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Magnesium in PDB 3oe1: Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp

Enzymatic activity of Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp

All present enzymatic activity of Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp:
4.1.1.1;

Protein crystallography data

The structure of Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp, PDB code: 3oe1 was solved by D.Meyer, P.Neumann, C.Parthier, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.58 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.493, 165.356, 95.869, 90.00, 108.93, 90.00
R / Rfree (%) 19.4 / 24.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp (pdb code 3oe1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp, PDB code: 3oe1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3oe1

Go back to Magnesium Binding Sites List in 3oe1
Magnesium binding site 1 out of 4 in the Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:23.4
occ:1.00
 OD1 A:ASN467 2.2 19.8 1.0
O1A A:TDL611 2.2 16.6 1.0
O A:GLY469 2.2 21.1 1.0
O3B A:TDL611 2.3 19.3 1.0
OD1 A:ASP440 2.3 17.8 1.0
O A:HOH1251 2.4 14.5 1.0
CG A:ASN467 3.1 21.9 1.0
PB A:TDL611 3.3 23.5 1.0
ND2 A:ASN467 3.4 22.1 1.0
PA A:TDL611 3.4 16.7 1.0
C A:GLY469 3.4 20.3 1.0
CG A:ASP440 3.5 23.8 1.0
O2B A:TDL611 3.5 26.5 1.0
O3A A:TDL611 3.7 23.9 1.0
O A:ILE465 4.0 15.7 1.0
N A:ASP440 4.0 19.8 1.0
OD2 A:ASP440 4.1 24.0 1.0
N A:THR471 4.1 22.4 1.0
N A:GLY469 4.2 20.8 1.0
N A:GLY441 4.2 18.9 1.0
O7 A:TDL611 4.3 21.0 1.0
CA A:GLY469 4.4 21.3 1.0
N A:TYR470 4.4 19.7 1.0
N A:ASN467 4.4 19.6 1.0
CA A:TYR470 4.4 22.7 1.0
CB A:ASN467 4.5 20.5 1.0
O2A A:TDL611 4.5 18.2 1.0
CA A:GLY439 4.6 19.6 1.0
O A:HOH708 4.6 18.0 1.0
O1B A:TDL611 4.6 24.2 1.0
C A:GLY439 4.7 20.6 1.0
CB A:ASP440 4.7 21.9 1.0
C A:ASN467 4.8 21.8 1.0
CA A:ASP440 4.8 20.2 1.0
CA A:ASN467 4.8 20.4 1.0
C A:TYR470 4.8 23.9 1.0
OG1 A:THR471 4.8 23.7 1.0
CB A:THR471 4.8 23.4 1.0
N A:TYR468 5.0 22.8 0.4
CA A:GLY441 5.0 19.6 1.0
N A:TYR468 5.0 22.5 0.6

Magnesium binding site 2 out of 4 in 3oe1

Go back to Magnesium Binding Sites List in 3oe1
Magnesium binding site 2 out of 4 in the Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:26.5
occ:1.00
 O B:GLY469 2.2 17.0 1.0
OD1 B:ASN467 2.2 17.0 1.0
O1A B:TDL611 2.2 19.5 1.0
OD1 B:ASP440 2.3 21.1 1.0
O3B B:TDL611 2.4 23.5 1.0
O B:HOH897 2.5 24.9 1.0
CG B:ASN467 3.1 18.4 1.0
C B:GLY469 3.4 20.5 1.0
CG B:ASP440 3.4 21.1 1.0
ND2 B:ASN467 3.5 14.3 1.0
PB B:TDL611 3.5 22.4 1.0
PA B:TDL611 3.5 19.2 1.0
O3A B:TDL611 3.9 17.3 1.0
OD2 B:ASP440 3.9 21.9 1.0
O2B B:TDL611 3.9 29.1 1.0
N B:GLY469 3.9 17.5 1.0
N B:GLY441 3.9 16.6 1.0
O B:ILE465 4.0 19.6 1.0
N B:ASP440 4.1 19.1 1.0
N B:THR471 4.2 28.0 1.0
CA B:GLY469 4.2 20.0 1.0
N B:TYR470 4.3 21.8 1.0
N B:ASN467 4.3 15.9 1.0
O7 B:TDL611 4.4 16.1 1.0
CA B:TYR470 4.4 25.3 1.0
CB B:ASN467 4.4 17.5 1.0
N B:TYR468 4.6 20.6 1.0
C B:ASN467 4.6 21.2 1.0
O B:HOH624 4.6 15.2 1.0
CB B:ASP440 4.6 18.4 1.0
CA B:GLY439 4.6 18.8 1.0
C B:GLY439 4.7 20.4 1.0
O2A B:TDL611 4.7 22.3 1.0
CA B:ASN467 4.7 20.0 1.0
CA B:GLY441 4.7 15.1 1.0
CA B:ASP440 4.7 15.2 1.0
OG1 B:THR471 4.7 27.4 1.0
O1B B:TDL611 4.8 28.3 1.0
C B:ASP440 4.8 18.9 1.0
C B:TYR470 4.9 25.1 1.0
C B:TYR468 4.9 20.8 1.0
O B:ASN467 5.0 23.6 1.0
CB B:THR471 5.0 26.8 1.0

Magnesium binding site 3 out of 4 in 3oe1

Go back to Magnesium Binding Sites List in 3oe1
Magnesium binding site 3 out of 4 in the Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:24.1
occ:1.00
 O1A C:TDL611 2.2 22.8 1.0
O3B C:TDL611 2.2 16.3 1.0
OD1 C:ASP440 2.3 22.9 1.0
OD1 C:ASN467 2.3 24.1 1.0
O C:GLY469 2.3 24.9 1.0
O C:HOH1252 2.4 20.0 1.0
CG C:ASN467 3.2 24.2 1.0
PB C:TDL611 3.3 23.8 1.0
PA C:TDL611 3.4 24.8 1.0
CG C:ASP440 3.5 27.3 1.0
ND2 C:ASN467 3.5 25.7 1.0
C C:GLY469 3.5 21.9 1.0
O3A C:TDL611 3.7 27.9 1.0
O2B C:TDL611 3.7 26.7 1.0
N C:ASP440 4.0 18.5 1.0
OD2 C:ASP440 4.0 31.2 1.0
O C:ILE465 4.1 25.5 1.0
N C:THR471 4.1 28.1 1.0
N C:GLY441 4.2 20.7 1.0
N C:GLY469 4.2 20.9 1.0
O7 C:TDL611 4.3 34.9 1.0
N C:ASN467 4.4 22.8 1.0
N C:TYR470 4.4 20.6 1.0
CA C:TYR470 4.4 25.7 1.0
CA C:GLY469 4.5 19.7 1.0
CB C:ASN467 4.5 22.2 1.0
O C:HOH603 4.6 37.4 1.0
O2A C:TDL611 4.6 31.7 1.0
CA C:GLY439 4.6 23.8 1.0
CB C:ASP440 4.6 22.4 1.0
O1B C:TDL611 4.6 23.9 1.0
C C:ASN467 4.7 24.7 1.0
OG1 C:THR471 4.7 32.1 1.0
C C:GLY439 4.7 21.1 1.0
CA C:ASP440 4.7 19.9 1.0
CA C:ASN467 4.7 21.5 1.0
CB C:THR471 4.7 29.5 1.0
C C:TYR470 4.8 30.6 1.0
N C:TYR468 4.8 25.9 1.0
O C:ASN467 5.0 23.8 1.0
C C:ASP440 5.0 21.0 1.0

Magnesium binding site 4 out of 4 in 3oe1

Go back to Magnesium Binding Sites List in 3oe1
Magnesium binding site 4 out of 4 in the Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate Decarboxylase Variant GLU473ASP From Z. Mobilis in Complex with Reaction Intermediate 2-Lactyl-Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:26.4
occ:1.00
 O2A D:TDL611 2.2 13.3 1.0
OD1 D:ASN467 2.2 20.9 1.0
O D:GLY469 2.2 22.6 1.0
OD1 D:ASP440 2.3 18.1 1.0
O3B D:TDL611 2.4 24.3 1.0
O D:HOH898 2.5 17.1 1.0
CG D:ASN467 3.1 20.5 1.0
PB D:TDL611 3.3 23.3 1.0
ND2 D:ASN467 3.3 17.3 1.0
C D:GLY469 3.4 21.1 1.0
PA D:TDL611 3.4 17.9 1.0
CG D:ASP440 3.5 19.9 1.0
O2B D:TDL611 3.5 25.5 1.0
O3A D:TDL611 3.8 18.6 1.0
OD2 D:ASP440 4.0 24.1 1.0
N D:GLY469 4.0 22.2 1.0
O D:ILE465 4.1 22.4 1.0
N D:GLY441 4.1 18.8 1.0
N D:ASP440 4.1 15.1 1.0
N D:THR471 4.1 23.7 1.0
CA D:GLY469 4.3 22.5 1.0
N D:TYR470 4.3 20.3 1.0
O7 D:TDL611 4.3 13.8 1.0
CA D:TYR470 4.4 23.3 1.0
N D:ASN467 4.4 14.3 1.0
CB D:ASN467 4.5 17.2 1.0
O D:HOH751 4.5 23.2 1.0
O1A D:TDL611 4.5 18.7 1.0
CB D:ASP440 4.7 15.2 1.0
CA D:GLY439 4.7 16.9 1.0
C D:ASN467 4.7 20.4 1.0
N D:TYR468 4.7 20.5 1.0
O1B D:TDL611 4.7 25.5 1.0
OG1 D:THR471 4.7 23.8 1.0
C D:GLY439 4.8 18.0 1.0
CA D:ASP440 4.8 13.1 1.0
CA D:ASN467 4.8 19.2 1.0
C D:TYR470 4.8 26.5 1.0
CB D:THR471 4.8 23.9 1.0
CA D:GLY441 4.9 19.2 1.0
C D:ASP440 5.0 15.2 1.0

Reference:

D.Meyer, P.Neumann, C.Parthier, R.Friedemann, N.Nemeria, F.Jordan, K.Tittmann. Double Duty For A Conserved Glutamate in Pyruvate Decarboxylase: Evidence of the Participation in Stereoelectronically Controlled Decarboxylation and in Protonation of the Nascent Carbanion/Enamine Intermediate . Biochemistry V. 49 8197 2010.
ISSN: ISSN 0006-2960
PubMed: 20715795
DOI: 10.1021/BI100828R
Page generated: Mon Dec 14 08:32:10 2020

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