Magnesium in PDB 4b5v: Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with 4-Hydroxyl-2-Ketoheptane-1,7-Dioate

All present enzymatic activity of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with 4-Hydroxyl-2-Ketoheptane-1,7-Dioate:
4.1.2.20;

The structure of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with 4-Hydroxyl-2-Ketoheptane-1,7-Dioate, PDB code: 4b5v 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)	37.94 / 2.04
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 (%)	15.3 / 17.9

The binding sites of Magnesium atom in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with 4-Hydroxyl-2-Ketoheptane-1,7-Dioate (pdb code 4b5v). 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 4-Hydroxyl-2-Ketoheptane-1,7-Dioate, PDB code: 4b5v:
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 4-Hydroxyl-2-Ketoheptane-1,7-Dioate


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 4-Hydroxyl-2-Ketoheptane-1,7-Dioate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1255 b:45.0 occ:1.00 O A:HOH2128 2.1 49.1 1.0 OE1 A:GLU149 2.3 63.1 1.0 OD2 A:ASP175 2.4 53.4 1.0 O A:HOH2123 2.6 37.5 1.0 O3 A:PYR1252 2.6 36.8 0.3 OAB A:E8U1253 2.7 41.3 0.3 O10 A:E8U1253 2.7 38.6 0.3 O2 A:PYR1252 2.7 41.2 0.3 O10 A:E8U1253 2.8 38.7 0.3 OAE A:E8U1253 2.8 41.8 0.3 HE22 A:GLN147 2.8 40.5 1.0 HB2 A:ASP175 3.1 42.3 1.0 CAL A:E8U1253 3.2 44.5 0.3 CAL A:E8U1253 3.3 44.5 0.3 HAC A:E8U1253 3.3 55.4 0.3 C2 A:PYR1252 3.3 43.0 0.3 CG A:ASP175 3.3 50.1 1.0 C1 A:PYR1252 3.3 42.5 0.3 CAJ A:E8U1253 3.4 42.1 0.3 CD A:GLU149 3.4 62.9 1.0 HH12 A:ARG70 3.4 43.2 1.0 CAJ A:E8U1253 3.4 42.0 0.3 NE2 A:GLN147 3.5 33.7 1.0 HE21 A:GLN147 3.7 40.5 1.0 CB A:ASP175 3.7 35.2 1.0 O A:HOH2124 3.7 32.2 1.0 OE2 A:GLU149 3.8 40.6 1.0 OAC A:E8U1253 4.0 46.2 0.3 HA3 A:GLY172 4.0 38.6 1.0 NH1 A:ARG70 4.0 36.0 1.0 OAC A:E8U1253 4.1 47.0 0.3 H A:ASP175 4.1 38.6 1.0 O A:HOH2163 4.2 42.8 0.3 HB3 A:ASP175 4.2 42.3 1.0 HH11 A:ARG70 4.2 43.2 1.0 OD1 A:ASP175 4.3 41.1 1.0 CAG A:E8U1253 4.3 44.9 0.3 HB3 A:GLU149 4.4 48.9 1.0 O1 A:PYR1252 4.5 40.0 0.3 CAG A:E8U1253 4.5 45.3 0.3 CAM A:E8U1253 4.6 43.5 0.3 HAM A:E8U1253 4.6 52.1 0.3 OAE A:E8U1253 4.6 40.4 0.3 CG A:GLU149 4.6 41.8 1.0 C3 A:PYR1252 4.7 40.9 0.3 OAB A:E8U1253 4.7 40.7 0.3 HD2 A:HIS45 4.7 34.5 1.0 CD A:GLN147 4.7 32.6 1.0 HAM A:E8U1253 4.7 51.5 0.3 HAG2 A:E8U1253 4.7 53.8 0.3 CAM A:E8U1253 4.7 42.9 0.3 OE1 A:GLU44 4.7 27.7 1.0 HG2 A:GLU149 4.7 50.1 1.0 HH22 A:ARG70 4.8 29.0 1.0 N A:ASP175 4.8 32.2 1.0 HAC A:E8U1253 4.8 56.4 0.3 H31 A:PYR1252 4.8 49.0 0.3 CA A:ASP175 4.9 34.4 1.0 HB1 A:ALA174 4.9 53.2 1.0 NE2 A:HIS45 4.9 34.0 1.0 CA A:GLY172 4.9 32.1 1.0 HE3 A:MET94 4.9 57.8 1.0 HE1 A:PHE170 5.0 26.8 1.0 HAG1 A:E8U1253 5.0 54.3 0.3

Magnesium binding site 2 out of 2 in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with 4-Hydroxyl-2-Ketoheptane-1,7-Dioate


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 4-Hydroxyl-2-Ketoheptane-1,7-Dioate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1255 b:40.2 occ:1.00 O B:HOH2121 2.1 42.5 1.0 O B:HOH2113 2.3 37.4 1.0 OE1 B:GLU149 2.4 53.9 1.0 OD2 B:ASP175 2.5 54.7 1.0 O3 B:PYR1253 2.6 37.8 0.3 O10 B:E8U1254 2.7 37.2 0.3 O2 B:PYR1253 2.7 35.1 0.3 OAB B:E8U1254 2.7 36.0 0.3 O10 B:E8U1254 2.7 37.0 0.3 OAE B:E8U1254 2.8 37.0 0.3 HE22 B:GLN147 2.9 37.7 1.0 HB2 B:ASP175 3.0 44.4 1.0 CAL B:E8U1254 3.1 39.5 0.3 CAL B:E8U1254 3.3 40.5 0.3 C2 B:PYR1253 3.3 38.7 0.3 C1 B:PYR1253 3.3 41.0 0.3 CG B:ASP175 3.3 52.5 1.0 CAJ B:E8U1254 3.3 41.0 0.3 HAC B:E8U1254 3.3 49.5 0.3 CAJ B:E8U1254 3.4 40.7 0.3 CD B:GLU149 3.4 61.4 1.0 HH12 B:ARG70 3.5 40.7 1.0 CB B:ASP175 3.6 37.0 1.0 NE2 B:GLN147 3.6 31.4 1.0 O B:HOH2115 3.7 32.7 1.0 HE21 B:GLN147 3.7 37.7 1.0 OE2 B:GLU149 3.7 44.5 1.0 H B:ASP175 3.9 43.1 1.0 HA3 B:GLY172 3.9 36.0 1.0 OAC B:E8U1254 4.0 41.5 0.3 OAC B:E8U1254 4.0 41.3 0.3 NH1 B:ARG70 4.1 33.9 1.0 O B:HOH2157 4.2 37.4 0.3 O B:HOH2114 4.2 62.5 1.0 HB3 B:ASP175 4.2 44.4 1.0 OD1 B:ASP175 4.3 43.0 1.0 HH11 B:ARG70 4.3 40.7 1.0 CAG B:E8U1254 4.3 40.0 0.3 HB3 B:GLU149 4.4 53.4 1.0 O1 B:PYR1253 4.4 37.1 0.3 OAB B:E8U1254 4.5 38.9 0.3 CAG B:E8U1254 4.5 41.8 0.3 N B:ASP175 4.6 35.9 1.0 OAE B:E8U1254 4.6 39.2 0.3 HAC B:E8U1254 4.6 49.8 0.3 CAM B:E8U1254 4.6 37.9 0.3 C3 B:PYR1253 4.6 36.3 0.3 HAG2 B:E8U1254 4.7 48.0 0.3 HB1 B:ALA174 4.7 49.7 1.0 HAM B:E8U1254 4.7 45.5 0.3 HD2 B:HIS45 4.7 37.7 1.0 CG B:GLU149 4.7 43.9 1.0 CA B:ASP175 4.7 39.3 1.0 OE1 B:GLU44 4.8 28.9 1.0 HH22 B:ARG70 4.8 30.2 1.0 CAM B:E8U1254 4.8 38.6 0.3 H31 B:PYR1253 4.8 43.5 0.3 CD B:GLN147 4.8 34.1 1.0 NE2 B:HIS45 4.8 29.8 1.0 CA B:GLY172 4.9 30.0 1.0 HAM B:E8U1254 4.9 46.3 0.3 HG2 B:GLU149 5.0 52.7 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