Sodium in PDB 2wl4: Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A.

All present enzymatic activity of Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A.:
2.3.1.9;

The structure of Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A., PDB code: 2wl4 was solved by G.Merilainen, V.Poikela, P.Kursula, R.K.Wierenga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.613 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.310, 79.140, 149.410, 90.00, 92.68, 90.00
R / Rfree (%)	23.07 / 27.02

The structure of Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A. also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A. (pdb code 2wl4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A., PDB code: 2wl4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1394 b:34.3 occ:1.00 O C:HOH2027 2.9 36.4 1.0 N C:SER118 2.9 34.8 1.0 O C:LEU58 3.1 34.6 1.0 OE2 C:GLU117 3.2 51.4 1.0 NE2 C:GLN56 3.3 53.3 1.0 O C:HOH2011 3.5 38.1 1.0 O C:SER118 3.6 44.5 1.0 CA C:GLU117 3.6 36.5 1.0 CB C:ALA27 3.7 49.9 1.0 C C:GLU117 3.8 38.1 1.0 C C:SER118 3.8 45.2 1.0 CA C:SER118 3.8 41.1 1.0 CD C:GLU117 3.8 43.8 1.0 CG C:GLU117 3.9 45.9 1.0 C C:LEU58 4.0 44.0 1.0 CB C:SER118 4.2 46.5 1.0 CB C:LEU58 4.3 56.8 1.0 CG C:GLN56 4.3 49.4 1.0 CD C:GLN56 4.3 53.5 1.0 CB C:GLU117 4.4 40.0 1.0 OE1 C:GLU62 4.5 44.0 1.0 CA C:LEU58 4.6 48.5 1.0 N C:MET119 4.6 44.3 1.0 N C:LEU58 4.6 54.3 1.0 O C:HOH2026 4.7 32.7 1.0 N C:GLU117 4.7 47.9 1.0 O C:MET116 4.7 48.5 1.0 OE1 C:GLU117 4.8 49.2 1.0 CA C:ALA27 4.9 40.2 1.0 CG C:LEU58 5.0 64.9 1.0 O C:GLU117 5.0 35.7 1.0 N C:PRO59 5.0 45.4 1.0

Sodium binding site 2 out of 3 in the Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1395 b:60.3 occ:1.00 CG1 C:VAL112 3.4 69.0 1.0 CB C:VAL38 3.4 79.3 1.0 CB C:ALA255 3.4 67.0 1.0 CA C:ILE35 3.5 55.1 1.0 O C:VAL34 3.5 62.5 1.0 CG2 C:VAL38 3.7 81.6 1.0 CG2 C:VAL112 3.7 71.2 1.0 CG1 C:VAL38 3.9 79.8 1.0 N C:ALA256 3.9 73.2 1.0 C C:VAL34 4.0 58.6 1.0 N C:ILE35 4.0 57.0 1.0 CB C:VAL112 4.1 64.8 1.0 CG1 C:VAL34 4.1 61.7 1.0 CB C:ILE35 4.2 47.8 1.0 CG2 C:ILE35 4.2 47.8 1.0 O C:ILE35 4.2 63.2 1.0 CG1 C:ILE35 4.3 42.0 1.0 C C:ALA255 4.3 69.9 1.0 C C:ALA256 4.3 75.3 1.0 C C:ILE35 4.3 58.6 1.0 O C:ALA256 4.3 76.1 1.0 CA C:ALA255 4.5 67.4 1.0 CA C:ALA256 4.5 75.9 1.0 CA C:VAL112 4.6 56.1 1.0 CA C:VAL38 4.7 75.4 1.0 N C:LEU257 4.8 71.1 1.0 N C:ALA113 4.8 60.6 1.0 N C:VAL38 4.9 70.0 1.0 C C:VAL112 4.9 61.4 1.0

Sodium binding site 3 out of 3 in the Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Biosynthetic Thiolase From Z. Ramigera. Complex of the H348A Mutant with Coenzyme A. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1398 b:38.5 occ:1.00 O D:GLN322 3.1 65.3 1.0 O D:GLY289 3.2 80.0 1.0 N D:VAL326 3.3 0.7 1.0 CG2 D:VAL326 3.4 0.4 1.0 CG1 D:ILE293 3.4 49.3 1.0 CD1 D:ILE293 3.6 51.3 1.0 CB D:ALA325 3.6 0.3 1.0 C D:ALA325 3.6 0.6 1.0 CA D:VAL326 3.7 0.5 1.0 CA D:THR290 3.8 58.0 1.0 C D:GLN322 3.9 58.4 1.0 C D:GLY289 4.0 72.8 1.0 O D:ALA325 4.1 0.8 1.0 CA D:ALA325 4.2 0.7 1.0 CB D:VAL326 4.2 0.8 1.0 CA D:GLN322 4.3 57.8 1.0 N D:THR290 4.3 67.5 1.0 O D:HOH2150 4.3 54.4 1.0 CB D:GLN322 4.5 49.1 1.0 CD D:PRO292 4.6 43.9 1.0 CB D:THR290 4.6 52.4 1.0 CG2 D:THR290 4.6 53.5 1.0 N D:ALA325 4.7 0.8 1.0 C D:THR290 4.7 48.2 1.0 CB D:ILE293 4.8 49.5 1.0 N D:ALA323 4.9 58.9 1.0 N D:ILE293 4.9 57.5 1.0

G.Merilainen, V.Poikela, P.Kursula, R.K.Wierenga. The Thiolase Reaction Mechanism: the Importance of ASN316 and HIS348 For Stabilizing the Enolate Intermediate of the Claisen Condensation. Biochemistry V. 48 11011 2009.
ISSN: ISSN 0006-2960
PubMed: 19842716
DOI: 10.1021/BI901069H