Sodium in PDB 6aid: Structural Insights Into the Unique Polylactate Degrading Mechanism of Thermobifida Alba Cutinase

The structure of Structural Insights Into the Unique Polylactate Degrading Mechanism of Thermobifida Alba Cutinase, PDB code: 6aid was solved by K.Kitadokoro, M.Kakara, S.Matsui, R.Osokoshi, U.Thumarat, F.Kawai, S.Kamitani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.265, 68.860, 78.594, 90.00, 90.00, 90.00
R / Rfree (%)	13.3 / 16.5

The structure of Structural Insights Into the Unique Polylactate Degrading Mechanism of Thermobifida Alba Cutinase also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the Structural Insights Into the Unique Polylactate Degrading Mechanism of Thermobifida Alba Cutinase (pdb code 6aid). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structural Insights Into the Unique Polylactate Degrading Mechanism of Thermobifida Alba Cutinase, PDB code: 6aid:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structural Insights Into the Unique Polylactate Degrading Mechanism of Thermobifida Alba Cutinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Insights Into the Unique Polylactate Degrading Mechanism of Thermobifida Alba Cutinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:14.0 occ:1.00 OG A:SER224 2.7 8.8 1.0 O A:ALA218 2.7 9.2 1.0 O A:PRO193 2.8 8.1 1.0 N A:SER224 3.2 8.5 1.0 O A:HOH589 3.3 8.9 1.0 CB A:HIS223 3.3 8.5 1.0 CB A:SER224 3.5 8.2 1.0 CB A:ALA218 3.6 8.7 1.0 N A:PRO193 3.6 7.6 1.0 C A:ALA218 3.7 8.8 1.0 C A:THR192 3.7 7.6 1.0 CD A:PRO193 3.8 7.6 1.0 CA A:SER224 3.8 8.3 1.0 C A:PRO193 3.9 7.9 1.0 O A:SER219 4.0 9.8 1.0 CA A:THR192 4.1 7.7 1.0 CG A:PRO193 4.1 7.7 1.0 O A:THR192 4.1 7.8 1.0 C A:HIS223 4.1 8.6 1.0 CA A:HIS223 4.2 8.7 1.0 C A:SER219 4.3 9.8 1.0 CA A:ALA218 4.3 8.9 1.0 CA A:PRO193 4.3 7.7 1.0 CA A:VAL220 4.3 9.6 1.0 CG A:HIS223 4.4 8.8 1.0 N A:VAL220 4.4 9.6 1.0 CG1 A:VAL220 4.5 10.0 1.0 OD2 A:ASP215 4.6 8.2 1.0 N A:SER219 4.7 9.4 1.0 CB A:THR192 4.8 7.7 1.0 CB A:PRO193 4.9 7.8 1.0 N A:HIS223 4.9 9.3 1.0 CB A:VAL220 5.0 9.9 1.0

Sodium binding site 2 out of 2 in the Structural Insights Into the Unique Polylactate Degrading Mechanism of Thermobifida Alba Cutinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Insights Into the Unique Polylactate Degrading Mechanism of Thermobifida Alba Cutinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:17.0 occ:1.00 O A:ALA212 2.9 9.4 1.0 N A:VAL220 3.0 9.6 1.0 O A:HOH686 3.0 14.6 1.0 O A:GLU213 3.1 10.5 1.0 N A:ASP215 3.3 10.1 1.0 O A:ASP215 3.3 14.3 1.0 CB A:ASP215 3.5 9.8 1.0 CG2 A:VAL220 3.5 10.5 1.0 CA A:SER219 3.6 9.9 1.0 C A:GLU213 3.6 9.1 1.0 O A:HOH553 3.6 28.0 1.0 CG1 A:VAL220 3.7 10.0 1.0 CA A:ASP215 3.8 9.8 1.0 C A:SER219 3.8 9.8 1.0 CB A:VAL220 3.9 9.9 1.0 CA A:VAL220 4.0 9.6 1.0 C A:ASP215 4.0 11.2 1.0 C A:ALA212 4.1 8.5 1.0 CB A:SER219 4.2 12.8 1.0 N A:TYR214 4.2 9.0 1.0 O A:HOH635 4.3 25.2 1.0 C A:TYR214 4.3 10.6 1.0 CA A:GLU213 4.4 8.9 1.0 CA A:TYR214 4.4 9.7 1.0 O A:ALA218 4.7 9.2 1.0 N A:SER219 4.7 9.4 1.0 N A:GLU213 4.7 8.5 1.0 CG A:ASP215 4.8 8.8 1.0 N A:THR221 4.8 9.8 1.0 O A:HOH589 4.8 8.9 1.0 O A:SER219 5.0 9.8 1.0 C A:VAL220 5.0 9.4 1.0

K.Kitadokoro, M.Kakara, S.Matsui, R.Osokoshi, U.Thumarat, F.Kawai, S.Kamitani. Structural Insights Into the Unique Polylactate-Degrading Mechanism of Thermobifida Alba Cutinase. Febs J. V. 286 2087 2019.
ISSN: ISSN 1742-464X
PubMed: 30761732
DOI: 10.1111/FEBS.14781