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Magnesium in PDB 2nxw: Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense

Enzymatic activity of Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense

All present enzymatic activity of Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense:
4.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense, PDB code: 2nxw was solved by W.Versees, S.Spaepen, J.Vanderleyden, J.Steyaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 99.411, 179.032, 120.925, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.6

Other elements in 2nxw:

The structure of Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense (pdb code 2nxw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense, PDB code: 2nxw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2nxw

Go back to Magnesium Binding Sites List in 2nxw
Magnesium binding site 1 out of 2 in the Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4002

b:10.3
occ:1.00
OD1 A:ASP429 2.1 10.4 1.0
O1B A:TPP2002 2.1 10.5 1.0
OD1 A:ASN456 2.1 11.7 1.0
O2A A:TPP2002 2.1 9.8 1.0
O A:SER458 2.1 10.1 1.0
O A:HOH4004 2.1 11.4 1.0
CG A:ASN456 3.1 10.8 1.0
CG A:ASP429 3.2 11.1 1.0
PB A:TPP2002 3.3 10.7 1.0
PA A:TPP2002 3.3 10.0 1.0
C A:SER458 3.3 10.3 1.0
O3A A:TPP2002 3.4 9.4 1.0
ND2 A:ASN456 3.5 12.6 1.0
OD2 A:ASP429 3.7 11.3 1.0
O7 A:TPP2002 3.9 9.6 1.0
N A:ASP429 4.0 9.0 1.0
N A:SER458 4.0 10.5 1.0
CA A:SER458 4.1 10.3 1.0
O2B A:TPP2002 4.1 13.3 1.0
N A:GLU460 4.1 10.5 1.0
O A:PHE454 4.2 12.4 1.0
N A:GLY430 4.3 9.8 1.0
N A:TRP459 4.3 10.1 1.0
N A:ASN456 4.3 11.5 1.0
CB A:ASP429 4.4 10.1 1.0
O3B A:TPP2002 4.4 11.5 1.0
O A:HOH4091 4.4 17.5 1.0
CB A:ASN456 4.4 11.6 1.0
O1A A:TPP2002 4.5 11.2 1.0
CA A:TRP459 4.5 10.1 1.0
CB A:SER458 4.5 12.1 1.0
CA A:ASP429 4.6 9.7 1.0
CB A:GLU460 4.7 11.0 1.0
CA A:ASN456 4.7 10.9 1.0
CA A:GLY428 4.8 9.8 1.0
C A:GLY428 4.8 9.4 1.0
N A:ALA457 4.8 11.5 1.0
C A:ASN456 4.8 11.5 1.0
C A:TRP459 4.9 11.1 1.0

Magnesium binding site 2 out of 2 in 2nxw

Go back to Magnesium Binding Sites List in 2nxw
Magnesium binding site 2 out of 2 in the Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Phenylpyruvate Decarboxylase of Azospirillum Brasilense within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4001

b:14.7
occ:1.00
O2A B:TPP2001 2.1 13.8 1.0
O1B B:TPP2001 2.1 15.4 1.0
OD1 B:ASP429 2.1 14.8 1.0
OD1 B:ASN456 2.1 15.1 1.0
O B:SER458 2.1 14.6 1.0
O B:HOH4005 2.1 15.5 1.0
CG B:ASN456 3.1 15.4 1.0
CG B:ASP429 3.1 15.2 1.0
PA B:TPP2001 3.2 14.0 1.0
PB B:TPP2001 3.3 14.9 1.0
C B:SER458 3.3 14.6 1.0
O3A B:TPP2001 3.4 13.5 1.0
ND2 B:ASN456 3.5 16.4 1.0
OD2 B:ASP429 3.6 15.0 1.0
O7 B:TPP2001 3.9 12.2 1.0
N B:ASP429 3.9 12.5 1.0
N B:SER458 4.0 15.2 1.0
CA B:SER458 4.1 15.8 1.0
N B:GLU460 4.2 14.4 1.0
O2B B:TPP2001 4.2 18.0 1.0
O B:PHE454 4.2 15.4 1.0
N B:GLY430 4.3 12.4 1.0
N B:TRP459 4.3 15.0 1.0
N B:ASN456 4.3 16.2 1.0
O3B B:TPP2001 4.3 15.6 1.0
CB B:ASP429 4.4 14.0 1.0
O B:HOH4081 4.4 19.9 1.0
O1A B:TPP2001 4.4 14.5 1.0
CB B:ASN456 4.5 16.3 1.0
CA B:TRP459 4.5 14.8 1.0
CA B:ASP429 4.6 13.0 1.0
CB B:GLU460 4.6 17.9 1.0
CB B:SER458 4.7 18.0 1.0
CA B:GLY428 4.7 12.8 1.0
C B:GLY428 4.7 12.3 1.0
CA B:ASN456 4.8 16.4 1.0
C B:ASN456 4.9 17.5 1.0
C B:TRP459 4.9 14.7 1.0
N B:ALA457 4.9 16.3 1.0
C B:ASP429 5.0 12.9 1.0

Reference:

W.Versees, S.Spaepen, J.Vanderleyden, J.Steyaert. The Crystal Structure of Phenylpyruvate Decarboxylase From Azospirillum Brasilense at 1.5 A Resolution. Implications For Its Catalytic and Regulatory Mechanism. Febs J. V. 274 2363 2007.
ISSN: ISSN 1742-464X
PubMed: 17403037
DOI: 10.1111/J.1742-4658.2007.05771.X
Page generated: Mon Dec 14 07:31:17 2020

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