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Magnesium in PDB 2wsb: Crystal Structure of the Short-Chain Dehydrogenase Galactitol-Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad

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

All present enzymatic activity of Crystal Structure of the Short-Chain Dehydrogenase Galactitol-Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad:
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, PDB code: 2wsb was solved by Y.Carius, H.Christian, A.Faust, P.Kornberger, 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) 19.94 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.790, 106.620, 109.330, 90.00, 90.00, 90.00
R / Rfree (%) 13.393 / 17.749

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 (pdb code 2wsb). 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 the Short-Chain Dehydrogenase Galactitol-Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad, PDB code: 2wsb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2wsb

Go back to Magnesium Binding Sites List in 2wsb
Magnesium binding site 1 out of 2 in the Crystal Structure of the Short-Chain Dehydrogenase Galactitol-Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg256

b:11.0
occ:1.00
 OXT B:TRP254 2.0 12.3 1.0
O A:HOH2465 2.0 20.8 1.0
OXT A:TRP254 2.1 11.6 1.0
O B:HOH2413 2.1 13.3 1.0
O A:HOH2467 2.1 12.8 1.0
O B:HOH2414 2.1 16.0 1.0
C B:TRP254 2.9 11.8 1.0
C A:TRP254 3.0 11.2 1.0
O A:TRP254 3.3 12.3 1.0
O B:TRP254 3.3 12.4 1.0
CA A:TRP254 4.3 12.1 1.0
CA B:TRP254 4.3 11.8 1.0
O B:HOH2411 4.3 20.7 1.0
O B:HOH2412 4.3 20.9 1.0
O A:HOH2463 4.3 26.0 1.0
O B:TYR251 4.4 11.8 1.0
CG2 A:ILE149 4.4 13.5 1.0
CG2 B:ILE149 4.4 13.7 1.0
O B:HOH2382 4.4 14.5 1.0
O A:TYR251 4.4 12.0 1.0
O A:HOH2431 4.6 15.5 1.0
O A:THR252 4.7 16.0 1.0
N B:TRP254 4.7 11.4 1.0
N A:TRP254 4.7 11.4 1.0
CB A:TRP254 4.8 13.0 1.0
O B:THR252 4.9 15.1 1.0
CB B:TRP254 4.9 12.7 1.0
C A:THR252 4.9 12.5 1.0
CA A:THR252 4.9 12.6 1.0
CA B:THR252 4.9 11.7 1.0
C B:THR252 5.0 12.3 1.0

Magnesium binding site 2 out of 2 in 2wsb

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg256

b:12.2
occ:1.00
 OXT C:TRP254 2.0 13.1 1.0
O D:HOH2418 2.0 21.6 1.0
OXT D:TRP254 2.0 12.6 1.0
O D:HOH2420 2.1 14.1 1.0
O C:HOH2452 2.1 13.7 1.0
O C:HOH2453 2.2 17.7 1.0
C C:TRP254 3.0 13.3 1.0
C D:TRP254 3.0 12.4 1.0
O D:TRP254 3.3 13.5 1.0
O C:TRP254 3.3 13.6 1.0
O C:HOH2449 4.3 23.1 1.0
CA C:TRP254 4.3 11.3 1.0
O D:HOH2419 4.3 25.3 1.0
O D:HOH2415 4.3 24.0 1.0
CA D:TRP254 4.3 11.8 1.0
CG2 D:ILE149 4.4 14.0 1.0
CG2 C:ILE149 4.4 13.5 1.0
O D:TYR251 4.4 12.3 1.0
O C:TYR251 4.4 12.2 1.0
O C:HOH2454 4.5 29.3 1.0
O C:HOH2415 4.5 15.0 1.0
O D:HOH2384 4.6 15.9 1.0
N C:TRP254 4.6 11.4 1.0
N D:TRP254 4.7 11.4 1.0
O D:THR252 4.7 16.6 1.0
O C:THR252 4.8 16.5 1.0
CB C:TRP254 4.8 12.5 1.0
CB D:TRP254 4.8 12.6 1.0
C D:THR252 4.9 13.4 1.0
CA C:THR252 4.9 11.9 1.0
CA D:THR252 4.9 12.9 1.0
C C:THR252 4.9 13.1 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: Wed Aug 14 06:12:27 2024

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