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Magnesium in PDB 1ovm: Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae

Enzymatic activity of Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae

All present enzymatic activity of Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae:
4.1.1.74;

Protein crystallography data

The structure of Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae, PDB code: 1ovm was solved by A.Schutz, T.Sandalova, S.Ricagno, G.Hubner, S.Konig, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.56 / 2.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 132.200, 151.620, 107.550, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae (pdb code 1ovm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae, PDB code: 1ovm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ovm

Go back to Magnesium Binding Sites List in 1ovm
Magnesium binding site 1 out of 4 in the Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae


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 Indolepyruvate Decarboxylase From Enterobacter Cloacae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:23.6
occ:1.00
 O A:HOH647 2.2 22.7 1.0
OD1 A:ASN462 2.2 35.6 1.0
OD1 A:ASP435 2.3 25.8 1.0
O A:GLY464 2.3 27.7 1.0
O2A A:TPP600 2.4 21.6 1.0
O3B A:TPP600 2.5 27.0 1.0
CG A:ASN462 3.0 31.5 1.0
PB A:TPP600 3.1 26.4 1.0
ND2 A:ASN462 3.2 30.5 1.0
O1B A:TPP600 3.2 25.5 1.0
CG A:ASP435 3.3 24.4 1.0
O3A A:TPP600 3.3 25.6 1.0
PA A:TPP600 3.5 23.5 1.0
C A:GLY464 3.6 30.8 1.0
O A:LEU460 3.7 28.7 1.0
N A:ASP435 3.7 26.7 1.0
OD2 A:ASP435 3.8 23.8 1.0
N A:GLY436 4.1 24.1 1.0
N A:GLY464 4.3 33.0 1.0
N A:ASN462 4.3 28.9 1.0
CA A:GLY434 4.4 26.3 1.0
O1A A:TPP600 4.4 26.4 1.0
CB A:ASP435 4.4 24.7 1.0
CB A:ASN462 4.4 30.4 1.0
O7 A:TPP600 4.4 24.5 1.0
CA A:GLY464 4.5 30.8 1.0
C A:GLY434 4.5 26.8 1.0
CG2 A:THR466 4.5 29.4 1.0
N A:TYR465 4.5 30.4 1.0
CA A:ASP435 4.5 24.5 1.0
N A:THR466 4.5 30.1 1.0
O2B A:TPP600 4.5 27.7 1.0
CA A:TYR465 4.6 29.3 1.0
CA A:ASN462 4.8 30.2 1.0
C A:ASP435 4.8 24.8 1.0
C A:LEU460 4.9 28.6 1.0
C A:ASN462 4.9 31.1 1.0

Magnesium binding site 2 out of 4 in 1ovm

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Magnesium binding site 2 out of 4 in the Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae


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 Indolepyruvate Decarboxylase From Enterobacter Cloacae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:19.9
occ:1.00
 OD1 B:ASN462 2.2 32.0 1.0
OD1 B:ASP435 2.3 23.8 1.0
O B:HOH660 2.3 18.9 1.0
O2A B:TPP600 2.4 22.3 1.0
O B:GLY464 2.4 29.0 1.0
O3B B:TPP600 2.6 24.9 1.0
CG B:ASN462 3.0 29.1 1.0
ND2 B:ASN462 3.1 27.3 1.0
PB B:TPP600 3.2 26.1 1.0
O1B B:TPP600 3.2 27.4 1.0
CG B:ASP435 3.2 23.3 1.0
O3A B:TPP600 3.4 25.0 1.0
PA B:TPP600 3.5 22.9 1.0
C B:GLY464 3.6 30.3 1.0
O B:LEU460 3.6 29.4 1.0
N B:ASP435 3.7 24.2 1.0
OD2 B:ASP435 3.7 20.5 1.0
N B:GLY436 4.1 23.6 1.0
N B:GLY464 4.3 30.8 1.0
N B:ASN462 4.3 28.0 1.0
CB B:ASP435 4.4 24.0 1.0
CA B:GLY434 4.4 24.4 1.0
O1A B:TPP600 4.4 23.2 1.0
CB B:ASN462 4.4 28.2 1.0
O7 B:TPP600 4.4 25.3 1.0
C B:GLY434 4.5 24.0 1.0
CA B:ASP435 4.5 23.6 1.0
CA B:GLY464 4.5 30.5 1.0
N B:TYR465 4.5 29.0 1.0
N B:THR466 4.5 30.3 1.0
CG2 B:THR466 4.6 27.0 1.0
O2B B:TPP600 4.6 25.7 1.0
CA B:TYR465 4.6 28.8 1.0
CA B:ASN462 4.8 29.1 1.0
C B:LEU460 4.8 28.4 1.0
C B:ASP435 4.8 24.0 1.0
C B:ASN462 4.9 30.0 1.0
O B:HOH603 5.0 20.8 1.0

Magnesium binding site 3 out of 4 in 1ovm

Go back to Magnesium Binding Sites List in 1ovm
Magnesium binding site 3 out of 4 in the Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:29.1
occ:1.00
 OD1 C:ASP435 2.3 32.0 1.0
OD1 C:ASN462 2.3 36.4 1.0
O2A C:TPP600 2.4 28.3 1.0
O C:GLY464 2.6 28.6 1.0
O3B C:TPP600 2.7 30.4 1.0
CG C:ASN462 3.0 33.6 1.0
O1B C:TPP600 3.0 31.0 1.0
CG C:ASP435 3.1 30.6 1.0
PB C:TPP600 3.2 32.7 1.0
ND2 C:ASN462 3.2 34.0 1.0
O C:LEU460 3.3 29.9 1.0
O3A C:TPP600 3.4 29.1 1.0
N C:ASP435 3.4 26.9 1.0
PA C:TPP600 3.5 27.1 1.0
OD2 C:ASP435 3.6 30.1 1.0
C C:GLY464 3.9 32.1 1.0
N C:GLY436 4.1 26.3 1.0
CA C:GLY434 4.1 26.8 1.0
C C:GLY434 4.2 25.8 1.0
CB C:ASP435 4.2 28.8 1.0
O1A C:TPP600 4.2 28.6 1.0
N C:ASN462 4.3 31.2 1.0
CA C:ASP435 4.3 27.8 1.0
CB C:ASN462 4.4 31.8 1.0
C C:LEU460 4.5 29.2 1.0
N C:GLY464 4.5 34.9 1.0
O7 C:TPP600 4.5 29.7 1.0
O2B C:TPP600 4.6 30.6 1.0
CG2 C:THR466 4.7 31.2 1.0
CA C:GLY464 4.7 32.6 1.0
C C:ASP435 4.7 27.2 1.0
CA C:ASN462 4.8 32.1 1.0
N C:THR466 4.8 32.4 1.0
N C:TYR465 4.8 31.6 1.0
CA C:TYR465 5.0 30.7 1.0
C C:ASN462 5.0 32.6 1.0

Magnesium binding site 4 out of 4 in 1ovm

Go back to Magnesium Binding Sites List in 1ovm
Magnesium binding site 4 out of 4 in the Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Indolepyruvate Decarboxylase From Enterobacter Cloacae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:27.1
occ:1.00
 OD1 D:ASP435 2.3 29.0 1.0
OD1 D:ASN462 2.3 36.4 1.0
O2A D:TPP600 2.4 27.5 1.0
O D:GLY464 2.5 30.6 1.0
O3B D:TPP600 2.5 26.9 1.0
O1B D:TPP600 3.0 29.9 1.0
PB D:TPP600 3.1 31.2 1.0
CG D:ASN462 3.1 32.8 1.0
ND2 D:ASN462 3.2 33.0 1.0
O3A D:TPP600 3.3 29.1 1.0
CG D:ASP435 3.3 28.6 1.0
PA D:TPP600 3.5 31.7 1.0
O D:LEU460 3.5 33.0 1.0
N D:ASP435 3.6 27.8 1.0
C D:GLY464 3.7 32.2 1.0
OD2 D:ASP435 4.0 28.9 1.0
N D:GLY436 4.1 26.9 1.0
CA D:GLY434 4.2 26.9 1.0
O1A D:TPP600 4.3 31.6 1.0
C D:GLY434 4.3 27.4 1.0
N D:ASN462 4.3 31.1 1.0
CB D:ASP435 4.4 28.2 1.0
CA D:ASP435 4.4 27.1 1.0
CB D:ASN462 4.5 30.5 1.0
N D:GLY464 4.5 35.0 1.0
O7 D:TPP600 4.5 31.4 1.0
O2B D:TPP600 4.5 28.9 1.0
CA D:GLY464 4.7 32.6 1.0
N D:THR466 4.7 32.8 1.0
CG2 D:THR466 4.7 30.1 1.0
N D:TYR465 4.7 31.7 1.0
C D:LEU460 4.7 31.4 1.0
CA D:TYR465 4.8 31.2 1.0
C D:ASP435 4.8 27.4 1.0
CA D:ASN462 4.9 31.6 1.0
O D:HOH602 4.9 18.9 1.0

Reference:

A.Schutz, T.Sandalova, S.Ricagno, G.Hubner, S.Konig, G.Schneider. Crystal Structure of Thiamindiphosphate-Dependent Indolepyruvate Decarboxylase From Enterobacter Cloacae, An Enzyme Involved in the Biosynthesis of the Plant Hormone Indole-3-Acetic Acid Eur.J.Biochem. V. 270 2312 2003.
ISSN: ISSN 0014-2956
PubMed: 12752451
DOI: 10.1046/J.1432-1033.2003.03601.X
Page generated: Tue Aug 13 10:43:38 2024

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