Magnesium in PDB 9msa: Alpha-Ketoisovalerate Decarboxylase (Kivd) From Synechocystis Sp. Pcc 6803 with Substitution S286T

The structure of Alpha-Ketoisovalerate Decarboxylase (Kivd) From Synechocystis Sp. Pcc 6803 with Substitution S286T, PDB code: 9msa was solved by A.Begum, H.Xie, L.H.Gunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	218.465, 81.731, 124.981, 90, 105.52, 90
R / Rfree (%)	18.9 / 23.4

The binding sites of Magnesium atom in the Alpha-Ketoisovalerate Decarboxylase (Kivd) From Synechocystis Sp. Pcc 6803 with Substitution S286T (pdb code 9msa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Alpha-Ketoisovalerate Decarboxylase (Kivd) From Synechocystis Sp. Pcc 6803 with Substitution S286T, PDB code: 9msa:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Alpha-Ketoisovalerate Decarboxylase (Kivd) From Synechocystis Sp. Pcc 6803 with Substitution S286T


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Alpha-Ketoisovalerate Decarboxylase (Kivd) From Synechocystis Sp. Pcc 6803 with Substitution S286T within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:61.0 occ:1.00 O1A A:TPP601 2.0 59.5 1.0 OD1 A:ASN456 2.1 70.1 1.0 OD1 A:ASP429 2.1 62.0 1.0 O3B A:TPP601 2.2 60.2 1.0 O A:GLY458 2.6 67.2 1.0 PB A:TPP601 3.0 63.5 1.0 CG A:ASN456 3.0 70.0 1.0 O2B A:TPP601 3.1 66.0 1.0 PA A:TPP601 3.1 59.8 1.0 O3A A:TPP601 3.3 64.8 1.0 CG A:ASP429 3.3 62.8 1.0 ND2 A:ASN456 3.3 68.7 1.0 O A:ILE454 3.5 66.5 1.0 N A:ASP429 3.7 60.8 1.0 C A:GLY458 3.8 70.0 1.0 CA A:GLY428 4.0 61.5 1.0 N A:GLY430 4.0 57.8 1.0 OD2 A:ASP429 4.1 64.9 1.0 O2A A:TPP601 4.1 57.4 1.0 C A:GLY428 4.2 63.2 1.0 O7 A:TPP601 4.3 68.1 1.0 N A:ASN456 4.3 66.4 1.0 CB A:ASN456 4.4 69.7 1.0 CB A:ASP429 4.4 60.5 1.0 O1B A:TPP601 4.4 60.1 1.0 CA A:ASP429 4.4 59.4 1.0 N A:THR460 4.6 74.4 1.0 N A:GLY458 4.6 64.5 1.0 C A:ILE454 4.7 62.2 1.0 N A:TYR459 4.7 69.8 1.0 CA A:ASN456 4.7 67.5 1.0 CA A:TYR459 4.8 68.1 1.0 C A:ASP429 4.8 61.0 1.0 CA A:GLY458 4.8 66.2 1.0 C A:ASN456 4.8 66.4 1.0 CA A:GLY430 4.9 53.5 1.0

Magnesium binding site 2 out of 2 in the Alpha-Ketoisovalerate Decarboxylase (Kivd) From Synechocystis Sp. Pcc 6803 with Substitution S286T


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Alpha-Ketoisovalerate Decarboxylase (Kivd) From Synechocystis Sp. Pcc 6803 with Substitution S286T within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:71.7 occ:1.00 O2A B:TPP601 1.9 71.0 1.0 OD1 B:ASP429 1.9 68.2 1.0 OD1 B:ASN456 2.0 70.0 1.0 O B:HOH702 2.1 37.0 0.5 O B:GLY458 2.2 76.9 1.0 O2B B:TPP601 2.3 66.5 1.0 CG B:ASN456 3.1 74.7 1.0 CG B:ASP429 3.2 69.1 1.0 PA B:TPP601 3.2 66.1 1.0 PB B:TPP601 3.3 64.1 1.0 O3A B:TPP601 3.4 66.5 1.0 C B:GLY458 3.4 79.2 1.0 ND2 B:ASN456 3.5 81.8 1.0 O3B B:TPP601 3.7 65.8 1.0 O B:ILE454 3.8 69.5 1.0 N B:ASP429 3.8 68.1 1.0 OD2 B:ASP429 3.8 68.0 1.0 N B:GLY430 3.9 60.7 1.0 O7 B:TPP601 4.2 64.8 1.0 N B:GLY458 4.2 73.8 1.0 O1A B:TPP601 4.2 58.6 1.0 CB B:ASP429 4.3 64.8 1.0 N B:ASN456 4.3 71.5 1.0 CA B:GLY428 4.3 67.7 1.0 N B:TYR459 4.3 76.8 1.0 CA B:GLY458 4.4 75.2 1.0 CB B:ASN456 4.4 77.8 1.0 C B:GLY428 4.4 67.4 1.0 CA B:ASP429 4.4 65.6 1.0 N B:THR460 4.4 73.9 1.0 CA B:TYR459 4.5 70.6 1.0 O1B B:TPP601 4.6 64.6 1.0 C B:ASN456 4.7 81.2 1.0 CA B:ASN456 4.7 77.0 1.0 C B:ASP429 4.7 65.7 1.0 CA B:GLY430 4.7 59.8 1.0 N B:ASP457 4.8 77.4 1.0 O B:ASN456 4.9 83.2 1.0 C B:ILE454 5.0 67.2 1.0

H.Xie, A.Begum, L.H.Gunn, P.Lindblad. Directed Evolution of Alpha-Ketoisovalerate Decarboxylase For Improved Isobutanol and 3-Methyl-1-Butanol Production in Cyanobacteria. Biotechnol Biofuels Bioprod V. 18 84 2025.
ISSN: ISSN 2731-3654
PubMed: 40745552
DOI: 10.1186/S13068-025-02687-6