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Cobalt in PDB 1a0c: Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes

Enzymatic activity of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes

All present enzymatic activity of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes:
5.3.1.5;

Protein crystallography data

The structure of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes, PDB code: 1a0c 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) 10.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.660, 153.730, 158.470, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 17.7

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes (pdb code 1a0c). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes, PDB code: 1a0c:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 1a0c

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Cobalt binding site 1 out of 8 in the Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co491

b:33.4
occ:1.00
 OD2 A:ASP338 2.1 15.7 1.0
OD2 A:ASP295 2.1 15.3 1.0
OE2 A:GLU231 2.2 16.0 1.0
OE1 A:GLU267 2.2 13.9 1.0
O A:HOH495 2.6 18.5 1.0
O A:HOH494 2.6 20.1 1.0
CD A:GLU231 3.0 15.0 1.0
OE1 A:GLU231 3.1 14.8 1.0
CG A:ASP338 3.3 13.6 1.0
CG A:ASP295 3.3 13.9 1.0
CD A:GLU267 3.5 13.0 1.0
O A:HOH493 3.9 11.5 1.0
CB A:ASP338 3.9 12.6 1.0
CE1 A:HIS270 4.0 11.3 1.0
CB A:ASP295 4.1 12.8 1.0
OD1 A:ASP338 4.3 12.1 1.0
OD1 A:ASP295 4.3 13.3 1.0
CG A:GLU267 4.3 12.6 1.0
OE2 A:GLU267 4.3 13.4 1.0
CB A:GLU267 4.3 11.1 1.0
CG A:GLU231 4.4 12.9 1.0
O A:HOH639 4.5 42.0 1.0
ND1 A:HIS270 4.7 10.8 1.0
ND2 A:ASN265 4.7 11.6 1.0
NE2 A:HIS270 4.7 10.1 1.0
O A:HOH496 4.7 17.0 1.0
CO A:CO492 4.9 15.7 1.0

Cobalt binding site 2 out of 8 in 1a0c

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Cobalt binding site 2 out of 8 in the Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co492

b:15.7
occ:1.00
 O A:HOH493 1.9 11.5 1.0
OE2 A:GLU267 2.0 13.4 1.0
OD2 A:ASP306 2.1 17.0 1.0
OD1 A:ASP308 2.1 13.0 1.0
OD1 A:ASP306 2.3 17.5 1.0
NE2 A:HIS270 2.4 10.1 1.0
CG A:ASP306 2.5 15.7 1.0
CG A:ASP308 3.0 12.5 1.0
CD A:GLU267 3.0 13.0 1.0
CD2 A:HIS270 3.1 10.6 1.0
OD2 A:ASP308 3.2 13.6 1.0
OE1 A:GLU267 3.4 13.9 1.0
CE1 A:HIS270 3.5 11.3 1.0
O A:HOH556 3.5 26.7 1.0
CB A:ASP306 4.0 14.3 1.0
ND2 A:ASN297 4.1 11.1 1.0
CG A:HIS270 4.3 11.0 1.0
CG A:GLU267 4.4 12.6 1.0
CB A:ASN269 4.4 10.2 1.0
ND1 A:HIS270 4.4 10.8 1.0
CB A:ASP308 4.5 11.4 1.0
OD2 A:ASP338 4.5 15.7 1.0
O A:HOH651 4.6 41.4 1.0
OD1 A:ASN269 4.8 11.1 1.0
CG A:ASN269 4.9 10.9 1.0
CA A:ASP308 4.9 12.4 1.0
O A:HOH639 4.9 42.0 1.0
CO A:CO491 4.9 33.4 1.0
CG A:ASP338 4.9 13.6 1.0
O A:HOH494 5.0 20.1 1.0
CA A:ASP306 5.0 13.1 1.0
N A:ASP308 5.0 12.5 1.0

Cobalt binding site 3 out of 8 in 1a0c

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Cobalt binding site 3 out of 8 in the Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co491

b:33.4
occ:1.00
 OD2 B:ASP338 2.1 15.7 1.0
OD2 B:ASP295 2.1 15.3 1.0
OE2 B:GLU231 2.2 16.0 1.0
OE1 B:GLU267 2.2 13.9 1.0
O B:HOH528 2.6 18.5 1.0
O B:HOH527 2.6 20.1 1.0
CD B:GLU231 3.0 15.0 1.0
OE1 B:GLU231 3.1 14.8 1.0
CG B:ASP338 3.3 13.6 1.0
CG B:ASP295 3.3 13.9 1.0
CD B:GLU267 3.5 13.0 1.0
O B:HOH526 3.9 11.5 1.0
CB B:ASP338 3.9 12.6 1.0
CE1 B:HIS270 4.0 11.3 1.0
CB B:ASP295 4.1 12.8 1.0
OD1 B:ASP338 4.3 12.1 1.0
OD1 B:ASP295 4.3 13.3 1.0
CG B:GLU267 4.3 12.6 1.0
OE2 B:GLU267 4.3 13.4 1.0
CB B:GLU267 4.3 11.1 1.0
CG B:GLU231 4.4 12.9 1.0
O B:HOH671 4.5 42.0 1.0
ND1 B:HIS270 4.7 10.8 1.0
ND2 B:ASN265 4.7 11.6 1.0
NE2 B:HIS270 4.7 10.1 1.0
O B:HOH529 4.7 17.0 1.0
CO B:CO492 4.9 15.7 1.0

Cobalt binding site 4 out of 8 in 1a0c

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Cobalt binding site 4 out of 8 in the Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co492

b:15.7
occ:1.00
 O B:HOH526 1.9 11.5 1.0
OE2 B:GLU267 2.0 13.4 1.0
OD2 B:ASP306 2.1 17.0 1.0
OD1 B:ASP308 2.1 13.0 1.0
OD1 B:ASP306 2.3 17.5 1.0
NE2 B:HIS270 2.4 10.1 1.0
CG B:ASP306 2.5 15.7 1.0
CG B:ASP308 3.0 12.5 1.0
CD B:GLU267 3.0 13.0 1.0
CD2 B:HIS270 3.1 10.6 1.0
OD2 B:ASP308 3.2 13.6 1.0
OE1 B:GLU267 3.4 13.9 1.0
CE1 B:HIS270 3.5 11.3 1.0
O B:HOH588 3.5 26.7 1.0
CB B:ASP306 4.0 14.3 1.0
ND2 B:ASN297 4.1 11.1 1.0
CG B:HIS270 4.3 11.0 1.0
CG B:GLU267 4.4 12.6 1.0
CB B:ASN269 4.4 10.2 1.0
ND1 B:HIS270 4.4 10.8 1.0
CB B:ASP308 4.5 11.4 1.0
OD2 B:ASP338 4.5 15.7 1.0
O B:HOH683 4.6 41.4 1.0
OD1 B:ASN269 4.8 11.1 1.0
CG B:ASN269 4.9 10.9 1.0
CA B:ASP308 4.9 12.4 1.0
O B:HOH671 4.9 42.0 1.0
CO B:CO491 4.9 33.4 1.0
CG B:ASP338 4.9 13.6 1.0
O B:HOH527 5.0 20.1 1.0
CA B:ASP306 5.0 13.1 1.0
N B:ASP308 5.0 12.5 1.0

Cobalt binding site 5 out of 8 in 1a0c

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Cobalt binding site 5 out of 8 in the Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co491

b:33.4
occ:1.00
 OD2 C:ASP338 2.1 15.7 1.0
OD2 C:ASP295 2.1 15.3 1.0
OE2 C:GLU231 2.2 16.0 1.0
OE1 C:GLU267 2.2 13.9 1.0
O C:HOH526 2.6 18.5 1.0
O C:HOH525 2.6 20.1 1.0
CD C:GLU231 3.0 15.0 1.0
OE1 C:GLU231 3.1 14.8 1.0
CG C:ASP338 3.3 13.6 1.0
CG C:ASP295 3.3 13.9 1.0
CD C:GLU267 3.5 13.0 1.0
O C:HOH524 3.9 11.5 1.0
CB C:ASP338 3.9 12.6 1.0
CE1 C:HIS270 4.0 11.3 1.0
CB C:ASP295 4.1 12.8 1.0
OD1 C:ASP338 4.3 12.1 1.0
OD1 C:ASP295 4.3 13.3 1.0
CG C:GLU267 4.3 12.6 1.0
CB C:GLU267 4.3 11.1 1.0
OE2 C:GLU267 4.3 13.4 1.0
CG C:GLU231 4.4 12.9 1.0
O C:HOH670 4.5 42.0 1.0
ND1 C:HIS270 4.7 10.8 1.0
ND2 C:ASN265 4.7 11.6 1.0
NE2 C:HIS270 4.7 10.1 1.0
O C:HOH527 4.7 17.0 1.0
CO C:CO492 4.9 15.7 1.0

Cobalt binding site 6 out of 8 in 1a0c

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Cobalt binding site 6 out of 8 in the Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co492

b:15.7
occ:1.00
 O C:HOH524 1.9 11.5 1.0
OE2 C:GLU267 2.0 13.4 1.0
OD2 C:ASP306 2.1 17.0 1.0
OD1 C:ASP308 2.1 13.0 1.0
OD1 C:ASP306 2.3 17.5 1.0
NE2 C:HIS270 2.4 10.1 1.0
CG C:ASP306 2.5 15.7 1.0
CG C:ASP308 3.0 12.5 1.0
CD C:GLU267 3.0 13.0 1.0
CD2 C:HIS270 3.1 10.6 1.0
OD2 C:ASP308 3.2 13.6 1.0
OE1 C:GLU267 3.4 13.9 1.0
CE1 C:HIS270 3.5 11.3 1.0
O C:HOH587 3.5 26.7 1.0
CB C:ASP306 4.0 14.3 1.0
ND2 C:ASN297 4.1 11.1 1.0
CG C:HIS270 4.3 11.0 1.0
CG C:GLU267 4.4 12.6 1.0
CB C:ASN269 4.4 10.2 1.0
ND1 C:HIS270 4.4 10.8 1.0
CB C:ASP308 4.5 11.4 1.0
OD2 C:ASP338 4.5 15.7 1.0
O C:HOH681 4.6 41.4 1.0
OD1 C:ASN269 4.8 11.1 1.0
CG C:ASN269 4.9 10.9 1.0
CA C:ASP308 4.9 12.4 1.0
O C:HOH670 4.9 42.0 1.0
CG C:ASP338 4.9 13.6 1.0
CO C:CO491 4.9 33.4 1.0
O C:HOH525 5.0 20.1 1.0
CA C:ASP306 5.0 13.1 1.0
N C:ASP308 5.0 12.5 1.0

Cobalt binding site 7 out of 8 in 1a0c

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Cobalt binding site 7 out of 8 in the Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co491

b:33.4
occ:1.00
 OD2 D:ASP338 2.1 15.7 1.0
OD2 D:ASP295 2.1 15.3 1.0
OE2 D:GLU231 2.2 16.0 1.0
OE1 D:GLU267 2.2 13.9 1.0
O D:HOH559 2.6 18.5 1.0
O D:HOH558 2.6 20.1 1.0
CD D:GLU231 3.0 15.0 1.0
OE1 D:GLU231 3.1 14.8 1.0
CG D:ASP338 3.3 13.6 1.0
CG D:ASP295 3.3 13.9 1.0
CD D:GLU267 3.5 13.0 1.0
O D:HOH557 3.9 11.5 1.0
CB D:ASP338 3.9 12.6 1.0
CE1 D:HIS270 4.0 11.3 1.0
CB D:ASP295 4.1 12.8 1.0
OD1 D:ASP338 4.3 12.1 1.0
OD1 D:ASP295 4.3 13.3 1.0
CG D:GLU267 4.3 12.6 1.0
OE2 D:GLU267 4.3 13.4 1.0
CB D:GLU267 4.3 11.1 1.0
CG D:GLU231 4.4 12.9 1.0
O D:HOH702 4.5 42.0 1.0
ND1 D:HIS270 4.7 10.8 1.0
ND2 D:ASN265 4.7 11.6 1.0
NE2 D:HIS270 4.7 10.1 1.0
O D:HOH560 4.7 17.0 1.0
CO D:CO492 4.9 15.7 1.0

Cobalt binding site 8 out of 8 in 1a0c

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Cobalt binding site 8 out of 8 in the Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Xylose Isomerase From Thermoanaerobacterium Thermosulfurigenes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co492

b:15.7
occ:1.00
 O D:HOH557 1.9 11.5 1.0
OE2 D:GLU267 2.0 13.4 1.0
OD2 D:ASP306 2.1 17.0 1.0
OD1 D:ASP308 2.1 13.0 1.0
OD1 D:ASP306 2.3 17.5 1.0
NE2 D:HIS270 2.4 10.1 1.0
CG D:ASP306 2.5 15.7 1.0
CG D:ASP308 3.0 12.5 1.0
CD D:GLU267 3.0 13.0 1.0
CD2 D:HIS270 3.1 10.6 1.0
OD2 D:ASP308 3.2 13.6 1.0
OE1 D:GLU267 3.4 13.9 1.0
CE1 D:HIS270 3.5 11.3 1.0
O D:HOH620 3.5 26.7 1.0
CB D:ASP306 4.0 14.3 1.0
ND2 D:ASN297 4.1 11.1 1.0
CG D:HIS270 4.3 11.0 1.0
CG D:GLU267 4.4 12.6 1.0
CB D:ASN269 4.4 10.2 1.0
ND1 D:HIS270 4.4 10.8 1.0
CB D:ASP308 4.5 11.4 1.0
OD2 D:ASP338 4.5 15.7 1.0
O D:HOH713 4.6 41.4 1.0
OD1 D:ASN269 4.8 11.1 1.0
CG D:ASN269 4.9 10.9 1.0
CA D:ASP308 4.9 12.4 1.0
O D:HOH702 4.9 42.0 1.0
CO D:CO491 4.9 33.4 1.0
CG D:ASP338 4.9 13.6 1.0
O D:HOH558 5.0 20.1 1.0
CA D:ASP306 5.0 13.1 1.0
N D:ASP308 5.0 12.5 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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