Magnesium in PDB 2v5k: Class II Aldolase Hpch - Magnesium - Oxamate Complex

The structure of Class II Aldolase Hpch - Magnesium - Oxamate Complex, PDB code: 2v5k was solved by D.Rea, V.Fulop, T.D.H.Bugg, D.I.Roper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.77 / 2.2
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	152.200, 152.200, 152.200, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.2

The binding sites of Magnesium atom in the Class II Aldolase Hpch - Magnesium - Oxamate Complex (pdb code 2v5k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Class II Aldolase Hpch - Magnesium - Oxamate Complex, PDB code: 2v5k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Class II Aldolase Hpch - Magnesium - Oxamate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Class II Aldolase Hpch - Magnesium - Oxamate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:50.1 occ:1.00 O1 A:OXM302 2.2 37.4 1.0 OD2 A:ASP175 2.2 41.9 1.0 O2 A:OXM302 2.3 40.4 1.0 OE1 A:GLU149 2.3 40.7 1.0 O A:HOH2027 2.4 28.5 1.0 C1 A:OXM302 2.9 40.7 1.0 C2 A:OXM302 3.0 41.1 1.0 CG A:ASP175 3.2 38.8 1.0 CD A:GLU149 3.4 39.6 1.0 CB A:ASP175 3.6 36.9 1.0 NE2 A:GLN147 3.6 35.7 1.0 OE2 A:GLU149 3.8 38.1 1.0 O A:HOH2028 4.0 31.2 1.0 NH1 A:ARG70 4.2 29.4 1.0 O3 A:OXM302 4.2 43.1 1.0 N1 A:OXM302 4.2 38.9 1.0 OD1 A:ASP175 4.3 39.9 1.0 N A:ASP175 4.6 36.3 1.0 O A:HOH2051 4.6 24.2 1.0 CA A:GLY172 4.6 32.6 1.0 CG A:GLU149 4.7 35.5 1.0 CA A:ASP175 4.7 36.6 1.0 OE1 A:GLU44 4.7 31.0 1.0 CD A:GLN147 4.8 32.8 1.0

Magnesium binding site 2 out of 2 in the Class II Aldolase Hpch - Magnesium - Oxamate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Class II Aldolase Hpch - Magnesium - Oxamate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:43.4 occ:1.00 O B:HOH2031 2.1 27.9 1.0 OD2 B:ASP175 2.1 36.1 1.0 OE1 B:GLU149 2.2 41.8 1.0 O1 B:OXM302 2.4 36.7 1.0 O2 B:OXM302 2.5 34.2 1.0 C1 B:OXM302 3.1 38.0 1.0 CG B:ASP175 3.2 34.0 1.0 C2 B:OXM302 3.2 38.4 1.0 CD B:GLU149 3.3 39.6 1.0 O B:HOH2125 3.6 34.9 1.0 CB B:ASP175 3.6 33.3 1.0 OE2 B:GLU149 3.7 37.0 1.0 NE2 B:GLN147 3.9 31.5 1.0 NH1 B:ARG70 4.1 24.8 1.0 OD1 B:ASP175 4.2 34.2 1.0 N1 B:OXM302 4.3 38.1 1.0 O3 B:OXM302 4.4 38.8 1.0 OE1 B:GLU44 4.4 28.1 1.0 O B:HOH2057 4.5 22.6 1.0 CG B:GLU149 4.6 33.9 1.0 NE2 B:HIS45 4.6 29.2 1.0 N B:ASP175 4.6 33.2 1.0 CA B:ASP175 4.8 33.3 1.0 CD2 B:HIS45 4.9 27.3 1.0 CD B:GLN147 4.9 28.7 1.0 CZ B:ARG70 5.0 27.5 1.0 CA B:GLY172 5.0 30.7 1.0

D.Rea, V.Fulop, T.D.H.Bugg, D.I.Roper. Structure and Mechanism of Hpch: A Metal Ion Dependent Class II Aldolase From the Homoprotocatechuate Degradation Pathway of Escherichia Coli. J.Mol.Biol. V. 373 866 2007.
ISSN: ISSN 0022-2836
PubMed: 17881002
DOI: 10.1016/J.JMB.2007.06.048