Cobalt in PDB 1a0e: Xylose Isomerase From Thermotoga Neapolitana

All present enzymatic activity of Xylose Isomerase From Thermotoga Neapolitana:
5.3.1.5;

The structure of Xylose Isomerase From Thermotoga Neapolitana, PDB code: 1a0e 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)	12.50 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.790, 121.870, 98.860, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.3

The binding sites of Cobalt atom in the Xylose Isomerase From Thermotoga Neapolitana (pdb code 1a0e). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Xylose Isomerase From Thermotoga Neapolitana, PDB code: 1a0e:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in the Xylose Isomerase From Thermotoga Neapolitana


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 Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Co491 b:48.2 occ:1.00 OD2 A:ASP338 1.9 38.5 1.0 OE2 A:GLU231 2.0 40.3 1.0 OE1 A:GLU267 2.1 35.6 1.0 OD2 A:ASP295 2.2 39.3 1.0 O A:HOH613 2.5 13.3 1.0 CD A:GLU231 3.0 36.1 1.0 CG A:ASP338 3.2 36.8 1.0 OE1 A:GLU231 3.3 40.9 1.0 CD A:GLU267 3.3 35.0 1.0 CG A:ASP295 3.3 34.9 1.0 O A:HOH612 3.8 39.5 1.0 CB A:ASP338 3.9 27.6 1.0 OE2 A:GLU267 3.9 38.5 1.0 CB A:ASP295 3.9 30.3 1.0 O A:HOH615 4.1 39.8 1.0 CE1 A:HIS270 4.1 19.2 1.0 OD1 A:ASP338 4.1 35.9 1.0 CO A:CO492 4.2 45.0 1.0 OD1 A:ASP295 4.3 36.8 1.0 CG A:GLU231 4.3 29.5 1.0 CG A:GLU267 4.4 24.1 1.0 CB A:GLU267 4.5 16.3 1.0 O A:HOH528 4.5 40.0 1.0 NE2 A:HIS270 4.6 21.0 1.0 ND2 A:ASN265 4.7 25.6 1.0 ND1 A:HIS270 4.9 25.4 1.0 O A:HOH614 5.0 21.3 1.0

Cobalt binding site 2 out of 6 in the Xylose Isomerase From Thermotoga Neapolitana


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 Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Co492 b:45.0 occ:1.00 OE2 A:GLU267 1.9 38.5 1.0 O A:HOH613 2.0 13.3 1.0 NE2 A:HIS270 2.4 21.0 1.0 O A:HOH616 2.4 20.0 1.0 O A:HOH615 2.6 39.8 1.0 O A:HOH614 2.8 21.3 1.0 CD A:GLU267 2.9 35.0 1.0 CD2 A:HIS270 3.2 17.4 1.0 OD2 A:ASP306 3.3 51.5 1.0 CE1 A:HIS270 3.3 19.2 1.0 OD1 A:ASP308 3.3 34.9 1.0 OE1 A:GLU267 3.4 35.6 1.0 OD2 A:ASP308 3.8 30.0 1.0 CG A:ASP308 4.0 29.4 1.0 OD2 A:ASP338 4.1 38.5 1.0 CO A:CO491 4.2 48.2 1.0 CG A:GLU267 4.2 24.1 1.0 O A:HOH612 4.3 39.5 1.0 CG A:ASP306 4.3 45.8 1.0 CG A:HIS270 4.4 24.4 1.0 ND1 A:HIS270 4.4 25.4 1.0 ND2 A:ASN297 4.4 26.8 1.0 NZ A:LYS233 4.4 21.8 1.0 CB A:ASP306 4.6 37.5 1.0 CG A:ASP338 4.7 36.8 1.0 CE A:LYS233 4.8 18.0 1.0 CD A:LYS233 4.9 15.7 1.0 OE2 A:GLU231 4.9 40.3 1.0 OD1 A:ASP338 4.9 35.9 1.0

Cobalt binding site 3 out of 6 in the Xylose Isomerase From Thermotoga Neapolitana


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 Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Co493 b:56.9 occ:1.00 OE2 A:GLU2 2.0 65.3 1.0 CD A:GLU2 2.7 56.3 1.0 CG A:GLU2 2.9 49.1 1.0 CB A:GLU2 3.2 43.6 1.0 OE1 A:GLU2 3.8 51.9 1.0 CA A:GLU2 4.7 45.2 1.0 CE2 A:PHE3 5.0 30.9 1.0

Cobalt binding site 4 out of 6 in the Xylose Isomerase From Thermotoga Neapolitana


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 Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ D:Co491 b:48.2 occ:1.00 OD2 D:ASP338 1.9 38.5 1.0 OE2 D:GLU231 2.0 40.3 1.0 OE1 D:GLU267 2.1 35.6 1.0 OD2 D:ASP295 2.2 39.3 1.0 O D:HOH618 2.5 13.3 1.0 CD D:GLU231 3.0 36.1 1.0 CG D:ASP338 3.2 36.8 1.0 OE1 D:GLU231 3.3 40.9 1.0 CD D:GLU267 3.3 35.0 1.0 CG D:ASP295 3.3 34.9 1.0 O D:HOH617 3.8 39.5 1.0 CB D:ASP338 3.9 27.6 1.0 OE2 D:GLU267 3.9 38.5 1.0 CB D:ASP295 3.9 30.3 1.0 O D:HOH620 4.1 39.8 1.0 CE1 D:HIS270 4.1 19.2 1.0 OD1 D:ASP338 4.1 35.9 1.0 CO D:CO492 4.2 45.0 1.0 OD1 D:ASP295 4.3 36.8 1.0 CG D:GLU231 4.3 29.5 1.0 CG D:GLU267 4.4 24.1 1.0 CB D:GLU267 4.5 16.3 1.0 O D:HOH533 4.5 40.0 1.0 NE2 D:HIS270 4.6 21.0 1.0 ND2 D:ASN265 4.7 25.6 1.0 ND1 D:HIS270 4.9 25.4 1.0 O D:HOH619 5.0 21.3 1.0

Cobalt binding site 5 out of 6 in the Xylose Isomerase From Thermotoga Neapolitana


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 Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ D:Co492 b:45.0 occ:1.00 OE2 D:GLU267 1.9 38.5 1.0 O D:HOH618 2.0 13.3 1.0 NE2 D:HIS270 2.4 21.0 1.0 O D:HOH621 2.4 20.0 1.0 O D:HOH620 2.6 39.8 1.0 O D:HOH619 2.8 21.3 1.0 CD D:GLU267 2.9 35.0 1.0 CD2 D:HIS270 3.2 17.4 1.0 OD2 D:ASP306 3.3 51.5 1.0 CE1 D:HIS270 3.3 19.2 1.0 OD1 D:ASP308 3.3 34.9 1.0 OE1 D:GLU267 3.4 35.6 1.0 OD2 D:ASP308 3.8 30.0 1.0 CG D:ASP308 4.0 29.4 1.0 OD2 D:ASP338 4.1 38.5 1.0 CO D:CO491 4.2 48.2 1.0 CG D:GLU267 4.2 24.1 1.0 O D:HOH617 4.3 39.5 1.0 CG D:ASP306 4.3 45.8 1.0 CG D:HIS270 4.4 24.4 1.0 ND1 D:HIS270 4.4 25.4 1.0 ND2 D:ASN297 4.4 26.8 1.0 NZ D:LYS233 4.4 21.8 1.0 CB D:ASP306 4.6 37.5 1.0 CG D:ASP338 4.7 36.8 1.0 CE D:LYS233 4.8 18.0 1.0 CD D:LYS233 4.9 15.7 1.0 OE2 D:GLU231 4.9 40.3 1.0 OD1 D:ASP338 4.9 35.9 1.0

Cobalt binding site 6 out of 6 in the Xylose Isomerase From Thermotoga Neapolitana


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 Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ D:Co493 b:56.9 occ:1.00 OE2 D:GLU2 2.0 65.3 1.0 CD D:GLU2 2.7 56.3 1.0 CG D:GLU2 2.9 49.1 1.0 CB D:GLU2 3.2 43.6 1.0 OE1 D:GLU2 3.8 51.9 1.0 CA D:GLU2 4.7 45.2 1.0 CE2 D:PHE3 5.0 30.9 1.0

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.