0 N A:ASN469 4.2 47.5 1.0 CA A:GLY471 4.2 66.5 1.0 N A:LEU443 4.3 27.9 1.0 CA A:GLY441 4.5 26.6 1.0 CB A:ASP442 4.5 30.1 1.0 C A:GLY441 4.5 26.7 1.0 CA A:ASP442 4.6 28.7 1.0 O1 A:AKG557 4.6 71.3 1.0 CB A:ASN469 4.7 51.2 1.0 C5 A:AKG557 4.8 70.9 1.0 CA A:ASN469 4.9 51.8 1.0 C A:ASP442 5.0 27.3 1.0 O A:HOH677 5.0 39.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg558 b:41.4 occ:1.00 OD1 D:ASP442 2.4 31.6 1.0 O5 D:AKG557 2.4 69.5 1.0 O2 D:AKG557 2.5 61.9 1.0 O3 D:AKG557 2.8 68.5 1.0 C2 D:AKG557 2.8 68.8 1.0 ND2 D:ASN469 2.9 59.7 1.0 OD1 D:ASN469 3.0 56.8 1.0 C1 D:AKG557 3.0 66.6 1.0 CG D:ASN469 3.2 57.1 1.0 CG D:ASP442 3.3 32.6 1.0 O D:VAL467 3.5 41.5 1.0 OD2 D:ASP442 3.6 37.7 1.0 C5 D:AKG557 3.7 68.6 1.0 C4 D:AKG557 3.8 69.1 1.0 C3 D:AKG557 3.9 68.2 1.0 N D:ASP442 4.0 32.1 1.0 N D:ASN469 4.1 51.2 1.0 O1 D:AKG557 4.3 66.1 1.0 CB D:ASN469 4.4 55.6 1.0 N D:LEU443 4.5 34.4 1.0 CB D:ASP442 4.6 32.3 1.0 CA D:GLY441 4.6 31.7 1.0 CA D:ASN469 4.7 56.0 1.0 C D:GLY441 4.7 31.9 1.0 CA D:ASP442 4.8 32.9 1.0 O4 D:AKG557 4.9 65.2 1.0 C D:ASN469 5.0 58.6 1.0

A.Priyadarshi, E.E.Kim, K.Y.Hwang. Structural and Functional Analysis of Vitamin K2 Synthesis Protein Mend. Biochem.Biophys.Res.Commun. V. 388 748 2009.
ISSN: ISSN 0006-291X
PubMed: 19703421
DOI: 10.1016/J.BBRC.2009.08.093