Sodium in PDB 7abo: Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn

The structure of Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn, PDB code: 7abo was solved by D.Leys, S.A.Marshall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.93 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.88, 55.57, 198.88, 90, 100, 90
R / Rfree (%)	21.4 / 24.6

The structure of Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn (pdb code 7abo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn, PDB code: 7abo:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:28.6 occ:1.00 OE2 C:GLU229 2.7 35.5 1.0 O C:MET221 2.7 35.7 1.0 O C:ALA219 2.8 32.5 1.0 O5' C:FMN501 2.9 36.9 1.0 O C:ALA218 3.0 36.5 1.0 O C:TRP166 3.0 36.8 1.0 O3P C:FMN501 3.1 39.2 1.0 C C:ALA219 3.3 33.4 1.0 CD C:GLU229 3.4 37.7 1.0 P C:FMN501 3.4 42.3 1.0 CA C:ALA219 3.5 34.0 1.0 H4' C:FMN501 3.6 44.0 1.0 O C:HOH637 3.6 35.7 1.0 CG C:GLU229 3.6 37.2 1.0 O2P C:FMN501 3.7 36.8 1.0 MN C:MN502 3.7 41.2 1.0 C C:MET221 3.8 33.7 1.0 N C:MET221 3.8 32.9 1.0 O4' C:FMN501 3.9 35.4 1.0 C C:ALA218 4.0 35.3 1.0 C4' C:FMN501 4.0 36.7 1.0 C5' C:FMN501 4.1 37.6 1.0 C C:TRP166 4.2 36.6 1.0 N C:GLY220 4.2 35.1 1.0 CA C:SER167 4.3 31.9 1.0 N C:ALA219 4.3 36.0 1.0 CA C:MET221 4.4 30.4 1.0 CB C:SER167 4.5 33.9 1.0 OE1 C:GLU229 4.5 35.2 1.0 HO4' C:FMN501 4.6 42.5 1.0 C C:GLY220 4.6 36.7 1.0 H5'1 C:FMN501 4.6 45.1 1.0 N C:SER167 4.7 34.3 1.0 CA C:GLY220 4.8 33.1 1.0 CB C:ALA219 4.8 34.1 1.0 N C:PRO222 4.8 34.6 1.0 H5'2 C:FMN501 4.8 45.1 1.0 N C:LEU223 4.9 37.0 1.0 O1P C:FMN501 4.9 38.6 1.0 CB C:MET221 4.9 32.7 1.0

Sodium binding site 2 out of 4 in the Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:31.6 occ:1.00 OE1 B:GLU229 2.6 37.7 1.0 O B:MET221 2.8 40.5 1.0 O B:ALA219 2.8 38.9 1.0 O5' B:FMN501 2.9 37.6 1.0 O B:TRP166 3.0 39.1 1.0 O B:ALA218 3.1 40.0 1.0 O1P B:FMN501 3.1 42.9 1.0 C B:ALA219 3.3 42.5 1.0 P B:FMN501 3.4 45.6 1.0 CD B:GLU229 3.4 41.2 1.0 O3P B:FMN501 3.5 35.8 1.0 CA B:ALA219 3.6 40.7 1.0 O B:HOH601 3.6 44.2 1.0 MN B:MN502 3.6 43.7 1.0 CG B:GLU229 3.7 44.3 1.0 H4' B:FMN501 3.7 52.2 1.0 C B:MET221 3.8 40.0 1.0 O4' B:FMN501 3.9 44.6 1.0 N B:MET221 3.9 39.8 1.0 C5' B:FMN501 4.1 41.4 1.0 C B:ALA218 4.1 39.8 1.0 C4' B:FMN501 4.1 43.5 1.0 HO4' B:FMN501 4.1 53.5 1.0 C B:TRP166 4.2 40.6 1.0 N B:GLY220 4.3 39.1 1.0 N B:ALA219 4.3 42.5 1.0 CA B:SER167 4.3 39.4 1.0 CA B:MET221 4.4 37.7 1.0 OE2 B:GLU229 4.5 39.3 1.0 CB B:SER167 4.6 39.2 1.0 H5'1 B:FMN501 4.6 49.7 1.0 C B:GLY220 4.7 42.2 1.0 CB B:ALA219 4.8 39.1 1.0 N B:SER167 4.8 37.4 1.0 H5'2 B:FMN501 4.8 49.7 1.0 N B:PRO222 4.8 39.1 1.0 O2P B:FMN501 4.9 44.2 1.0 N B:LEU223 4.9 42.9 1.0 CA B:GLY220 4.9 35.6 1.0 O B:HOH684 5.0 38.9 1.0 CB B:MET221 5.0 38.6 1.0

Sodium binding site 3 out of 4 in the Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ D:Na503 b:26.2 occ:1.00 O D:MET221 2.6 29.6 1.0 OE2 D:GLU229 2.7 32.2 1.0 O D:ALA219 2.9 35.6 1.0 O D:ALA218 3.0 32.1 1.0 O5' D:FMN501 3.0 34.7 1.0 O1P D:FMN501 3.0 38.0 1.0 O D:TRP166 3.2 33.8 1.0 CD D:GLU229 3.3 35.9 1.0 H4' D:FMN501 3.3 41.0 1.0 P D:FMN501 3.4 37.9 1.0 C D:ALA219 3.4 32.6 1.0 O D:HOH622 3.4 30.6 1.0 CG D:GLU229 3.6 34.3 1.0 C D:MET221 3.6 30.1 1.0 O3P D:FMN501 3.6 35.1 1.0 CA D:ALA219 3.7 33.4 1.0 N D:MET221 3.7 27.8 1.0 MN D:MN502 3.7 33.9 1.0 O4' D:FMN501 3.8 35.3 1.0 C4' D:FMN501 3.9 34.2 1.0 C5' D:FMN501 4.0 33.9 1.0 C D:ALA218 4.0 33.0 1.0 HO4' D:FMN501 4.1 42.3 1.0 CA D:MET221 4.2 31.0 1.0 OE1 D:GLU229 4.3 35.0 1.0 N D:GLY220 4.3 34.7 1.0 N D:ALA219 4.3 32.2 1.0 C D:TRP166 4.4 33.5 1.0 CA D:SER167 4.5 31.8 1.0 C D:GLY220 4.6 33.9 1.0 CB D:SER167 4.6 32.6 1.0 N D:PRO222 4.7 31.8 1.0 H5'1 D:FMN501 4.7 40.6 1.0 H5'2 D:FMN501 4.7 40.6 1.0 N D:LEU223 4.7 32.5 1.0 CB D:MET221 4.8 31.5 1.0 CA D:GLY220 4.8 29.1 1.0 O2P D:FMN501 4.8 37.3 1.0 CB D:ALA219 4.9 30.4 1.0 CA D:PRO222 4.9 33.2 1.0 N D:SER167 4.9 35.6 1.0

Sodium binding site 4 out of 4 in the Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the N318H Variant of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:27.7 occ:1.00 O A:MET221 2.7 37.7 1.0 OE2 A:GLU229 2.7 35.0 1.0 O A:ALA219 2.8 39.2 1.0 O5' A:FMN501 2.9 41.9 1.0 O1P A:FMN501 3.0 46.2 1.0 O A:ALA218 3.0 35.3 1.0 O A:TRP166 3.2 36.7 1.0 H4' A:FMN501 3.2 48.4 1.0 C A:ALA219 3.2 35.8 1.0 P A:FMN501 3.4 46.0 1.0 CD A:GLU229 3.4 42.9 1.0 CA A:ALA219 3.5 34.0 1.0 CG A:GLU229 3.7 40.8 1.0 O A:HOH617 3.7 37.5 1.0 O4' A:FMN501 3.7 38.5 1.0 C A:MET221 3.7 36.7 1.0 N A:MET221 3.8 32.7 1.0 MN A:MN502 3.8 36.5 1.0 C4' A:FMN501 3.8 40.4 1.0 O3P A:FMN501 3.8 42.9 1.0 C5' A:FMN501 3.9 39.5 1.0 C A:ALA218 4.0 34.6 1.0 N A:GLY220 4.2 36.0 1.0 HO4' A:FMN501 4.2 46.2 1.0 N A:ALA219 4.3 34.8 1.0 C A:TRP166 4.3 39.0 1.0 CA A:MET221 4.3 33.1 1.0 CA A:SER167 4.3 33.7 1.0 OE1 A:GLU229 4.4 43.3 1.0 CB A:SER167 4.5 34.8 1.0 C A:GLY220 4.5 38.4 1.0 H5'1 A:FMN501 4.6 47.4 1.0 H5'2 A:FMN501 4.7 47.4 1.0 CA A:GLY220 4.7 36.5 1.0 CB A:ALA219 4.7 38.8 1.0 N A:PRO222 4.8 31.1 1.0 O2P A:FMN501 4.8 44.4 1.0 N A:SER167 4.8 35.3 1.0 N A:LEU223 4.9 36.9 1.0 CB A:MET221 4.9 37.3 1.0 CA A:PRO222 5.0 37.1 1.0

K.A.P.Payne, S.A.Marshall, K.Fisher, S.E.J.Rigby, M.J.Cliff, R.Spiess, D.M.Cannas, I.Larrosa, S.Hay, D.Leys. Structure and Mechanism of Pseudomonas Aeruginosa PA0254/Huda, A Prfmn-Dependent Pyrrole-2-Carboxylic Acid Decarboxylase Linked to Virulence. Acs Catalysis V. 11 2865 2021.
ISSN: ESSN 2155-5435
PubMed: 33763291
DOI: 10.1021/ACSCATAL.0C05042