Atomistry » Magnesium » PDB 3o1n-3oha » 3oe1
Atomistry »
  Magnesium »
    PDB 3o1n-3oha »
      3oe1 »

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: Thu Aug 15 08:17:32 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy