Sodium in PDB 4y96: Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus

All present enzymatic activity of Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus:
5.3.1.1;

The structure of Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus, PDB code: 4y96 was solved by S.Romero-Romero, A.Rodriguez-Romero, D.A.Fernandez-Velasco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.36 / 1.58
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	124.778, 124.778, 134.231, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20.1

The structure of Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus (pdb code 4y96). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus, PDB code: 4y96:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:16.4 occ:1.00 O A:HOH530 2.9 29.1 1.0 O A:HOH637 3.0 30.9 1.0 NE2 A:HIS99 3.2 14.1 1.0 ND2 A:ASN14 3.2 13.7 1.0 CE A:LYS16 3.7 17.7 1.0 CB A:ASN14 3.8 13.3 1.0 CG A:LEU236 3.9 18.3 1.0 CD2 A:HIS99 3.9 13.1 1.0 CG A:ASN14 4.0 13.2 1.0 CA A:GLY238 4.0 17.6 1.0 CD2 A:LEU236 4.1 21.9 1.0 N A:GLY238 4.2 17.7 1.0 CE1 A:HIS99 4.2 15.7 1.0 NZ A:LYS16 4.2 18.6 1.0 OE1 A:GLU171 4.3 49.8 1.0 C A:VAL237 4.4 16.8 1.0 O A:VAL237 4.4 17.1 1.0 O A:LEU236 4.5 18.1 1.0 CD1 A:LEU236 4.6 20.5 1.0 C A:LEU236 4.8 17.6 1.0 O4 A:PO4303 4.9 49.0 1.0 O A:HOH506 4.9 27.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:61.1 occ:1.00 CB A:PHE112 3.8 14.8 1.0 CG A:PHE112 3.8 18.0 1.0 CD1 A:PHE112 3.9 22.5 1.0 O B:HOH653 4.0 42.4 1.0 O A:HOH444 4.1 24.2 1.0 CA A:PHE112 4.3 15.6 1.0 CD2 A:PHE112 4.4 21.4 1.0 OG A:SER109 4.5 18.3 1.0 N A:PHE112 4.5 17.7 1.0 CE1 A:PHE112 4.6 20.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Triosephosphate Isomerase From Gemmata Obscuriglobus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:18.1 occ:1.00 OE1 B:GLU171 2.9 27.3 1.0 O B:HOH622 3.0 27.0 1.0 NE2 B:HIS99 3.2 19.7 1.0 ND2 B:ASN14 3.4 18.2 1.0 OE2 B:GLU171 3.6 26.3 1.0 CD B:GLU171 3.6 27.1 1.0 CE B:LYS16 3.7 18.4 1.0 CG B:LEU236 3.8 22.3 1.0 CB B:ASN14 3.9 19.5 1.0 CA B:GLY238 4.0 21.3 1.0 CD2 B:HIS99 4.0 18.1 1.0 CD2 B:LEU236 4.1 20.7 1.0 NZ B:LYS16 4.1 20.0 1.0 CG B:ASN14 4.1 18.4 1.0 N B:GLY238 4.2 18.3 1.0 CE1 B:HIS99 4.3 16.1 1.0 C B:VAL237 4.4 24.6 1.0 CD1 B:LEU236 4.4 23.4 1.0 O B:VAL237 4.4 24.3 1.0 O B:LEU236 4.5 20.6 1.0 O3 B:PO4302 4.6 46.8 1.0 C B:LEU236 4.8 18.6 1.0 O B:HOH516 4.9 23.2 1.0 CB B:LEU236 4.9 19.6 1.0

S.Romero-Romero, M.Costas, A.Rodriguez-Romero, D.Alejandro Fernandez-Velasco. Reversibility and Two State Behaviour in the Thermal Unfolding of Oligomeric Tim Barrel Proteins. Phys Chem Chem Phys V. 17 20699 2015.
ISSN: ESSN 1463-9084
PubMed: 26206330
DOI: 10.1039/C5CP01599E