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Magnesium in PDB 3lqf: Crystal Structure of the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol

Enzymatic activity of Crystal Structure of the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol

All present enzymatic activity of Crystal Structure of the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol:
1.1.1.16;

Protein crystallography data

The structure of Crystal Structure of the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol, PDB code: 3lqf was solved by Y.Carius, H.Christian, A.Faust, P.Kornberger, U.Zander, B.U.Klink, G.W.Kohring, F.Giffhorn, A.J.Scheidig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.863, 113.838, 123.234, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol (pdb code 3lqf). 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 the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol, PDB code: 3lqf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3lqf

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol


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 the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg255

b:12.0
occ:0.50
 MG A:MG255 0.0 12.0 0.5
MG A:MG255 0.8 11.1 0.5
OXT A:TRP254 1.8 14.5 1.0
O B:HOH301 1.9 16.2 1.0
O A:HOH344 2.1 16.4 1.0
O A:HOH336 2.2 16.4 1.0
OXT B:TRP254 2.4 14.7 1.0
O A:HOH317 2.4 16.0 1.0
C A:TRP254 2.9 16.2 1.0
C B:TRP254 3.2 14.7 1.0
O A:TRP254 3.3 15.2 1.0
O B:TRP254 3.3 13.9 1.0
O A:TYR251 4.0 14.9 1.0
CA A:TRP254 4.1 15.3 1.0
O A:HOH305 4.2 17.2 1.0
O A:HOH363 4.2 25.4 1.0
CG2 A:ILE149 4.4 15.5 1.0
CG2 B:ILE149 4.4 15.6 1.0
N A:TRP254 4.5 14.3 1.0
O A:THR252 4.6 14.8 1.0
CA B:TRP254 4.6 15.1 1.0
CB A:TRP254 4.6 15.9 1.0
O B:HOH406 4.6 32.3 1.0
C A:THR252 4.6 14.3 1.0
O B:HOH355 4.6 19.3 1.0
CA A:THR252 4.6 14.1 1.0
O B:TYR251 4.8 14.1 1.0
O A:HOH365 4.8 29.6 1.0

Magnesium binding site 2 out of 4 in 3lqf

Go back to Magnesium Binding Sites List in 3lqf
Magnesium binding site 2 out of 4 in the Crystal Structure of the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol


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 the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg255

b:11.1
occ:0.50
 MG A:MG255 0.0 11.1 0.5
MG A:MG255 0.8 12.0 0.5
O A:HOH317 1.9 16.0 1.0
OXT B:TRP254 1.9 14.7 1.0
O A:HOH336 2.0 16.4 1.0
OXT A:TRP254 2.2 14.5 1.0
O A:HOH344 2.3 16.4 1.0
O B:HOH301 2.5 16.2 1.0
C B:TRP254 3.0 14.7 1.0
C A:TRP254 3.2 16.2 1.0
O B:TRP254 3.3 13.9 1.0
O A:TRP254 3.4 15.2 1.0
O B:HOH406 4.1 32.3 1.0
O B:TYR251 4.2 14.1 1.0
O A:HOH363 4.2 25.4 1.0
CG2 B:ILE149 4.2 15.6 1.0
CG2 A:ILE149 4.3 15.5 1.0
CA B:TRP254 4.3 15.1 1.0
O B:HOH355 4.3 19.3 1.0
O B:THR252 4.4 16.8 1.0
C B:THR252 4.5 16.5 1.0
N B:TRP254 4.6 15.4 1.0
CA B:THR252 4.6 15.6 1.0
CA A:TRP254 4.6 15.3 1.0
O A:TYR251 4.7 14.9 1.0
CB B:TRP254 4.8 15.5 1.0
O A:HOH305 4.8 17.2 1.0
O A:THR252 4.9 14.8 1.0

Magnesium binding site 3 out of 4 in 3lqf

Go back to Magnesium Binding Sites List in 3lqf
Magnesium binding site 3 out of 4 in the Crystal Structure of the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol


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 the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg255

b:12.7
occ:0.50
 MG C:MG255 0.0 12.7 0.5
MG C:MG255 0.7 12.4 0.5
O C:HOH339 1.9 13.3 1.0
OXT D:TRP254 2.0 12.8 1.0
O D:HOH327 2.0 13.9 1.0
O D:HOH339 2.1 17.8 1.0
OXT C:TRP254 2.2 13.7 1.0
O D:HOH307 2.5 13.5 1.0
C D:TRP254 3.0 13.8 1.0
C C:TRP254 3.1 12.3 1.0
O C:TRP254 3.2 12.1 1.0
O D:TRP254 3.4 12.3 1.0
O D:TYR251 4.1 13.6 1.0
O D:HOH394 4.2 26.5 1.0
CG2 D:ILE149 4.2 11.7 1.0
O D:HOH325 4.3 17.3 1.0
CA D:TRP254 4.3 14.0 1.0
CA C:TRP254 4.5 12.8 1.0
N D:TRP254 4.5 13.4 1.0
CG2 C:ILE149 4.5 16.0 1.0
O D:THR252 4.5 14.4 1.0
CA D:THR252 4.6 13.9 1.0
C D:THR252 4.6 13.1 1.0
O C:HOH418 4.7 31.1 1.0
CB D:TRP254 4.7 14.6 1.0
O C:TYR251 4.8 13.8 1.0
O C:HOH389 4.8 13.8 1.0
N C:TRP254 4.9 13.2 1.0
CB D:ILE149 5.0 12.4 1.0

Magnesium binding site 4 out of 4 in 3lqf

Go back to Magnesium Binding Sites List in 3lqf
Magnesium binding site 4 out of 4 in the Crystal Structure of the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol


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 the Short-Chain Dehydrogenase Galactitol- Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad and Erythritol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg255

b:12.4
occ:0.50
 MG C:MG255 0.0 12.4 0.5
MG C:MG255 0.7 12.7 0.5
O D:HOH307 1.9 13.5 1.0
OXT C:TRP254 1.9 13.7 1.0
O D:HOH327 2.0 13.9 1.0
O D:HOH339 2.0 17.8 1.0
OXT D:TRP254 2.3 12.8 1.0
O C:HOH339 2.5 13.3 1.0
C C:TRP254 3.0 12.3 1.0
C D:TRP254 3.1 13.8 1.0
O D:TRP254 3.3 12.3 1.0
O C:TRP254 3.4 12.1 1.0
O C:TYR251 4.1 13.8 1.0
CA C:TRP254 4.2 12.8 1.0
CG2 D:ILE149 4.3 11.7 1.0
CG2 C:ILE149 4.3 16.0 1.0
O D:HOH394 4.3 26.5 1.0
O C:HOH389 4.4 13.8 1.0
N C:TRP254 4.5 13.2 1.0
CA D:TRP254 4.5 14.0 1.0
O C:THR252 4.6 15.9 1.0
CA C:THR252 4.7 13.9 1.0
C C:THR252 4.7 14.9 1.0
O D:TYR251 4.7 13.6 1.0
O D:HOH325 4.7 17.3 1.0
CB C:TRP254 4.8 12.8 1.0
N D:TRP254 4.9 13.4 1.0
O C:HOH418 4.9 31.1 1.0
O D:THR252 4.9 14.4 1.0

Reference:

Y.Carius, H.Christian, A.Faust, U.Zander, B.U.Klink, P.Kornberger, G.W.Kohring, F.Giffhorn, A.J.Scheidig. Structural Insight Into Substrate Differentiation of the Sugar-Metabolizing Enzyme Galactitol Dehydrogenase From Rhodobacter Sphaeroides D. J.Biol.Chem. V. 285 20006 2010.
ISSN: ISSN 0021-9258
PubMed: 20410293
DOI: 10.1074/JBC.M110.113738
Page generated: Mon Dec 14 08:24:36 2020

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