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Manganese in PDB 1a0d: Xylose Isomerase From Bacillus Stearothermophilus

Enzymatic activity of Xylose Isomerase From Bacillus Stearothermophilus

All present enzymatic activity of Xylose Isomerase From Bacillus Stearothermophilus:
5.3.1.5;

Protein crystallography data

The structure of Xylose Isomerase From Bacillus Stearothermophilus, PDB code: 1a0d was solved by O.Gallay, R.Chopra, E.Conti, P.Brick, D.Blow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.290, 141.850, 160.660, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 20.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Xylose Isomerase From Bacillus Stearothermophilus (pdb code 1a0d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Xylose Isomerase From Bacillus Stearothermophilus, PDB code: 1a0d:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1a0d

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Manganese binding site 1 out of 8 in the Xylose Isomerase From Bacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Xylose Isomerase From Bacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn491

b:26.4
occ:0.80
 OE2 A:GLU229 2.1 20.4 1.0
OD2 A:ASP336 2.2 23.1 1.0
OE1 A:GLU265 2.3 16.9 1.0
OD2 A:ASP293 2.4 10.5 1.0
O A:HOH538 2.7 25.9 1.0
CD A:GLU229 3.0 16.9 1.0
OE1 A:GLU229 3.1 23.6 1.0
CG A:ASP336 3.3 15.7 1.0
CD A:GLU265 3.5 12.1 1.0
O A:HOH544 3.5 28.5 1.0
CG A:ASP293 3.6 14.1 1.0
CE1 A:HIS268 4.1 21.2 1.0
MN A:MN492 4.2 35.1 0.5
OD1 A:ASP336 4.2 19.3 1.0
CB A:ASP336 4.2 13.9 1.0
O A:HOH493 4.2 36.8 0.7
OE2 A:GLU265 4.3 13.8 1.0
CG A:GLU229 4.4 10.9 1.0
CB A:ASP293 4.4 13.0 1.0
CG A:GLU265 4.5 6.5 1.0
CB A:GLU265 4.5 6.4 1.0
OD1 A:ASP293 4.6 16.4 1.0
NE2 A:HIS268 4.6 14.7 1.0
ND1 A:HIS268 4.9 19.4 1.0
OD1 A:ASN263 5.0 13.8 1.0

Manganese binding site 2 out of 8 in 1a0d

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Manganese binding site 2 out of 8 in the Xylose Isomerase From Bacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Xylose Isomerase From Bacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn492

b:35.1
occ:0.50
 OE2 A:GLU265 2.2 13.8 1.0
OD2 A:ASP304 2.3 34.0 1.0
OD1 A:ASP306 2.6 21.0 1.0
O A:HOH493 2.7 36.8 0.7
O A:HOH544 2.7 28.5 1.0
CD A:GLU265 2.9 12.1 1.0
OE1 A:GLU265 3.0 16.9 1.0
NE2 A:HIS268 3.3 14.7 1.0
CG A:ASP306 3.4 22.6 1.0
OD2 A:ASP306 3.5 27.0 1.0
CG A:ASP304 3.5 31.0 1.0
CD2 A:HIS268 4.0 12.2 1.0
OD1 A:ASN295 4.1 24.0 1.0
CE1 A:HIS268 4.1 21.2 1.0
MN A:MN491 4.2 26.4 0.8
OD2 A:ASP336 4.2 23.1 1.0
OD1 A:ASP336 4.3 19.3 1.0
OD1 A:ASP304 4.3 39.5 1.0
CG A:GLU265 4.4 6.5 1.0
CG A:ASP336 4.4 15.7 1.0
CB A:ASP304 4.5 20.9 1.0
O A:ASP336 4.8 19.0 1.0
CB A:ASP306 4.8 18.4 1.0
NZ A:LYS231 4.9 20.0 1.0

Manganese binding site 3 out of 8 in 1a0d

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Manganese binding site 3 out of 8 in the Xylose Isomerase From Bacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Xylose Isomerase From Bacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn491

b:26.4
occ:0.80
 OE2 B:GLU229 2.1 20.4 1.0
OD2 B:ASP336 2.2 23.1 1.0
OE1 B:GLU265 2.3 16.9 1.0
OD2 B:ASP293 2.4 10.5 1.0
O B:HOH542 2.7 25.9 1.0
CD B:GLU229 3.0 16.9 1.0
OE1 B:GLU229 3.1 23.6 1.0
CG B:ASP336 3.3 15.7 1.0
CD B:GLU265 3.5 12.1 1.0
O B:HOH548 3.5 28.5 1.0
CG B:ASP293 3.6 14.1 1.0
CE1 B:HIS268 4.1 21.2 1.0
MN B:MN492 4.2 35.1 0.5
OD1 B:ASP336 4.2 19.3 1.0
CB B:ASP336 4.2 13.9 1.0
O B:HOH496 4.2 36.8 0.7
OE2 B:GLU265 4.3 13.8 1.0
CG B:GLU229 4.4 10.9 1.0
CB B:ASP293 4.4 13.0 1.0
CG B:GLU265 4.5 6.5 1.0
CB B:GLU265 4.5 6.4 1.0
OD1 B:ASP293 4.6 16.4 1.0
NE2 B:HIS268 4.6 14.7 1.0
ND1 B:HIS268 4.9 19.4 1.0
OD1 B:ASN263 5.0 13.8 1.0

Manganese binding site 4 out of 8 in 1a0d

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Manganese binding site 4 out of 8 in the Xylose Isomerase From Bacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Xylose Isomerase From Bacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn492

b:35.1
occ:0.50
 OE2 B:GLU265 2.2 13.8 1.0
OD2 B:ASP304 2.3 34.0 1.0
OD1 B:ASP306 2.6 21.0 1.0
O B:HOH496 2.7 36.8 0.7
O B:HOH548 2.7 28.5 1.0
CD B:GLU265 2.9 12.1 1.0
OE1 B:GLU265 3.0 16.9 1.0
NE2 B:HIS268 3.3 14.7 1.0
CG B:ASP306 3.4 22.6 1.0
OD2 B:ASP306 3.5 27.0 1.0
CG B:ASP304 3.5 31.0 1.0
CD2 B:HIS268 4.0 12.2 1.0
OD1 B:ASN295 4.1 24.0 1.0
CE1 B:HIS268 4.1 21.2 1.0
MN B:MN491 4.2 26.4 0.8
OD2 B:ASP336 4.2 23.1 1.0
OD1 B:ASP336 4.3 19.3 1.0
OD1 B:ASP304 4.3 39.5 1.0
CG B:GLU265 4.4 6.5 1.0
CG B:ASP336 4.4 15.7 1.0
CB B:ASP304 4.5 20.9 1.0
O B:ASP336 4.8 19.0 1.0
CB B:ASP306 4.8 18.4 1.0
NZ B:LYS231 4.9 20.0 1.0

Manganese binding site 5 out of 8 in 1a0d

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Manganese binding site 5 out of 8 in the Xylose Isomerase From Bacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Xylose Isomerase From Bacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn491

b:26.4
occ:0.80
 OE2 C:GLU229 2.1 20.4 1.0
OD2 C:ASP336 2.2 23.1 1.0
OE1 C:GLU265 2.3 16.9 1.0
OD2 C:ASP293 2.4 10.5 1.0
O C:HOH541 2.7 25.9 1.0
CD C:GLU229 3.0 16.9 1.0
OE1 C:GLU229 3.1 23.6 1.0
CG C:ASP336 3.3 15.7 1.0
CD C:GLU265 3.5 12.1 1.0
O C:HOH547 3.5 28.5 1.0
CG C:ASP293 3.6 14.1 1.0
CE1 C:HIS268 4.1 21.2 1.0
MN C:MN492 4.2 35.1 0.5
OD1 C:ASP336 4.2 19.3 1.0
CB C:ASP336 4.2 13.9 1.0
O C:HOH497 4.2 36.8 0.7
OE2 C:GLU265 4.3 13.8 1.0
CG C:GLU229 4.4 10.9 1.0
CB C:ASP293 4.4 13.0 1.0
CG C:GLU265 4.5 6.5 1.0
CB C:GLU265 4.5 6.4 1.0
OD1 C:ASP293 4.6 16.4 1.0
NE2 C:HIS268 4.6 14.7 1.0
ND1 C:HIS268 4.9 19.4 1.0
OD1 C:ASN263 5.0 13.8 1.0

Manganese binding site 6 out of 8 in 1a0d

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Manganese binding site 6 out of 8 in the Xylose Isomerase From Bacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Xylose Isomerase From Bacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn492

b:35.1
occ:0.50
 OE2 C:GLU265 2.2 13.8 1.0
OD2 C:ASP304 2.3 34.0 1.0
OD1 C:ASP306 2.6 21.0 1.0
O C:HOH497 2.7 36.8 0.7
O C:HOH547 2.7 28.5 1.0
CD C:GLU265 2.9 12.1 1.0
OE1 C:GLU265 3.0 16.9 1.0
NE2 C:HIS268 3.3 14.7 1.0
CG C:ASP306 3.4 22.6 1.0
OD2 C:ASP306 3.5 27.0 1.0
CG C:ASP304 3.5 31.0 1.0
CD2 C:HIS268 4.0 12.2 1.0
OD1 C:ASN295 4.1 24.0 1.0
CE1 C:HIS268 4.1 21.2 1.0
MN C:MN491 4.2 26.4 0.8
OD2 C:ASP336 4.2 23.1 1.0
OD1 C:ASP336 4.3 19.3 1.0
OD1 C:ASP304 4.3 39.5 1.0
CG C:GLU265 4.4 6.5 1.0
CG C:ASP336 4.4 15.7 1.0
CB C:ASP304 4.5 20.9 1.0
CB C:ASP306 4.8 18.4 1.0
O C:ASP336 4.8 19.0 1.0
NZ C:LYS231 4.9 20.0 1.0

Manganese binding site 7 out of 8 in 1a0d

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Manganese binding site 7 out of 8 in the Xylose Isomerase From Bacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Xylose Isomerase From Bacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn491

b:26.4
occ:0.80
 OE2 D:GLU229 2.1 20.4 1.0
OD2 D:ASP336 2.2 23.1 1.0
OE1 D:GLU265 2.3 16.9 1.0
OD2 D:ASP293 2.4 10.5 1.0
O D:HOH544 2.7 25.9 1.0
CD D:GLU229 3.0 16.9 1.0
OE1 D:GLU229 3.1 23.6 1.0
CG D:ASP336 3.3 15.7 1.0
CD D:GLU265 3.5 12.1 1.0
O D:HOH550 3.5 28.5 1.0
CG D:ASP293 3.6 14.1 1.0
CE1 D:HIS268 4.1 21.2 1.0
MN D:MN492 4.2 35.1 0.5
OD1 D:ASP336 4.2 19.3 1.0
CB D:ASP336 4.2 13.9 1.0
O D:HOH499 4.2 36.8 0.7
OE2 D:GLU265 4.3 13.8 1.0
CG D:GLU229 4.4 10.9 1.0
CB D:ASP293 4.4 13.0 1.0
CG D:GLU265 4.5 6.5 1.0
CB D:GLU265 4.5 6.4 1.0
OD1 D:ASP293 4.6 16.4 1.0
NE2 D:HIS268 4.6 14.7 1.0
ND1 D:HIS268 4.9 19.4 1.0
OD1 D:ASN263 5.0 13.8 1.0

Manganese binding site 8 out of 8 in 1a0d

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Manganese binding site 8 out of 8 in the Xylose Isomerase From Bacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Xylose Isomerase From Bacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn492

b:35.1
occ:0.50
 OE2 D:GLU265 2.2 13.8 1.0
OD2 D:ASP304 2.3 34.0 1.0
OD1 D:ASP306 2.6 21.0 1.0
O D:HOH499 2.7 36.8 0.7
O D:HOH550 2.7 28.5 1.0
CD D:GLU265 2.9 12.1 1.0
OE1 D:GLU265 3.0 16.9 1.0
NE2 D:HIS268 3.3 14.7 1.0
CG D:ASP306 3.4 22.6 1.0
OD2 D:ASP306 3.5 27.0 1.0
CG D:ASP304 3.5 31.0 1.0
CD2 D:HIS268 4.0 12.2 1.0
OD1 D:ASN295 4.1 24.0 1.0
CE1 D:HIS268 4.1 21.2 1.0
MN D:MN491 4.2 26.4 0.8
OD2 D:ASP336 4.2 23.1 1.0
OD1 D:ASP336 4.3 19.3 1.0
OD1 D:ASP304 4.3 39.5 1.0
CG D:GLU265 4.4 6.5 1.0
CG D:ASP336 4.4 15.7 1.0
CB D:ASP304 4.5 20.9 1.0
O D:ASP336 4.8 19.0 1.0
CB D:ASP306 4.8 18.4 1.0
NZ D:LYS231 4.9 20.0 1.0

Reference:

O.Gallay, R.Chopra, E.Conti, P.Brick, R.Jackson, B.Hartley, C.Vieille, J.G.Zeikus, D.Blow. Crystal Structures of Class II Xylose Isomerases From Two Thermophiles and A Hyperthermophile To Be Published.
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