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Manganese in PDB 4xis: 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: 4xis 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 / 1.60
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

Manganese Binding Sites:

The binding sites of Manganese 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 4xis). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese 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: 4xis:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4xis

Go back to Manganese Binding Sites List in 4xis
Manganese binding site 1 out of 3 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 Manganese with other atoms in the Mn 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:Mn391

b:10.0
occ:0.96
 MN A:MN391 0.0 10.0 1.0
MN A:MN391 1.8 12.1 0.2
OE2 A:GLU217 2.1 8.7 1.0
OD1 A:ASP255 2.3 9.7 1.0
OD2 A:ASP255 2.3 12.7 1.0
OD1 A:ASP257 2.3 9.7 1.0
O A:HOH737 2.3 9.8 1.0
NE2 A:HIS220 2.4 9.7 1.0
CG A:ASP255 2.6 9.8 1.0
CD A:GLU217 3.0 11.4 1.0
CD2 A:HIS220 3.1 6.2 1.0
OE1 A:GLU217 3.2 9.6 1.0
CG A:ASP257 3.3 9.9 1.0
OD2 A:ASP257 3.4 13.8 1.0
CE1 A:HIS220 3.5 7.6 1.0
O1 A:XLS393 3.7 14.1 1.0
OD1 A:ASN247 4.0 11.9 1.0
O2 A:XLS393 4.1 9.9 1.0
O A:HOH476 4.1 9.6 1.0
CB A:ASP255 4.1 7.4 1.0
CG A:HIS220 4.2 3.7 1.0
CG A:GLU217 4.4 6.3 1.0
ND1 A:HIS220 4.5 8.5 1.0
CB A:ASP257 4.6 7.7 1.0
C1 A:XLS393 4.7 16.4 0.8
O A:HOH663 4.7 23.6 0.9
OD2 A:ASP287 4.7 12.2 1.0
C2 A:XLS393 4.8 14.6 0.8
NZ A:LYS183 4.8 11.7 1.0
CE A:LYS183 4.8 9.5 1.0
MN A:MN392 4.9 8.9 1.0
O2 A:XYS394 5.0 32.1 0.2

Manganese binding site 2 out of 3 in 4xis

Go back to Manganese Binding Sites List in 4xis
Manganese binding site 2 out of 3 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 Manganese with other atoms in the Mn 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:Mn391

b:12.1
occ:0.17
 MN A:MN391 0.0 12.1 0.2
MN A:MN391 1.8 10.0 1.0
O A:HOH737 1.9 9.8 1.0
NE2 A:HIS220 2.1 9.7 1.0
O2 A:XLS393 2.3 9.9 1.0
CE1 A:HIS220 2.5 7.6 1.0
OE1 A:GLU217 2.5 9.6 1.0
O1 A:XLS393 2.6 14.1 1.0
OE2 A:GLU217 2.7 8.7 1.0
CD A:GLU217 3.0 11.4 1.0
OD2 A:ASP255 3.1 12.7 1.0
C2 A:XLS393 3.1 14.6 0.8
CD2 A:HIS220 3.3 6.2 1.0
C1 A:XLS393 3.3 16.4 0.8
MN A:MN392 3.5 8.9 1.0
OD1 A:ASP257 3.7 9.7 1.0
O2 A:XYS394 3.7 32.1 0.2
ND1 A:HIS220 3.7 8.5 1.0
OD2 A:ASP287 3.7 12.2 1.0
OD1 A:ASP255 3.8 9.7 1.0
CG A:ASP255 3.9 9.8 1.0
CG A:HIS220 4.1 3.7 1.0
OD2 A:ASP257 4.1 13.8 1.0
OE2 A:GLU181 4.2 9.6 1.0
CG A:GLU217 4.4 6.3 1.0
CG A:ASP257 4.4 9.9 1.0
C3 A:XLS393 4.4 10.5 0.8
C2 A:XYS394 4.5 24.8 0.2
O3 A:XLS393 4.7 15.9 0.8
NZ A:LYS183 4.7 11.7 1.0
CG A:ASP287 4.7 9.9 1.0
CE A:LYS183 4.8 9.5 1.0
CD A:LYS183 4.9 5.7 1.0
O3 A:XYS394 4.9 23.2 0.2
CB A:GLU217 4.9 5.5 1.0

Manganese binding site 3 out of 3 in 4xis

Go back to Manganese Binding Sites List in 4xis
Manganese binding site 3 out of 3 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 Manganese with other atoms in the Mn binding site number 3 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:Mn392

b:8.9
occ:0.99
 OE2 A:GLU181 2.1 9.6 1.0
OE1 A:GLU217 2.2 9.6 1.0
OD2 A:ASP245 2.2 11.8 1.0
OD2 A:ASP287 2.2 12.2 1.0
O3 A:XYS394 2.3 23.2 0.2
O2 A:XLS393 2.3 9.9 1.0
O4 A:XLS393 2.3 7.4 0.8
CD A:GLU181 3.0 8.9 1.0
CG A:ASP287 3.3 9.9 1.0
OE1 A:GLU181 3.3 10.3 1.0
CG A:ASP245 3.4 9.9 1.0
CD A:GLU217 3.4 11.4 1.0
C4 A:XLS393 3.4 9.5 0.8
C2 A:XLS393 3.4 14.6 0.8
C3 A:XYS394 3.5 25.1 0.2
O2 A:XYS394 3.5 32.1 0.2
MN A:MN391 3.5 12.1 0.2
C3 A:XLS393 3.7 10.5 0.8
C2 A:XYS394 3.7 24.8 0.2
CB A:ASP287 3.7 7.8 1.0
O3 A:XLS393 3.7 15.9 0.8
CB A:ASP245 4.0 5.0 1.0
O A:HOH737 4.0 9.8 1.0
O A:HOH738 4.1 13.7 0.9
CG A:GLU217 4.1 6.3 1.0
CE1 A:HIS220 4.1 7.6 1.0
CB A:GLU217 4.2 5.5 1.0
OE2 A:GLU217 4.2 8.7 1.0
OD1 A:ASP245 4.3 8.8 1.0
OD1 A:ASP287 4.4 9.5 1.0
CG A:GLU181 4.4 7.3 1.0
C4 A:XYS394 4.4 28.4 0.2
C5 A:XLS393 4.7 13.0 0.8
NE2 A:HIS220 4.7 9.7 1.0
C1 A:XLS393 4.8 16.4 0.8
ND1 A:HIS220 4.9 8.5 1.0
MN A:MN391 4.9 10.0 1.0
OD1 A:ASN215 4.9 11.0 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: Sat Oct 5 22:55:02 2024

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