Atomistry » Magnesium » PDB 2wb4-2wkk » 2wdz
Atomistry »
  Magnesium »
    PDB 2wb4-2wkk »
      2wdz »

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

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