Magnesium in PDB 4b5s: Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate

All present enzymatic activity of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate:
4.1.2.20;

The structure of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate, PDB code: 4b5s was solved by M.Coincon, W.Wang, S.Y.K.Seah, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.55 / 1.68
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	151.740, 151.740, 151.740, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.9

The structure of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Magnesium atom in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate (pdb code 4b5s). 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 Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate, PDB code: 4b5s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1257 b:55.7 occ:0.70 CO A:CO1253 0.0 21.8 0.3 O3 A:PYR1256 2.1 33.0 1.0 OD2 A:ASP175 2.2 39.4 1.0 OE1 A:GLU149 2.2 42.8 1.0 O A:HOH2144 2.3 39.8 1.0 O2 A:PYR1256 2.3 36.9 1.0 O A:HOH2140 2.3 28.8 1.0 HE22 A:GLN147 2.9 40.2 1.0 C2 A:PYR1256 2.9 42.8 1.0 C1 A:PYR1256 3.0 55.0 1.0 HB2 A:ASP175 3.1 42.8 1.0 CG A:ASP175 3.2 48.0 1.0 CD A:GLU149 3.3 57.5 1.0 HH12 A:ARG70 3.3 30.8 1.0 NE2 A:GLN147 3.6 33.5 1.0 OE2 A:GLU149 3.7 32.8 1.0 CB A:ASP175 3.7 35.7 1.0 HE21 A:GLN147 3.8 40.2 1.0 HA3 A:GLY172 3.9 36.9 1.0 O A:HOH2141 3.9 30.1 1.0 H A:ASP175 4.0 39.4 1.0 NH1 A:ARG70 4.0 25.7 1.0 HH11 A:ARG70 4.2 30.8 1.0 O1 A:PYR1256 4.3 39.9 1.0 O A:HOH2210 4.3 51.2 1.0 HB3 A:ASP175 4.3 42.8 1.0 OD1 A:ASP175 4.3 33.4 1.0 HB3 A:GLU149 4.3 39.5 1.0 C3 A:PYR1256 4.3 36.5 1.0 CG A:GLU149 4.6 36.0 1.0 OE1 A:GLU44 4.6 24.1 1.0 HH22 A:ARG70 4.6 27.2 1.0 N A:ASP175 4.7 32.8 1.0 CD A:GLN147 4.7 32.5 1.0 HD2 A:HIS45 4.7 28.1 1.0 HG2 A:GLU149 4.7 43.2 1.0 HB1 A:ALA174 4.7 50.3 1.0 CA A:GLY172 4.8 30.7 1.0 CA A:ASP175 4.8 32.2 1.0 NE2 A:HIS45 4.9 27.1 1.0 CZ A:ARG70 4.9 23.9 1.0 OE1 A:GLN147 5.0 34.7 1.0 HE1 A:PHE170 5.0 29.3 1.0 HA2 A:GLY172 5.0 36.9 1.0 CB A:GLU149 5.0 32.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1257 b:22.6 occ:0.70 CO B:CO1253 0.0 31.4 0.3 O3 B:PYR1256 2.1 32.8 1.0 OE1 B:GLU149 2.2 34.4 1.0 OD2 B:ASP175 2.2 37.0 1.0 O B:HOH2149 2.2 36.0 1.0 O2 B:PYR1256 2.2 36.0 1.0 O B:HOH2143 2.3 26.4 1.0 C2 B:PYR1256 2.9 46.0 1.0 HE22 B:GLN147 2.9 41.0 1.0 C1 B:PYR1256 2.9 47.1 1.0 HB2 B:ASP175 3.1 42.9 1.0 CD B:GLU149 3.2 58.3 1.0 CG B:ASP175 3.2 44.4 1.0 HH12 B:ARG70 3.4 28.1 1.0 OE2 B:GLU149 3.6 30.6 1.0 NE2 B:GLN147 3.6 34.2 1.0 CB B:ASP175 3.7 35.8 1.0 HA3 B:GLY172 3.8 38.3 1.0 HE21 B:GLN147 3.8 41.0 1.0 O B:HOH2144 3.9 32.7 1.0 H B:ASP175 3.9 38.0 1.0 NH1 B:ARG70 4.0 23.5 1.0 O B:HOH2145 4.1 59.0 1.0 O1 B:PYR1256 4.2 40.3 1.0 HH11 B:ARG70 4.3 28.1 1.0 HB3 B:ASP175 4.3 42.9 1.0 OD1 B:ASP175 4.3 34.4 1.0 C3 B:PYR1256 4.3 32.5 1.0 O B:HOH2215 4.3 41.4 1.0 HB3 B:GLU149 4.4 45.6 1.0 CG B:GLU149 4.5 32.0 1.0 N B:ASP175 4.6 31.7 1.0 OE1 B:GLU44 4.6 23.6 1.0 HH22 B:ARG70 4.6 22.8 1.0 HG2 B:GLU149 4.6 38.4 1.0 CD B:GLN147 4.7 31.3 1.0 CA B:GLY172 4.7 31.9 1.0 HD2 B:HIS45 4.7 26.5 1.0 CA B:ASP175 4.8 33.3 1.0 HB1 B:ALA174 4.8 47.6 1.0 HA2 B:GLY172 4.9 38.3 1.0 CZ B:ARG70 5.0 20.7 1.0 OE1 B:GLN147 5.0 32.4 1.0 NE2 B:HIS45 5.0 22.6 1.0 HE1 B:PHE170 5.0 28.4 1.0

M.Coincon, W.Wang, J.Sygusch, S.Y.K.Seah. Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity J.Biol.Chem. V. 287 36208 2012.
ISSN: ISSN 0021-9258
PubMed: 22908224
DOI: 10.1074/JBC.M112.400705