Sodium in PDB 4y90: Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans

All present enzymatic activity of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans:
5.3.1.1;

The structure of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans, PDB code: 4y90 was solved by S.Romero-Romero, A.Rodriguez-Romero, D.A.Fernadez-Velasco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.13 / 2.10
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	169.620, 169.620, 202.266, 90.00, 90.00, 120.00
R / Rfree (%)	13.6 / 18.6

The structure of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans (pdb code 4y90). 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 Deinococcus Radiodurans, PDB code: 4y90:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans


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 Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:14.1 occ:1.00 HE2 C:HIS96 2.5 23.2 1.0 HD22 C:ASN11 2.5 24.9 1.0 HG C:LEU228 2.9 26.3 1.0 OE2 C:GLU164 3.0 24.1 1.0 O C:HOH497 3.1 32.4 1.0 HB3 C:ASN11 3.2 26.8 1.0 HE3 C:LYS13 3.3 24.7 1.0 NE2 C:HIS96 3.3 19.3 1.0 ND2 C:ASN11 3.3 20.7 1.0 HE2 C:LYS13 3.5 24.7 1.0 OE1 C:GLU164 3.7 32.1 1.0 HA2 C:GLY230 3.8 25.1 1.0 CG C:LEU228 3.8 21.9 1.0 CD C:GLU164 3.8 38.6 1.0 HD21 C:ASN11 3.8 24.9 1.0 HD21 C:LEU228 3.8 36.7 1.0 CE C:LYS13 3.8 20.6 1.0 CB C:ASN11 3.9 22.3 1.0 HD2 C:HIS96 3.9 18.1 1.0 HZ1 C:LYS13 3.9 23.1 1.0 HB2 C:ASN11 4.0 26.8 1.0 CD2 C:HIS96 4.0 15.1 1.0 HA3 C:GLY230 4.1 25.1 1.0 CG C:ASN11 4.1 24.2 1.0 HD23 C:LEU228 4.1 36.7 1.0 CD2 C:LEU228 4.1 30.6 1.0 N C:GLY230 4.1 23.8 1.0 HD11 C:LEU228 4.2 22.6 1.0 CA C:GLY230 4.2 20.9 1.0 C C:VAL229 4.3 24.5 1.0 H C:GLY230 4.3 28.5 1.0 CE1 C:HIS96 4.4 25.3 1.0 O C:LEU228 4.4 22.9 1.0 NZ C:LYS13 4.4 19.2 1.0 CD1 C:LEU228 4.4 18.8 1.0 O C:VAL229 4.5 24.7 1.0 C C:LEU228 4.5 19.3 1.0 HE1 C:HIS96 4.6 30.3 1.0 HD12 C:LEU228 4.6 22.6 1.0 N C:VAL229 4.7 18.0 1.0 HB3 C:LEU228 4.8 29.5 1.0 CB C:LEU228 4.8 24.6 1.0 HZ2 C:LYS13 4.9 23.1 1.0 HG3 C:LYS13 4.9 26.7 1.0 H C:VAL229 4.9 21.6 1.0 CA C:VAL229 5.0 20.3 1.0 O C:HOH529 5.0 33.7 1.0 HA C:VAL229 5.0 24.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans


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 Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ C:Na305 b:33.0 occ:1.00 O C:HOH577 2.4 51.3 1.0 O C:LYS221 2.5 23.6 1.0 O C:VAL224 2.6 27.7 1.0 O C:CYS219 2.6 27.8 1.0 O C:HOH515 3.3 35.4 1.0 O C:HOH576 3.4 43.4 1.0 C C:LYS221 3.6 20.8 1.0 C C:CYS219 3.7 27.2 1.0 HA2 C:GLY220 3.8 33.9 1.0 C C:VAL224 3.8 28.7 1.0 C C:GLY220 3.9 30.2 1.0 HA C:PRO222 3.9 31.0 1.0 H C:VAL224 4.0 29.4 1.0 O C:GLY220 4.0 24.8 1.0 HA C:ASN225 4.1 32.8 1.0 HD22 C:ASN225 4.1 28.4 1.0 N C:LYS221 4.1 27.2 1.0 CA C:GLY220 4.2 28.2 1.0 HB C:VAL224 4.3 19.7 1.0 H C:LYS221 4.4 32.7 1.0 N C:VAL224 4.4 24.5 1.0 N C:GLY220 4.4 20.3 1.0 CA C:PRO222 4.4 25.9 1.0 C C:PRO222 4.4 27.9 1.0 O C:PRO222 4.5 22.1 1.0 N C:PRO222 4.5 26.8 1.0 CA C:LYS221 4.5 20.5 1.0 CA C:VAL224 4.6 19.8 1.0 HA C:CYS219 4.6 26.7 1.0 ND2 C:ASN225 4.7 23.6 1.0 N C:ASN225 4.7 25.4 1.0 CA C:CYS219 4.8 22.2 1.0 HD21 C:ASN225 4.8 28.4 1.0 CA C:ASN225 4.8 27.3 1.0 CB C:VAL224 5.0 16.4 1.0 HB3 C:CYS219 5.0 33.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans


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 Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:12.4 occ:1.00 HD22 D:ASN11 2.4 20.8 1.0 HE2 D:HIS96 2.5 26.8 1.0 HG D:LEU228 3.0 23.7 1.0 OE2 D:GLU164 3.0 28.7 1.0 O D:HOH520 3.1 28.3 1.0 ND2 D:ASN11 3.2 17.3 1.0 HE3 D:LYS13 3.2 23.1 1.0 HB3 D:ASN11 3.3 24.6 1.0 NE2 D:HIS96 3.3 22.3 1.0 HE2 D:LYS13 3.4 23.1 1.0 HZ1 D:LYS13 3.6 23.9 1.0 HD21 D:ASN11 3.7 20.8 1.0 CE D:LYS13 3.7 19.2 1.0 OE1 D:GLU164 3.7 28.6 1.0 HD2 D:HIS96 3.7 22.0 1.0 CD D:GLU164 3.8 34.9 1.0 HD21 D:LEU228 3.8 24.5 1.0 HA2 D:GLY230 3.8 22.4 1.0 CG D:LEU228 3.9 19.8 1.0 HA3 D:GLY230 3.9 22.4 1.0 CD2 D:HIS96 3.9 18.4 1.0 HD23 D:LEU228 4.0 24.5 1.0 CB D:ASN11 4.0 20.5 1.0 N D:GLY230 4.0 20.6 1.0 CG D:ASN11 4.1 14.8 1.0 CD2 D:LEU228 4.1 20.4 1.0 HB2 D:ASN11 4.1 24.6 1.0 CA D:GLY230 4.1 18.7 1.0 NZ D:LYS13 4.2 19.9 1.0 H D:GLY230 4.2 24.7 1.0 C D:VAL229 4.3 19.1 1.0 O D:LEU228 4.3 20.9 1.0 HD11 D:LEU228 4.4 19.7 1.0 CE1 D:HIS96 4.4 21.7 1.0 O D:VAL229 4.5 19.8 1.0 C D:LEU228 4.6 20.6 1.0 CD1 D:LEU228 4.7 16.4 1.0 HZ2 D:LYS13 4.7 23.9 1.0 HE1 D:HIS96 4.7 26.0 1.0 HZ3 D:LYS13 4.8 23.9 1.0 HB3 D:LEU228 4.8 17.6 1.0 N D:VAL229 4.8 20.1 1.0 HD12 D:LEU228 4.8 19.7 1.0 CB D:LEU228 4.9 14.7 1.0 CA D:VAL229 5.0 19.0 1.0 HG3 D:LYS13 5.0 22.6 1.0 HA D:VAL229 5.0 22.8 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