Magnesium in PDB 5tma: Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3

All present enzymatic activity of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3:
4.1.1.1;

The structure of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3, PDB code: 5tma was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	101.18 / 1.67
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	124.440, 124.440, 173.825, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.3

The binding sites of Magnesium atom in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3 (pdb code 5tma). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3, PDB code: 5tma:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:20.7 occ:1.00 O1A A:TPP601 2.0 22.0 0.9 O2B A:TPP601 2.0 21.9 0.9 O A:GLY469 2.1 24.3 1.0 OD1 A:ASP440 2.1 22.1 1.0 O A:HOH961 2.2 24.2 1.0 OD1 A:ASN467 2.2 25.4 1.0 PA A:TPP601 3.1 22.6 0.9 CG A:ASN467 3.2 28.9 1.0 PB A:TPP601 3.2 27.8 0.9 C A:GLY469 3.3 29.0 1.0 CG A:ASP440 3.4 23.3 1.0 O3A A:TPP601 3.5 23.7 0.9 ND2 A:ASN467 3.5 24.7 1.0 OD2 A:ASP440 3.9 28.1 1.0 O7 A:TPP601 4.0 23.3 0.9 N A:ASP440 4.0 16.6 1.0 N A:GLY469 4.1 27.2 1.0 N A:GLY441 4.1 18.4 1.0 O3B A:TPP601 4.1 27.0 0.9 N A:THR471 4.1 28.3 1.0 CA A:GLY469 4.2 26.3 1.0 N A:TYR470 4.3 24.4 1.0 O A:HOH719 4.3 38.0 1.0 CA A:TYR470 4.4 26.0 1.0 O1B A:TPP601 4.4 34.8 0.9 O2A A:TPP601 4.4 21.5 0.9 O A:ILE465 4.4 18.7 1.0 CB A:ASN467 4.5 25.9 1.0 CB A:ASP440 4.6 19.5 1.0 CA A:GLY439 4.6 15.4 1.0 OG1 A:THR471 4.6 36.2 1.0 N A:ASN467 4.7 21.7 1.0 O A:HOH784 4.7 26.3 1.0 C A:GLY439 4.7 15.3 1.0 C A:ASN467 4.7 29.3 1.0 CA A:ASP440 4.7 18.4 1.0 CB A:THR471 4.8 32.6 1.0 C A:TYR470 4.8 26.1 1.0 CA A:ASN467 4.8 26.6 1.0 CA A:GLY441 4.9 17.8 1.0 O A:ASN467 4.9 27.7 1.0 N A:TYR468 4.9 27.9 1.0 C A:ASP440 4.9 18.2 1.0

Magnesium binding site 2 out of 2 in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:24.7 occ:1.00 O2A B:TPP601 2.0 17.9 0.8 O1B B:TPP601 2.1 21.1 0.8 OD1 B:ASP440 2.2 24.5 1.0 OD1 B:ASN467 2.2 23.3 1.0 O B:HOH962 2.2 23.9 1.0 O B:GLY469 2.2 26.3 1.0 CG B:ASN467 3.1 26.6 1.0 PA B:TPP601 3.1 21.5 0.8 PB B:TPP601 3.3 24.1 0.8 CG B:ASP440 3.4 24.1 1.0 C B:GLY469 3.4 29.6 1.0 O3A B:TPP601 3.4 23.8 0.8 ND2 B:ASN467 3.4 28.9 1.0 N B:ASP440 4.0 19.2 1.0 OD2 B:ASP440 4.0 31.8 1.0 O7 B:TPP601 4.0 22.2 0.8 N B:GLY441 4.1 20.2 1.0 N B:GLY469 4.1 26.8 1.0 O2B B:TPP601 4.2 26.7 0.8 N B:THR471 4.2 28.2 1.0 O B:ILE465 4.3 21.6 1.0 N B:TYR470 4.3 27.6 1.0 CA B:GLY469 4.3 27.1 1.0 O1A B:TPP601 4.3 23.0 0.8 CA B:TYR470 4.4 29.6 1.0 O3B B:TPP601 4.4 28.9 0.8 CB B:ASN467 4.5 23.7 1.0 CA B:GLY439 4.5 17.7 1.0 N B:ASN467 4.5 23.0 1.0 CB B:ASP440 4.6 21.9 1.0 C B:GLY439 4.6 19.5 1.0 CA B:ASP440 4.6 19.5 1.0 O B:HOH1021 4.7 29.0 1.0 C B:ASN467 4.7 25.9 1.0 CA B:ASN467 4.8 21.5 1.0 OG1 B:THR471 4.8 33.4 1.0 C B:TYR470 4.8 30.7 1.0 C B:ASP440 4.9 20.9 1.0 O B:HOH777 4.9 40.0 1.0 CA B:GLY441 4.9 20.0 1.0 N B:TYR468 4.9 28.4 1.0

D.W.Sammond, N.Kastelowitz, B.S.Donohoe, M.Alahuhta, V.V.Lunin, D.Chung, N.S.Sarai, H.Yin, A.Mittal, M.E.Himmel, A.M.Guss, Y.J.Bomble. An Iterative Computational Design Approach to Increase the Thermal Endurance of A Mesophilic Enzyme. Biotechnol Biofuels V. 11 189 2018.
ISSN: ESSN 1754-6834
PubMed: 30002729
DOI: 10.1186/S13068-018-1178-9