Manganese in PDB 7abn: Structure of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda

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

Resolution Low / High (Å)	53.64 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.81, 55.48, 199.53, 90, 99.92, 90
R / Rfree (%)	20.1 / 23.5

The structure of Structure of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Manganese atom in the Structure of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda (pdb code 7abn). 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 Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda, PDB code: 7abn:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda


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 Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn501 b:14.4 occ:1.00 O3P D:4LU503 2.1 13.4 1.0 O D:HOH623 2.1 12.7 1.0 O D:HOH648 2.2 12.3 1.0 OE2 D:GLU229 2.2 10.4 1.0 O D:HOH706 2.2 14.8 1.0 ND1 D:HIS188 2.2 14.0 1.0 CE1 D:HIS188 3.1 16.2 1.0 CD D:GLU229 3.2 14.1 1.0 CG D:HIS188 3.3 15.0 1.0 P D:4LU503 3.4 13.6 1.0 OE1 D:GLU229 3.5 13.0 1.0 O2P D:4LU503 3.7 15.1 1.0 K D:K502 3.7 15.3 1.0 CB D:HIS188 3.8 16.0 1.0 O D:LEU223 4.2 13.2 1.0 NE2 D:HIS188 4.2 15.2 1.0 O1P D:4LU503 4.3 15.0 1.0 CZ2 D:TRP163 4.3 21.3 1.0 O D:VAL227 4.4 18.0 1.0 CD2 D:HIS188 4.4 15.0 1.0 CG D:GLU229 4.5 15.6 1.0 OG D:SER165 4.5 16.7 1.0 O5' D:4LU503 4.5 14.8 1.0 NE1 D:TRP163 4.6 20.4 1.0 CB D:LEU223 4.7 15.8 1.0 O D:PRO224 4.7 18.5 1.0 O D:TRP166 4.8 15.8 1.0 O D:MET221 4.8 13.4 1.0 CE2 D:TRP163 4.9 21.9 1.0 C D:LEU223 4.9 15.7 1.0

Manganese binding site 2 out of 4 in the Structure of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda


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 Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:15.2 occ:1.00 O3P A:4LU503 2.1 14.4 1.0 O A:HOH659 2.1 13.8 1.0 O A:HOH744 2.2 15.7 1.0 ND1 A:HIS188 2.2 11.8 1.0 O A:HOH654 2.3 14.4 1.0 OE2 A:GLU229 2.3 13.7 1.0 CE1 A:HIS188 3.1 14.8 1.0 CD A:GLU229 3.3 13.7 1.0 CG A:HIS188 3.3 15.1 1.0 P A:4LU503 3.4 15.0 1.0 OE1 A:GLU229 3.6 13.7 1.0 O2P A:4LU503 3.7 15.8 1.0 K A:K502 3.8 15.1 1.0 CB A:HIS188 3.8 15.9 1.0 O A:LEU223 4.1 14.8 1.0 CZ2 A:TRP163 4.3 19.9 1.0 NE2 A:HIS188 4.3 13.4 1.0 O A:VAL227 4.3 18.2 1.0 O1P A:4LU503 4.3 15.2 1.0 O5' A:4LU503 4.4 14.2 1.0 CD2 A:HIS188 4.4 14.2 1.0 OG A:SER165 4.5 18.0 1.0 CG A:GLU229 4.7 15.5 1.0 NE1 A:TRP163 4.7 21.8 1.0 O A:PRO224 4.7 17.5 1.0 CB A:LEU223 4.7 15.8 1.0 O A:TRP166 4.8 15.2 1.0 O A:MET221 4.8 13.5 1.0 CE2 A:TRP163 4.9 19.4 1.0 C A:LEU223 4.9 14.5 1.0 N A:LEU223 5.0 13.3 1.0

Manganese binding site 3 out of 4 in the Structure of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda


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 Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn501 b:14.6 occ:1.00 O3P H:4LU503 2.1 13.6 1.0 O H:HOH639 2.1 13.0 1.0 OE2 H:GLU229 2.2 12.8 1.0 O H:HOH644 2.2 14.4 1.0 O H:HOH635 2.2 15.2 1.0 ND1 H:HIS188 2.3 12.3 1.0 CE1 H:HIS188 3.1 14.2 1.0 CD H:GLU229 3.2 17.6 1.0 CG H:HIS188 3.3 13.9 1.0 P H:4LU503 3.3 16.5 1.0 OE1 H:GLU229 3.5 16.5 1.0 O2P H:4LU503 3.6 16.1 1.0 CB H:HIS188 3.7 14.8 1.0 K H:K502 3.7 16.0 1.0 O H:LEU223 4.2 15.6 1.0 CZ2 H:TRP163 4.2 22.0 1.0 NE2 H:HIS188 4.3 13.1 1.0 O1P H:4LU503 4.3 14.8 1.0 O H:VAL227 4.3 19.0 1.0 O5' H:4LU503 4.4 14.2 1.0 OG H:SER165 4.4 17.9 1.0 CD2 H:HIS188 4.4 13.4 1.0 CG H:GLU229 4.5 16.6 1.0 O H:PRO224 4.7 16.2 1.0 CB H:LEU223 4.7 18.3 1.0 NE1 H:TRP163 4.7 24.1 1.0 O H:MET221 4.8 15.3 1.0 CE2 H:TRP163 4.9 20.8 1.0 O H:TRP166 4.9 14.6 1.0 C H:LEU223 4.9 15.9 1.0 N H:LEU223 4.9 14.6 1.0

Manganese binding site 4 out of 4 in the Structure of the Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda


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 Reversible Pyrrole-2-Carboxylic Acid Decarboxylase PA0254/Huda within 5.0Å range: probe atom residue distance (Å) B Occ M:Mn502 b:15.3 occ:1.00 O3P M:4LU504 2.1 15.6 1.0 O M:HOH617 2.2 13.3 1.0 O M:HOH708 2.2 13.7 1.0 OE2 M:GLU229 2.2 12.0 1.0 O M:HOH718 2.3 16.1 1.0 ND1 M:HIS188 2.3 14.1 1.0 CE1 M:HIS188 3.1 15.1 1.0 CD M:GLU229 3.3 16.5 1.0 P M:4LU504 3.3 14.3 1.0 CG M:HIS188 3.3 14.4 1.0 O2P M:4LU504 3.6 14.2 1.0 OE1 M:GLU229 3.7 16.0 1.0 CB M:HIS188 3.7 14.5 1.0 K M:K503 3.8 15.9 1.0 CZ2 M:TRP163 4.2 23.2 1.0 O M:LEU223 4.2 17.0 1.0 NE2 M:HIS188 4.3 17.1 1.0 O1P M:4LU504 4.3 18.4 1.0 O5' M:4LU504 4.4 15.2 1.0 OG M:SER165 4.4 18.0 1.0 CD2 M:HIS188 4.4 15.8 1.0 O M:VAL227 4.4 18.4 1.0 CG M:GLU229 4.6 16.2 1.0 O M:PRO224 4.6 18.4 1.0 NE1 M:TRP163 4.7 23.5 1.0 O M:MET221 4.8 15.4 1.0 CB M:LEU223 4.8 18.8 1.0 O M:TRP166 4.8 15.6 1.0 CE2 M:TRP163 4.9 23.0 1.0 C M:LEU223 4.9 16.9 1.0 N M:LEU223 4.9 15.3 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