Magnesium in PDB 2vbf: The Holostructure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis

The structure of The Holostructure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis, PDB code: 2vbf was solved by C.L.Berthold, D.Gocke, M.D.Wood, F.Leeper, M.Pohl, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.603, 108.421, 146.593, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20

The binding sites of Magnesium atom in the The Holostructure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis (pdb code 2vbf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Holostructure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis, PDB code: 2vbf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Holostructure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Holostructure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1548 b:13.5 occ:1.00 O2A B:TPP1549 2.0 12.0 1.0 O B:GLY458 2.0 12.7 1.0 OD1 B:ASP429 2.1 12.5 1.0 O3B B:TPP1549 2.1 11.2 1.0 OD1 B:ASN456 2.2 12.1 1.0 O B:HOH2447 2.2 11.4 1.0 CG B:ASN456 3.1 13.0 1.0 PA B:TPP1549 3.2 13.2 1.0 CG B:ASP429 3.2 13.1 1.0 PB B:TPP1549 3.2 12.9 1.0 C B:GLY458 3.2 14.3 1.0 ND2 B:ASN456 3.5 12.9 1.0 O3A B:TPP1549 3.5 11.8 1.0 O2B B:TPP1549 3.7 13.8 1.0 OD2 B:ASP429 3.7 13.9 1.0 N B:ASP429 4.0 12.3 1.0 O B:ILE454 4.0 14.4 1.0 N B:GLY430 4.1 12.8 1.0 N B:THR460 4.1 15.3 1.0 N B:GLY458 4.1 15.5 1.0 N B:TYR459 4.2 13.3 1.0 O7 B:TPP1549 4.2 14.2 1.0 CA B:GLY458 4.2 14.6 1.0 CA B:TYR459 4.3 14.7 1.0 O1A B:TPP1549 4.3 12.1 1.0 N B:ASN456 4.4 14.0 1.0 CB B:ASP429 4.5 11.1 1.0 CB B:ASN456 4.5 13.7 1.0 O B:HOH2450 4.5 14.6 1.0 O1B B:TPP1549 4.5 12.7 1.0 CA B:ASP429 4.6 11.7 1.0 CA B:GLY428 4.6 12.3 1.0 C B:GLY428 4.7 12.3 1.0 C B:ASN456 4.7 14.0 1.0 C B:TYR459 4.7 15.5 1.0 OG1 B:THR460 4.8 15.2 1.0 CA B:ASN456 4.8 13.3 1.0 C B:ASP429 4.9 11.6 1.0 CA B:GLY430 4.9 11.8 1.0 CB B:THR460 4.9 15.2 1.0 N B:ASP457 5.0 15.6 1.0 O B:ASN456 5.0 15.3 1.0

Magnesium binding site 2 out of 2 in the The Holostructure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Holostructure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1550 b:12.9 occ:1.00 OD1 A:ASP429 2.0 11.5 1.0 O A:GLY458 2.1 10.9 1.0 O2A B:TPP1551 2.1 11.0 1.0 O A:HOH2431 2.1 9.2 1.0 O3B B:TPP1551 2.1 12.8 1.0 OD1 A:ASN456 2.1 11.3 1.0 CG A:ASN456 3.1 12.5 1.0 CG A:ASP429 3.1 12.2 1.0 PB B:TPP1551 3.2 13.2 1.0 PA B:TPP1551 3.3 12.8 1.0 C A:GLY458 3.3 11.9 1.0 ND2 A:ASN456 3.5 12.4 1.0 O3A B:TPP1551 3.5 11.5 1.0 OD2 A:ASP429 3.7 14.3 1.0 O2B B:TPP1551 3.7 12.2 1.0 O A:ILE454 4.0 15.9 1.0 N A:ASP429 4.0 11.5 1.0 N A:GLY430 4.1 10.8 1.0 N A:THR460 4.2 12.7 1.0 N A:GLY458 4.2 13.1 1.0 O7 B:TPP1551 4.2 13.7 1.0 N A:TYR459 4.2 11.9 1.0 CA A:GLY458 4.2 12.7 1.0 CA A:TYR459 4.3 12.8 1.0 O1A B:TPP1551 4.4 13.3 1.0 N A:ASN456 4.4 13.2 1.0 CB A:ASP429 4.4 11.5 1.0 CB A:ASN456 4.5 11.8 1.0 O1B B:TPP1551 4.5 13.1 1.0 CA A:GLY428 4.6 11.6 1.0 O A:HOH2437 4.6 13.1 1.0 CA A:ASP429 4.6 11.7 1.0 C A:GLY428 4.7 11.0 1.0 CA A:ASN456 4.7 12.2 1.0 OG1 A:THR460 4.7 14.9 1.0 C A:ASN456 4.8 10.8 1.0 C A:TYR459 4.8 11.8 1.0 CB A:THR460 4.9 14.7 1.0 C A:ASP429 4.9 11.1 1.0 CA A:GLY430 5.0 11.5 1.0

C.L.Berthold, D.Gocke, M.D.Wood, F.Leeper, M.Pohl, G.Schneider. Crystal Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis Provides Insights Into the Structural Basis For the Chemo- and Enantioselective Carboligation Reaction Acta Crystallogr.,Sect.D V. 63 1217 2007.
ISSN: ISSN 0907-4449
PubMed: 18084069
DOI: 10.1107/S0907444907050433