Cobalt in PDB 4b5t: Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Ketobutyrate

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

The structure of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Ketobutyrate, PDB code: 4b5t 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)	37.83 / 1.92
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	151.327, 151.327, 151.327, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.6

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

Magnesium

(Mg)

2 atoms

The binding sites of Cobalt atom in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Ketobutyrate (pdb code 4b5t). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Ketobutyrate, PDB code: 4b5t:
Jump to Cobalt binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Ketobutyrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1000 b:41.5 occ:0.30 MG A:MG1003 0.2 41.5 0.7 OE1 A:GLU149 2.1 43.5 1.0 O3 A:2KT4000 2.2 41.4 1.0 OD2 A:ASP175 2.2 41.9 1.0 O A:HOH2117 2.3 38.8 1.0 O A:HOH2121 2.6 42.6 1.0 HE22 A:GLN147 2.7 41.2 1.0 O1 A:2KT4000 2.8 48.5 1.0 C2 A:2KT4000 3.0 47.8 1.0 CD A:GLU149 3.1 45.5 1.0 HB2 A:ASP175 3.3 44.4 1.0 C1 A:2KT4000 3.3 49.8 1.0 CG A:ASP175 3.3 44.5 1.0 HH12 A:ARG70 3.4 32.9 1.0 NE2 A:GLN147 3.4 34.3 1.0 OE2 A:GLU149 3.5 34.9 1.0 HE21 A:GLN147 3.5 41.2 1.0 O A:HOH2118 3.8 37.7 1.0 CB A:ASP175 3.8 37.0 1.0 HA3 A:GLY172 3.9 37.6 1.0 NH1 A:ARG70 4.0 27.4 1.0 HE2 A:HIS45 4.2 41.7 1.0 HH11 A:ARG70 4.2 32.9 1.0 HB3 A:GLU149 4.3 40.5 1.0 HB3 A:ASP175 4.3 44.4 1.0 HE3 A:MET94 4.4 60.3 1.0 OD1 A:ASP175 4.4 40.9 1.0 C3 A:2KT4000 4.4 42.0 1.0 CG A:GLU149 4.4 34.4 1.0 H A:ASP175 4.5 43.7 1.0 O2 A:2KT4000 4.5 46.8 1.0 CD A:GLN147 4.5 28.8 1.0 O A:HOH2167 4.6 44.4 1.0 HG2 A:GLU149 4.6 41.2 1.0 HH22 A:ARG70 4.7 27.3 1.0 OE1 A:GLU44 4.8 26.2 1.0 HD2 A:HIS45 4.8 31.2 1.0 CA A:GLY172 4.8 31.3 1.0 HE1 A:PHE170 4.8 28.7 1.0 CB A:GLU149 4.9 33.8 1.0 OE1 A:GLN147 4.9 34.8 1.0 C4 A:2KT4000 4.9 56.9 1.0 CZ A:ARG70 5.0 29.8 1.0 NE2 A:HIS45 5.0 34.8 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase, Hpai, in Complex with Ketobutyrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1000 b:35.1 occ:0.30 MG B:MG1001 0.2 37.0 0.7 O B:HOH2105 2.1 41.1 1.0 OD2 B:ASP175 2.1 44.3 1.0 OE1 B:GLU149 2.3 50.3 1.0 O B:HOH2098 2.3 34.5 1.0 O3 B:2KT4000 2.3 40.6 1.0 O1 B:2KT4000 2.6 38.7 1.0 HE22 B:GLN147 2.9 41.2 1.0 C2 B:2KT4000 3.0 44.9 1.0 C1 B:2KT4000 3.2 46.8 1.0 CG B:ASP175 3.2 41.5 1.0 HB2 B:ASP175 3.3 40.4 1.0 HH12 B:ARG70 3.3 29.6 1.0 CD B:GLU149 3.4 48.3 1.0 O B:HOH2099 3.5 34.6 1.0 NE2 B:GLN147 3.6 34.4 1.0 HE21 B:GLN147 3.8 41.2 1.0 CB B:ASP175 3.8 33.7 1.0 OE2 B:GLU149 3.8 35.3 1.0 HE2 B:HIS45 4.0 37.8 1.0 NH1 B:ARG70 4.0 24.7 1.0 HA3 B:GLY172 4.1 39.7 1.0 O B:HOH2147 4.1 41.4 1.0 OD1 B:ASP175 4.3 36.4 1.0 HH11 B:ARG70 4.3 29.6 1.0 H B:ASP175 4.3 38.3 1.0 HB3 B:ASP175 4.3 40.4 1.0 O2 B:2KT4000 4.4 43.5 1.0 C3 B:2KT4000 4.4 42.5 1.0 OE1 B:GLU44 4.6 24.2 1.0 HH22 B:ARG70 4.6 26.2 1.0 HD2 B:HIS45 4.6 34.4 1.0 HB3 B:GLU149 4.6 38.2 1.0 CG B:GLU149 4.6 30.3 1.0 HG2 B:GLU149 4.7 36.4 1.0 NE2 B:HIS45 4.7 31.5 1.0 CD B:GLN147 4.8 28.9 1.0 CZ B:ARG70 4.9 28.1 1.0 N B:ASP175 5.0 31.9 1.0 CD2 B:HIS45 5.0 28.7 1.0 CA B:ASP175 5.0 36.1 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