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Magnesium in PDB 2wdz: Crystal Structure of the Short Chain Dehydrogenase Galactitol-Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad+ and 1,2-Pentandiol

Enzymatic activity of Crystal Structure of the Short Chain Dehydrogenase Galactitol-Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad+ and 1,2-Pentandiol

All present enzymatic activity of Crystal Structure of the Short Chain Dehydrogenase Galactitol-Dehydrogenase (Gatdh) of Rhodobacter Sphaeroides in Complex with Nad+ and 1,2-Pentandiol:
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 1,2-Pentandiol, PDB code: 2wdz 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) 19.86 / 1.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.720, 113.620, 256.925, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24

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 1,2-Pentandiol (pdb code 2wdz). 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 1,2-Pentandiol, PDB code: 2wdz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2wdz

Go back to Magnesium Binding Sites List in 2wdz
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 1,2-Pentandiol


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 1,2-Pentandiol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg255

b:25.6
occ:0.50
 OXT A:TRP254 2.0 17.0 1.0
O A:HOH2143 2.3 26.5 1.0
O A:HOH2146 2.4 32.3 0.5
O A:HOH2145 2.6 27.8 0.5
C A:TRP254 2.9 17.4 1.0
O A:TRP254 3.2 16.0 1.0
O A:HOH2141 4.2 24.1 1.0
CA A:TRP254 4.3 18.4 1.0
O A:TYR251 4.5 17.5 1.0
CG2 A:ILE149 4.5 20.0 1.0
CB A:TRP254 4.7 19.7 1.0
N A:TRP254 4.7 18.4 1.0
O A:THR252 4.7 17.0 1.0

Magnesium binding site 2 out of 4 in 2wdz

Go back to Magnesium Binding Sites List in 2wdz
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 1,2-Pentandiol


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 1,2-Pentandiol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg255

b:27.5
occ:0.50
 OXT B:TRP254 2.2 19.0 1.0
O B:HOH2116 2.2 30.0 0.5
O B:HOH2111 2.2 13.8 1.0
O B:HOH2114 2.4 26.4 0.5
C B:TRP254 3.1 19.4 1.0
O B:TRP254 3.2 20.3 1.0
CA B:TRP254 4.4 17.3 1.0
CG2 B:ILE149 4.4 20.0 1.0
O B:TYR251 4.4 15.6 1.0
O B:THR252 4.4 17.7 1.0
O B:HOH2094 4.7 23.0 1.0
N B:TRP254 4.8 17.1 1.0
CB B:TRP254 4.9 17.0 1.0
C B:THR252 4.9 16.7 1.0
CA B:THR252 5.0 16.4 1.0

Magnesium binding site 3 out of 4 in 2wdz

Go back to Magnesium Binding Sites List in 2wdz
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 1,2-Pentandiol


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 1,2-Pentandiol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg256

b:20.2
occ:0.50
 OXT C:TRP254 1.9 25.7 1.0
O C:HOH2106 2.1 22.5 1.0
O C:HOH2104 2.2 30.0 1.0
O C:HOH2101 2.2 20.1 1.0
O C:HOH2105 2.4 26.5 1.0
C C:TRP254 3.0 25.6 1.0
O C:TRP254 3.3 24.4 1.0
O C:THR252 4.2 23.1 1.0
CA C:TRP254 4.3 25.1 1.0
O C:TYR251 4.4 19.8 1.0
CG2 C:ILE149 4.5 20.0 1.0
N C:TRP254 4.6 23.9 1.0
O C:HOH2102 4.6 19.4 1.0
C C:THR252 4.7 23.3 1.0
CB C:TRP254 4.8 24.6 1.0
CA C:THR252 4.9 22.0 1.0

Magnesium binding site 4 out of 4 in 2wdz

Go back to Magnesium Binding Sites List in 2wdz
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 1,2-Pentandiol


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 1,2-Pentandiol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg256

b:20.2
occ:0.50
 OXT D:TRP254 2.3 19.8 1.0
C D:TRP254 3.2 19.8 1.0
O D:TRP254 3.3 19.3 1.0
O D:HOH2113 4.2 43.0 1.0
CG2 D:ILE149 4.4 20.0 1.0
O D:TYR251 4.5 17.1 1.0
O D:HOH2093 4.5 26.8 1.0
CA D:TRP254 4.5 19.7 1.0
O D:THR252 4.8 19.6 1.0
N D:TRP254 4.8 19.4 1.0
CB D:TRP254 5.0 20.0 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 06:04:17 2024

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