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Magnesium in PDB 2xis: A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 Angstroms Streptomyces Rubiginosus Structures with Xylitol and D-Xylose

Enzymatic activity of A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 Angstroms Streptomyces Rubiginosus Structures with Xylitol and D-Xylose

All present enzymatic activity of A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 Angstroms Streptomyces Rubiginosus Structures with Xylitol and D-Xylose:
5.3.1.5;

Protein crystallography data

The structure of A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 Angstroms Streptomyces Rubiginosus Structures with Xylitol and D-Xylose, PDB code: 2xis was solved by M.Whitlow, A.J.Howard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.71
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.640, 99.970, 103.970, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 Angstroms Streptomyces Rubiginosus Structures with Xylitol and D-Xylose (pdb code 2xis). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 Angstroms Streptomyces Rubiginosus Structures with Xylitol and D-Xylose, PDB code: 2xis:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2xis

Go back to Magnesium Binding Sites List in 2xis
Magnesium binding site 1 out of 2 in the A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 Angstroms Streptomyces Rubiginosus Structures with Xylitol and D-Xylose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 Angstroms Streptomyces Rubiginosus Structures with Xylitol and D-Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg391

b:41.5
occ:1.00
 OD2 A:ASP255 2.2 22.4 0.6
OD1 A:ASP255 2.5 19.5 0.6
CG A:ASP255 2.5 18.1 0.6
NE2 A:HIS220 2.8 11.5 1.0
O1 A:XYL390 2.8 11.5 1.0
OD1 A:ASP257 2.9 12.3 1.0
O A:HOH511 2.9 16.8 0.9
OD2 A:ASP255 3.1 7.3 0.4
OE2 A:GLU217 3.1 10.0 1.0
O A:HOH513 3.1 23.1 0.9
CD2 A:HIS220 3.4 2.5 1.0
OD2 A:ASP257 3.6 22.9 1.0
C1 A:XYL390 3.6 15.2 1.0
CG A:ASP257 3.7 12.7 1.0
NZ A:LYS183 3.8 10.2 1.0
CB A:ASP255 3.9 13.2 1.0
CG A:ASP255 3.9 4.5 0.4
CE1 A:HIS220 4.0 6.7 1.0
CE A:LYS183 4.0 8.1 1.0
O2 A:XYL390 4.0 14.3 1.0
CD A:GLU217 4.2 10.3 1.0
C2 A:XYL390 4.5 10.3 1.0
O A:HOH663 4.7 38.0 0.9
CG A:HIS220 4.7 4.7 1.0
OE1 A:GLU217 4.8 8.8 1.0
CD A:LYS183 4.8 4.5 1.0
OD1 A:ASN247 4.9 10.3 1.0
ND1 A:HIS220 4.9 5.8 1.0

Magnesium binding site 2 out of 2 in 2xis

Go back to Magnesium Binding Sites List in 2xis
Magnesium binding site 2 out of 2 in the A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 Angstroms Streptomyces Rubiginosus Structures with Xylitol and D-Xylose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 Angstroms Streptomyces Rubiginosus Structures with Xylitol and D-Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg392

b:10.4
occ:1.00
 OE2 A:GLU181 2.0 14.7 1.0
OE1 A:GLU217 2.1 8.8 1.0
O2 A:XYL390 2.2 14.3 1.0
OD2 A:ASP287 2.2 12.2 1.0
O4 A:XYL390 2.2 14.1 1.0
OD2 A:ASP245 2.3 7.6 1.0
CD A:GLU181 3.0 12.6 1.0
OE1 A:GLU181 3.2 9.1 1.0
CD A:GLU217 3.3 10.3 1.0
C2 A:XYL390 3.3 10.3 1.0
CG A:ASP287 3.3 9.9 1.0
CG A:ASP245 3.3 5.2 1.0
C4 A:XYL390 3.3 11.8 1.0
C3 A:XYL390 3.6 13.8 1.0
O3 A:XYL390 3.6 12.2 1.0
CB A:ASP287 3.8 7.2 1.0
O A:HOH448 3.9 18.0 0.9
OE2 A:GLU217 3.9 10.0 1.0
CB A:ASP245 3.9 4.2 1.0
O A:HOH511 4.1 16.8 0.9
CE1 A:HIS220 4.2 6.7 1.0
CG A:GLU217 4.2 7.4 1.0
CB A:GLU217 4.4 7.0 1.0
OD1 A:ASP287 4.4 8.1 1.0
OD1 A:ASP245 4.4 7.6 1.0
CG A:GLU181 4.4 10.1 1.0
C1 A:XYL390 4.5 15.2 1.0
NE2 A:HIS220 4.6 11.5 1.0
C5 A:XYL390 4.6 8.8 1.0
OD1 A:ASN215 4.7 8.3 1.0

Reference:

M.Whitlow, A.J.Howard, B.C.Finzel, T.L.Poulos, E.Winborne, G.L.Gilliland. A Metal-Mediated Hydride Shift Mechanism For Xylose Isomerase Based on the 1.6 A Streptomyces Rubiginosus Structures with Xylitol and D-Xylose. Proteins V. 9 153 1991.
ISSN: ISSN 0887-3585
PubMed: 2006134
DOI: 10.1002/PROT.340090302
Page generated: Wed Aug 14 07:09:27 2024

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