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Magnesium in PDB 4fee: High-Resolution Structure of Pyruvate Oxidase in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate Carbanion-Enamine, Crystal B

Enzymatic activity of High-Resolution Structure of Pyruvate Oxidase in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate Carbanion-Enamine, Crystal B

All present enzymatic activity of High-Resolution Structure of Pyruvate Oxidase in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate Carbanion-Enamine, Crystal B:
1.2.3.3;

Protein crystallography data

The structure of High-Resolution Structure of Pyruvate Oxidase in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate Carbanion-Enamine, Crystal B, PDB code: 4fee was solved by D.Meyer, P.Neumann, E.Koers, H.Sjuts, S.Luedtke, G.M.Sheldrick, R.Ficner, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.13
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 119.070, 154.460, 165.820, 90.00, 90.00, 90.00
R / Rfree (%) n/a / 14.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the High-Resolution Structure of Pyruvate Oxidase in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate Carbanion-Enamine, Crystal B (pdb code 4fee). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the High-Resolution Structure of Pyruvate Oxidase in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate Carbanion-Enamine, Crystal B, PDB code: 4fee:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4fee

Go back to Magnesium Binding Sites List in 4fee
Magnesium binding site 1 out of 2 in the High-Resolution Structure of Pyruvate Oxidase in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate Carbanion-Enamine, Crystal B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High-Resolution Structure of Pyruvate Oxidase in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate Carbanion-Enamine, Crystal B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg710

b:5.6
occ:1.00
 OD1 A:ASP447 2.0 6.5 1.0
O1A A:TDM708 2.0 5.2 1.0
O A:GLN476 2.1 5.9 1.0
O A:HOH8082 2.1 6.5 1.0
OD1 A:ASN474 2.1 6.1 1.0
O2B A:TDM708 2.1 5.7 1.0
CG A:ASN474 3.1 6.6 1.0
PA A:TDM708 3.3 5.4 1.0
PB A:TDM708 3.3 5.3 1.0
CG A:ASP447 3.3 6.4 1.0
C A:GLN476 3.3 5.3 1.0
ND2 A:ASN474 3.4 8.1 1.0
O3A A:TDM708 3.4 5.7 1.0
O1B A:TDM708 3.8 6.0 1.0
OD2 A:ASP447 3.9 8.4 1.0
N A:GLN476 3.9 5.5 1.0
N A:ASP447 3.9 5.7 1.0
O7 A:TDM708 4.1 6.1 1.0
N A:GLY448 4.1 5.5 1.0
CA A:GLN476 4.1 5.3 1.0
N A:GLY478 4.2 5.6 1.0
O A:PHE472 4.2 7.3 1.0
N A:TYR477 4.2 5.2 1.0
CA A:TYR477 4.4 5.6 1.0
CB A:ASP447 4.4 5.8 1.0
O2A A:TDM708 4.4 6.3 1.0
CB A:ASN474 4.4 6.9 1.0
N A:ASN474 4.4 6.0 1.0
O3B A:TDM708 4.5 5.5 1.0
CA A:ASP447 4.6 5.8 1.0
CZ A:PHE497 4.6 9.3 1.0
CB A:GLN476 4.6 6.7 1.0
N A:CYS475 4.8 6.3 1.0
C A:GLY446 4.8 5.7 1.0
CA A:GLY446 4.8 5.9 1.0
CA A:ASN474 4.8 6.6 1.0
C A:ASP447 4.8 5.4 1.0
C A:TYR477 4.8 5.0 1.0
C A:ASN474 5.0 6.4 1.0

Magnesium binding site 2 out of 2 in 4fee

Go back to Magnesium Binding Sites List in 4fee
Magnesium binding site 2 out of 2 in the High-Resolution Structure of Pyruvate Oxidase in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate Carbanion-Enamine, Crystal B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High-Resolution Structure of Pyruvate Oxidase in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate Carbanion-Enamine, Crystal B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg708

b:5.3
occ:1.00
 O1A B:TDM704 2.0 5.1 1.0
OD1 B:ASP447 2.1 6.2 1.0
O B:GLN476 2.1 5.5 1.0
OD1 B:ASN474 2.1 5.6 1.0
O3B B:TDM704 2.1 5.2 1.0
O B:HOH940 2.1 5.8 1.0
CG B:ASN474 3.1 5.5 1.0
PA B:TDM704 3.2 5.0 1.0
PB B:TDM704 3.2 5.0 1.0
CG B:ASP447 3.3 5.5 1.0
C B:GLN476 3.3 4.9 1.0
ND2 B:ASN474 3.4 7.5 1.0
O3A B:TDM704 3.4 4.9 1.0
O2B B:TDM704 3.8 5.7 1.0
OD2 B:ASP447 3.9 7.7 1.0
N B:GLN476 3.9 5.4 1.0
N B:ASP447 4.0 5.2 1.0
O7 B:TDM704 4.0 5.7 1.0
N B:GLY448 4.1 5.5 1.0
CA B:GLN476 4.1 5.2 1.0
N B:GLY478 4.2 4.9 1.0
N B:TYR477 4.2 4.8 1.0
O B:PHE472 4.2 6.8 1.0
O2A B:TDM704 4.4 5.8 1.0
CA B:TYR477 4.4 4.7 1.0
CB B:ASP447 4.4 5.3 1.0
CB B:ASN474 4.4 6.2 1.0
N B:ASN474 4.5 5.7 1.0
O1B B:TDM704 4.5 5.5 1.0
CA B:ASP447 4.6 5.4 1.0
CB B:GLN476 4.6 6.5 1.0
CZ B:PHE497 4.6 9.1 1.0
C B:GLY446 4.7 4.5 1.0
CA B:GLY446 4.8 5.0 1.0
N B:CYS475 4.8 5.9 1.0
C B:ASP447 4.8 5.3 1.0
CA B:ASN474 4.8 6.0 1.0
C B:TYR477 4.8 5.0 1.0
C B:ASN474 5.0 5.7 1.0
CA B:GLY448 5.0 6.3 1.0

Reference:

D.Meyer, P.Neumann, E.Koers, H.Sjuts, S.Ludtke, G.M.Sheldrick, R.Ficner, K.Tittmann. Unexpected Tautomeric Equilibria of the Carbanion-Enamine Intermediate in Pyruvate Oxidase Highlight Unrecognized Chemical Versatility of Thiamin. Proc.Natl.Acad.Sci.Usa V. 109 10867 2012.
ISSN: ISSN 0027-8424
PubMed: 22730460
DOI: 10.1073/PNAS.1201280109
Page generated: Fri Aug 16 14:55:36 2024

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