Calcium in PDB 5nh5: Crystal Structure of Native Xylose Isomerase From Piromyces E2

All present enzymatic activity of Crystal Structure of Native Xylose Isomerase From Piromyces E2:
5.3.1.5;

The structure of Crystal Structure of Native Xylose Isomerase From Piromyces E2, PDB code: 5nh5 was solved by H.J.Rozeboom, D.B.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.20 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.720, 79.360, 92.210, 115.33, 90.31, 117.00
R / Rfree (%)	12.3 / 14.8

The structure of Crystal Structure of Native Xylose Isomerase From Piromyces E2 also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Iron	(Fe)	4 atoms

The binding sites of Calcium atom in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 (pdb code 5nh5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Native Xylose Isomerase From Piromyces E2, PDB code: 5nh5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:21.0 occ:0.37 MG A:MG503 0.5 8.0 0.4 FE A:FE2502 0.8 12.2 0.3 OE1 A:GLU269 2.0 14.7 1.0 O3 A:GOL507 2.0 22.6 1.0 OD2 A:ASP340 2.0 15.3 1.0 OE2 A:GLU233 2.3 15.3 1.0 O2 A:GOL507 2.5 15.9 1.0 OD2 A:ASP297 2.6 14.1 1.0 C3 A:GOL507 2.9 22.6 1.0 C2 A:GOL507 3.1 19.1 1.0 CG A:ASP340 3.2 12.7 1.0 CD A:GLU269 3.2 13.6 1.0 CD A:GLU233 3.2 13.4 1.0 OE1 A:GLU233 3.6 13.0 1.0 CG A:ASP297 3.7 13.0 1.0 O A:HOH673 3.7 32.6 1.0 CB A:ASP340 3.9 11.4 1.0 CE1 A:HIS272 3.9 12.7 1.0 OE2 A:GLU269 4.0 15.0 1.0 OD1 A:ASP340 4.2 12.8 1.0 CB A:ASP297 4.2 11.5 1.0 CG A:GLU269 4.3 11.8 1.0 NE2 A:HIS272 4.3 12.3 1.0 CB A:GLU269 4.4 10.7 1.0 CG A:GLU233 4.5 12.4 1.0 C1 A:GOL507 4.6 17.6 1.0 OD1 A:ASP297 4.7 11.7 1.0 ND1 A:HIS272 4.9 12.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:18.5 occ:0.45 MG B:MG503 0.7 6.9 0.4 FE B:FE2502 0.8 13.5 0.3 O3 B:GOL506 2.0 23.7 1.0 OE1 B:GLU269 2.1 14.7 1.0 OD2 B:ASP340 2.1 13.8 1.0 OE2 B:GLU233 2.2 13.7 1.0 O2 B:GOL506 2.4 15.8 1.0 OD2 B:ASP297 2.6 14.0 1.0 C3 B:GOL506 2.9 23.4 1.0 C2 B:GOL506 3.0 18.9 1.0 CD B:GLU233 3.2 13.1 1.0 CG B:ASP340 3.3 11.2 1.0 CD B:GLU269 3.3 13.5 1.0 OE1 B:GLU233 3.5 13.7 1.0 CG B:ASP297 3.8 11.7 1.0 CE1 B:HIS272 3.9 9.0 1.0 CB B:ASP340 4.0 10.3 1.0 OE2 B:GLU269 4.0 14.8 1.0 OD1 B:ASP340 4.2 11.3 1.0 CB B:ASP297 4.3 10.3 1.0 NE2 B:HIS272 4.3 9.5 1.0 CG B:GLU269 4.4 11.4 1.0 CB B:GLU269 4.4 10.0 1.0 C1 B:GOL506 4.5 17.1 1.0 CG B:GLU233 4.5 11.7 1.0 OD1 B:ASP297 4.8 11.5 1.0 ND1 B:HIS272 4.9 9.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:23.1 occ:0.36 MG C:MG503 0.3 5.9 0.4 FE C:FE2502 0.7 11.7 0.3 OE1 C:GLU269 2.0 15.0 1.0 OD2 C:ASP340 2.0 13.2 1.0 O1 C:GOL505 2.2 26.2 1.0 OE2 C:GLU233 2.3 14.4 1.0 OD2 C:ASP297 2.4 12.7 1.0 O2 C:GOL505 2.5 18.0 1.0 C1 C:GOL505 3.0 23.0 1.0 CG C:ASP340 3.1 12.1 1.0 C2 C:GOL505 3.1 20.9 1.0 CD C:GLU269 3.2 13.7 1.0 CD C:GLU233 3.3 12.6 1.0 CG C:ASP297 3.5 11.6 1.0 OE1 C:GLU233 3.6 13.2 1.0 CB C:ASP340 3.8 11.1 1.0 OE2 C:GLU269 3.9 14.2 1.0 CE1 C:HIS272 4.0 11.0 1.0 CB C:ASP297 4.1 10.6 1.0 OD1 C:ASP340 4.1 13.0 1.0 CG C:GLU269 4.2 11.8 1.0 CB C:GLU269 4.3 10.7 1.0 NE2 C:HIS272 4.4 11.0 1.0 OD1 C:ASP297 4.6 10.9 1.0 CG C:GLU233 4.6 11.7 1.0 C3 C:GOL505 4.6 18.7 1.0 O C:HOH642 4.6 34.1 1.0 ND1 C:HIS272 4.9 10.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:13.4 occ:0.44 MG D:MG503 0.1 14.5 0.3 FE D:FE2502 0.7 10.4 0.3 OD2 D:ASP297 1.8 12.8 1.0 OE1 D:GLU269 2.2 12.3 1.0 OE2 D:GLU233 2.2 14.8 1.0 O2 D:GOL505 2.2 17.9 1.0 OD2 D:ASP340 2.2 14.6 1.0 O3 D:GOL505 2.5 22.9 1.0 CD D:GLU233 3.0 11.7 1.0 CG D:ASP297 3.0 11.1 1.0 OE1 D:GLU233 3.2 12.6 1.0 C2 D:GOL505 3.3 20.2 1.0 CG D:ASP340 3.3 10.9 1.0 C3 D:GOL505 3.4 23.1 1.0 CD D:GLU269 3.4 11.0 1.0 CB D:ASP297 3.6 9.8 1.0 CB D:ASP340 3.8 10.2 1.0 OD1 D:ASP297 4.0 11.2 1.0 CG D:GLU269 4.2 10.0 1.0 CB D:GLU269 4.2 9.0 1.0 OE2 D:GLU269 4.3 11.7 1.0 CG D:GLU233 4.3 10.9 1.0 CE1 D:HIS272 4.3 9.4 1.0 OD1 D:ASP340 4.4 11.3 1.0 C1 D:GOL505 4.6 18.3 1.0 ND2 D:ASN267 4.6 10.5 1.0 O D:HOH604 4.6 34.4 1.0 NE2 D:HIS272 4.8 10.3 1.0

M.Lee, H.J.Rozeboom, P.P.De Waal, R.M.De Jong, H.M.Dudek, D.B.Janssen. Metal Dependence of the Xylose Isomerase From Piromyces Sp. E2 Explored By Activity Profiling and Protein Crystallography. Biochemistry V. 56 5991 2017.
ISSN: ISSN 1520-4995
PubMed: 29045784
DOI: 10.1021/ACS.BIOCHEM.7B00777