Magnesium in PDB 2vbg: The Complex Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis with 2R-1- Hydroxyethyl-Deazathdp

The structure of The Complex Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis with 2R-1- Hydroxyethyl-Deazathdp, PDB code: 2vbg 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 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.977, 108.578, 146.529, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20.5

The binding sites of Magnesium atom in the The Complex Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis with 2R-1- Hydroxyethyl-Deazathdp (pdb code 2vbg). 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 Complex Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis with 2R-1- Hydroxyethyl-Deazathdp, PDB code: 2vbg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Complex Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis with 2R-1- Hydroxyethyl-Deazathdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Complex Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis with 2R-1- Hydroxyethyl-Deazathdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1548 b:9.9 occ:1.00 OD1 A:ASP429 2.1 10.0 1.0 O A:GLY458 2.1 9.2 1.0 O1A A:R1T1549 2.1 9.1 1.0 O1B A:R1T1549 2.1 6.6 1.0 O A:HOH2367 2.2 7.4 1.0 OD1 A:ASN456 2.2 9.6 1.0 CG A:ASN456 3.2 9.5 1.0 CG A:ASP429 3.2 9.6 1.0 PB A:R1T1549 3.2 9.0 1.0 C A:GLY458 3.3 9.9 1.0 PA A:R1T1549 3.3 8.8 1.0 ND2 A:ASN456 3.5 8.7 1.0 O3A A:R1T1549 3.5 7.7 1.0 OD2 A:ASP429 3.7 9.5 1.0 O3B A:R1T1549 3.7 8.8 1.0 O A:ILE454 4.0 10.4 1.0 N A:ASP429 4.0 9.0 1.0 N A:GLY430 4.1 8.1 1.0 N A:THR460 4.1 9.4 1.0 N A:TYR459 4.2 9.5 1.0 N A:GLY458 4.2 9.9 1.0 O7 A:R1T1549 4.2 9.3 1.0 CA A:GLY458 4.2 9.6 1.0 CA A:TYR459 4.3 9.5 1.0 O2A A:R1T1549 4.4 8.3 1.0 CB A:ASP429 4.5 8.7 1.0 N A:ASN456 4.5 10.3 1.0 CB A:ASN456 4.5 9.4 1.0 O A:HOH2369 4.5 9.9 1.0 O2B A:R1T1549 4.5 8.4 1.0 CA A:GLY428 4.6 9.0 1.0 CA A:ASP429 4.6 8.8 1.0 C A:GLY428 4.7 9.0 1.0 C A:TYR459 4.7 9.7 1.0 OG1 A:THR460 4.8 9.6 1.0 CA A:ASN456 4.8 9.8 1.0 C A:ASN456 4.8 9.8 1.0 C A:ASP429 4.9 8.7 1.0 CB A:THR460 4.9 9.8 1.0 CA A:GLY430 4.9 8.3 1.0

Magnesium binding site 2 out of 2 in the The Complex Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis with 2R-1- Hydroxyethyl-Deazathdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Complex Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis with 2R-1- Hydroxyethyl-Deazathdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1548 b:11.7 occ:1.00 O1A B:R1T1549 2.0 7.2 1.0 OD1 B:ASP429 2.0 8.2 1.0 O B:GLY458 2.1 10.8 1.0 O1B B:R1T1549 2.1 8.3 1.0 O B:HOH2374 2.1 6.8 1.0 OD1 B:ASN456 2.2 9.6 1.0 CG B:ASN456 3.2 9.9 1.0 CG B:ASP429 3.2 9.2 1.0 PA B:R1T1549 3.2 9.2 1.0 C B:GLY458 3.3 11.3 1.0 PB B:R1T1549 3.3 9.2 1.0 ND2 B:ASN456 3.5 7.8 1.0 O3A B:R1T1549 3.5 8.7 1.0 OD2 B:ASP429 3.7 11.1 1.0 O3B B:R1T1549 3.7 10.0 1.0 N B:ASP429 3.9 9.5 1.0 O B:ILE454 4.0 10.8 1.0 N B:GLY430 4.0 8.8 1.0 N B:THR460 4.2 11.2 1.0 N B:TYR459 4.2 11.5 1.0 N B:GLY458 4.2 11.7 1.0 O7 B:R1T1549 4.2 10.0 1.0 CA B:GLY458 4.2 11.5 1.0 CA B:TYR459 4.3 11.1 1.0 O2A B:R1T1549 4.4 9.1 1.0 CB B:ASP429 4.4 9.2 1.0 N B:ASN456 4.5 10.5 1.0 CA B:GLY428 4.5 9.0 1.0 CB B:ASN456 4.6 10.1 1.0 CA B:ASP429 4.6 9.0 1.0 C B:GLY428 4.6 9.1 1.0 O2B B:R1T1549 4.6 8.8 1.0 O B:HOH2377 4.6 10.7 1.0 C B:TYR459 4.8 11.1 1.0 C B:ASN456 4.8 10.8 1.0 C B:ASP429 4.8 9.2 1.0 CA B:ASN456 4.9 10.3 1.0 OG1 B:THR460 4.9 10.3 1.0 CA B:GLY430 4.9 9.0 1.0 O B:ASN456 5.0 11.3 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