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Magnesium in PDB 2q5l: X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp

Enzymatic activity of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp

All present enzymatic activity of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp:
4.1.1.43;

Protein crystallography data

The structure of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp, PDB code: 2q5l was solved by W.Versees, S.Spaepen, M.D.Wood, F.J.Leeper, J.Vanderleyden, J.Steyaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.50 / 1.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 99.978, 179.050, 120.858, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.4

Other elements in 2q5l:

The structure of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp (pdb code 2q5l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp, PDB code: 2q5l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2q5l

Go back to Magnesium Binding Sites List in 2q5l
Magnesium binding site 1 out of 2 in the X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:15.1
occ:1.00
O1B A:S1T2002 2.0 16.1 0.5
OD1 A:ASP429 2.1 13.4 1.0
O1B A:R1T2004 2.1 11.1 0.5
O2A A:S1T2002 2.1 10.5 0.5
O2A A:R1T2004 2.1 11.5 0.5
O A:SER458 2.1 12.1 1.0
OD1 A:ASN456 2.1 11.0 1.0
O A:HOH4095 2.2 14.6 1.0
CG A:ASN456 3.1 12.5 1.0
CG A:ASP429 3.2 13.3 1.0
PB A:S1T2002 3.2 17.1 0.5
PA A:S1T2002 3.2 10.8 0.5
PA A:R1T2004 3.3 14.0 0.5
PB A:R1T2004 3.3 10.4 0.5
C A:SER458 3.3 14.2 1.0
O3A A:S1T2002 3.4 13.7 0.5
ND2 A:ASN456 3.5 14.0 1.0
O3A A:R1T2004 3.5 12.2 0.5
OD2 A:ASP429 3.7 12.5 1.0
O7 A:S1T2002 3.9 9.3 0.5
O7 A:R1T2004 3.9 14.4 0.5
N A:ASP429 4.0 11.9 1.0
N A:SER458 4.0 14.1 1.0
N A:GLU460 4.1 15.0 1.0
CA A:SER458 4.1 13.3 1.0
O2B A:S1T2002 4.1 16.9 0.5
O2B A:R1T2004 4.2 9.3 0.5
O A:PHE454 4.2 13.5 1.0
N A:GLY430 4.3 13.1 1.0
O3B A:S1T2002 4.3 18.0 0.5
N A:TRP459 4.3 13.0 1.0
O A:HOH4057 4.3 16.0 1.0
N A:ASN456 4.4 13.5 1.0
O3B A:R1T2004 4.4 9.5 0.5
CB A:ASP429 4.4 11.6 1.0
O1A A:S1T2002 4.4 8.7 0.5
O1A A:R1T2004 4.5 15.1 0.5
CA A:TRP459 4.5 14.1 1.0
CB A:ASN456 4.5 12.2 1.0
CB A:SER458 4.6 12.8 1.0
CB A:GLU460 4.6 14.4 1.0
CA A:ASP429 4.6 12.0 1.0
CA A:GLY428 4.7 12.6 1.0
C A:GLY428 4.8 14.2 1.0
CA A:ASN456 4.8 13.4 1.0
C A:TRP459 4.8 14.3 1.0
N A:ALA457 4.9 13.3 1.0
C A:ASN456 4.9 13.6 1.0
C A:ASP429 5.0 12.8 1.0

Magnesium binding site 2 out of 2 in 2q5l

Go back to Magnesium Binding Sites List in 2q5l
Magnesium binding site 2 out of 2 in the X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Phenylpyruvate Decarboxylase in Complex with 2-(1- Hydroxyethyl)-3-Deaza-Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:19.8
occ:1.00
O B:HOH4284 2.0 17.7 1.0
OD1 B:ASP429 2.1 16.6 1.0
O1B B:S1T2001 2.1 20.8 0.5
O2A B:S1T2001 2.1 17.1 0.5
O2A B:R1T2003 2.1 14.5 0.5
O1B B:R1T2003 2.1 16.6 0.5
OD1 B:ASN456 2.2 17.9 1.0
O B:SER458 2.2 18.4 1.0
CG B:ASN456 3.1 20.5 1.0
CG B:ASP429 3.2 16.2 1.0
PA B:S1T2001 3.3 16.7 0.5
PB B:S1T2001 3.3 20.4 0.5
PB B:R1T2003 3.3 17.3 0.5
PA B:R1T2003 3.3 17.0 0.5
C B:SER458 3.4 17.6 1.0
O3A B:R1T2003 3.4 16.3 0.5
O3A B:S1T2001 3.5 19.2 0.5
ND2 B:ASN456 3.6 20.7 1.0
OD2 B:ASP429 3.7 15.1 1.0
O7 B:S1T2001 3.9 15.8 0.5
N B:ASP429 3.9 17.8 1.0
O7 B:R1T2003 4.0 18.2 0.5
N B:SER458 4.0 18.6 1.0
O B:PHE454 4.0 19.0 1.0
O2B B:R1T2003 4.1 16.1 0.5
CA B:SER458 4.2 20.4 1.0
N B:GLU460 4.2 20.0 1.0
O2B B:S1T2001 4.3 22.5 0.5
N B:GLY430 4.3 16.0 1.0
O B:HOH4037 4.3 19.9 1.0
N B:ASN456 4.3 19.2 1.0
O3B B:S1T2001 4.3 20.6 0.5
N B:TRP459 4.4 17.9 1.0
CB B:ASP429 4.4 16.2 1.0
O1A B:R1T2003 4.4 17.8 0.5
O3B B:R1T2003 4.5 15.9 0.5
O1A B:S1T2001 4.5 12.1 0.5
CB B:ASN456 4.5 19.8 1.0
CA B:TRP459 4.6 18.5 1.0
CA B:ASP429 4.6 16.3 1.0
CB B:GLU460 4.6 22.4 1.0
CA B:GLY428 4.6 16.7 1.0
C B:GLY428 4.7 16.6 1.0
CB B:SER458 4.7 21.4 1.0
CA B:ASN456 4.8 20.5 1.0
C B:ASN456 4.9 21.6 1.0
N B:ALA457 4.9 20.9 1.0
C B:ASP429 5.0 16.1 1.0
C B:TRP459 5.0 18.5 1.0

Reference:

W.Versees, S.Spaepen, M.D.Wood, F.J.Leeper, J.Vanderleyden, J.Steyaert. Molecular Mechanism of Allosteric Substrate Activation in A Thiamine Diphosphate-Dependent Decarboxylase. J.Biol.Chem. V. 282 35269 2007.
ISSN: ISSN 0021-9258
PubMed: 17905741
DOI: 10.1074/JBC.M706048200
Page generated: Mon Dec 14 07:35:58 2020

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