Manganese 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:

Sodium

(Na)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn502 b:41.2 occ:1.00 O C:HOH654 2.1 36.4 1.0 ND1 C:HIS188 2.1 37.7 1.0 O C:HOH678 2.2 35.9 1.0 O C:HOH637 2.2 35.7 1.0 O3P C:FMN501 2.2 39.2 1.0 OE2 C:GLU229 2.3 35.5 1.0 CE1 C:HIS188 2.9 40.5 1.0 CG C:HIS188 3.2 42.7 1.0 CD C:GLU229 3.3 37.7 1.0 P C:FMN501 3.4 42.3 1.0 O2P C:FMN501 3.5 36.8 1.0 OE1 C:GLU229 3.6 35.2 1.0 CB C:HIS188 3.7 43.1 1.0 NA C:NA503 3.7 28.6 1.0 NE2 C:HIS188 4.1 42.5 1.0 O C:LEU223 4.1 39.5 1.0 OG C:SER165 4.2 46.4 1.0 CD2 C:HIS188 4.3 42.7 1.0 CZ2 C:TRP163 4.3 45.7 1.0 O1P C:FMN501 4.4 38.6 1.0 O C:VAL227 4.4 44.8 1.0 O5' C:FMN501 4.5 36.9 1.0 CG C:GLU229 4.6 37.2 1.0 O C:TRP166 4.7 36.8 1.0 O C:PRO224 4.7 42.5 1.0 NE1 C:TRP163 4.8 45.5 1.0 O C:MET221 4.8 35.7 1.0 N C:LEU223 4.9 37.0 1.0 CB C:LEU223 4.9 36.5 1.0 C C:LEU223 4.9 39.5 1.0 CE2 C:TRP163 4.9 47.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn502 b:43.7 occ:1.00 O B:HOH636 2.1 42.2 1.0 O B:HOH684 2.1 38.9 1.0 ND1 B:HIS188 2.2 44.7 1.0 OE1 B:GLU229 2.3 37.7 1.0 O1P B:FMN501 2.3 42.9 1.0 O B:HOH601 2.4 44.2 1.0 CE1 B:HIS188 2.9 46.0 1.0 O3P B:FMN501 3.3 35.8 1.0 CD B:GLU229 3.3 41.2 1.0 CG B:HIS188 3.3 47.7 1.0 P B:FMN501 3.4 45.6 1.0 OE2 B:GLU229 3.6 39.3 1.0 NA B:NA503 3.6 31.6 1.0 CB B:HIS188 3.8 48.4 1.0 O B:LEU223 4.0 43.3 1.0 NE2 B:HIS188 4.1 47.6 1.0 CZ2 B:TRP163 4.3 51.3 1.0 CD2 B:HIS188 4.3 45.8 1.0 O B:VAL227 4.4 45.9 1.0 O2P B:FMN501 4.4 44.2 1.0 O5' B:FMN501 4.5 37.6 1.0 OG B:SER165 4.6 48.4 1.0 O B:PRO224 4.6 46.2 1.0 CG B:GLU229 4.7 44.3 1.0 NE1 B:TRP163 4.7 52.5 1.0 O B:TRP166 4.8 39.1 1.0 O B:MET221 4.8 40.5 1.0 C B:LEU223 4.8 46.5 1.0 N B:LEU223 4.8 42.9 1.0 CE2 B:TRP163 4.9 52.8 1.0 CB B:SER165 5.0 45.4 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn502 b:33.9 occ:1.00 ND1 D:HIS188 2.1 36.8 1.0 O1P D:FMN501 2.2 38.0 1.0 O D:HOH652 2.2 34.5 1.0 O D:HOH611 2.3 31.1 1.0 OE2 D:GLU229 2.3 32.2 1.0 O D:HOH622 2.4 30.6 1.0 CE1 D:HIS188 2.8 37.8 1.0 CG D:HIS188 3.3 39.5 1.0 CD D:GLU229 3.3 35.9 1.0 P D:FMN501 3.4 37.9 1.0 O3P D:FMN501 3.5 35.1 1.0 OE1 D:GLU229 3.6 35.0 1.0 NA D:NA503 3.7 26.2 1.0 CB D:HIS188 3.8 39.5 1.0 O D:LEU223 4.0 34.6 1.0 NE2 D:HIS188 4.0 39.1 1.0 OG D:SER165 4.2 37.0 1.0 CZ2 D:TRP163 4.2 44.6 1.0 O D:VAL227 4.2 40.9 1.0 CD2 D:HIS188 4.3 38.9 1.0 O2P D:FMN501 4.3 37.3 1.0 O5' D:FMN501 4.5 34.7 1.0 O D:PRO224 4.6 41.8 1.0 NE1 D:TRP163 4.6 44.8 1.0 CG D:GLU229 4.7 34.3 1.0 CB D:LEU223 4.7 34.4 1.0 O D:MET221 4.8 29.6 1.0 C D:LEU223 4.8 34.7 1.0 N D:LEU223 4.8 32.5 1.0 CE2 D:TRP163 4.8 47.2 1.0 O D:TRP166 4.9 33.8 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn502 b:36.5 occ:1.00 O1P A:FMN501 2.0 46.2 1.0 O A:HOH682 2.1 44.6 1.0 O A:HOH602 2.2 31.6 1.0 ND1 A:HIS188 2.2 42.2 1.0 OE2 A:GLU229 2.3 35.0 1.0 O A:HOH617 2.4 37.5 1.0 CE1 A:HIS188 3.0 44.6 1.0 P A:FMN501 3.3 46.0 1.0 CD A:GLU229 3.3 42.9 1.0 CG A:HIS188 3.3 45.2 1.0 OE1 A:GLU229 3.6 43.3 1.0 O3P A:FMN501 3.6 42.9 1.0 OG A:SER165 3.8 44.3 1.0 CB A:HIS188 3.8 43.0 1.0 NA A:NA503 3.8 27.7 1.0 CZ2 A:TRP163 4.0 50.3 1.0 O A:LEU223 4.0 40.1 1.0 O2P A:FMN501 4.1 44.4 1.0 NE2 A:HIS188 4.2 45.6 1.0 O A:VAL227 4.3 44.6 1.0 CD2 A:HIS188 4.4 44.8 1.0 O5' A:FMN501 4.4 41.9 1.0 CG A:GLU229 4.7 40.8 1.0 NE1 A:TRP163 4.7 53.0 1.0 O A:PRO224 4.7 46.5 1.0 CE2 A:TRP163 4.8 50.5 1.0 O A:MET221 4.8 37.7 1.0 N A:LEU223 4.8 36.9 1.0 C A:LEU223 4.8 42.1 1.0 CB A:LEU223 4.8 40.2 1.0 CH2 A:TRP163 5.0 49.4 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