Manganese in PDB 5o3n: Crystal Structure of E. Cloacae 3,4-Dihydroxybenzoic Acid Decarboxylase (Aroy) Reconstituted with Prfmn

The structure of Crystal Structure of E. Cloacae 3,4-Dihydroxybenzoic Acid Decarboxylase (Aroy) Reconstituted with Prfmn, PDB code: 5o3n was solved by S.A.Marshall, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.07 / 2.05
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	208.310, 208.310, 157.910, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 20.5

The structure of Crystal Structure of E. Cloacae 3,4-Dihydroxybenzoic Acid Decarboxylase (Aroy) Reconstituted with Prfmn also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of E. Cloacae 3,4-Dihydroxybenzoic Acid Decarboxylase (Aroy) Reconstituted with Prfmn (pdb code 5o3n). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of E. Cloacae 3,4-Dihydroxybenzoic Acid Decarboxylase (Aroy) Reconstituted with Prfmn, PDB code: 5o3n:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of E. Cloacae 3,4-Dihydroxybenzoic Acid Decarboxylase (Aroy) Reconstituted with Prfmn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of E. Cloacae 3,4-Dihydroxybenzoic Acid Decarboxylase (Aroy) Reconstituted with Prfmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:61.3 occ:1.00 OE2 A:GLU233 2.2 75.1 1.0 O2P A:4LU508 2.2 30.0 1.0 OD2 A:ASP166 2.2 52.7 1.0 ND1 A:HIS189 2.3 53.8 1.0 O A:HOH665 2.4 40.5 1.0 O A:HOH621 2.4 64.1 1.0 CG A:ASP166 3.1 50.9 1.0 CE1 A:HIS189 3.2 53.7 1.0 NA A:NA502 3.2 46.4 1.0 CD A:GLU233 3.2 64.8 1.0 P A:4LU508 3.3 30.0 1.0 OD1 A:ASP166 3.3 49.0 1.0 O1P A:4LU508 3.3 30.0 1.0 CG A:HIS189 3.4 54.0 1.0 CB A:HIS189 3.7 48.9 1.0 OE1 A:GLU233 3.9 68.4 1.0 O A:HOH675 4.1 55.4 1.0 CG A:GLU233 4.2 53.1 1.0 O5' A:4LU508 4.2 30.0 1.0 NE2 A:HIS189 4.3 55.1 1.0 O3P A:4LU508 4.3 30.0 1.0 O A:TYR231 4.4 56.3 1.0 O A:THR227 4.4 52.5 1.0 CD2 A:HIS189 4.5 54.6 1.0 O A:HOH607 4.5 40.1 1.0 CB A:ASP166 4.5 50.3 1.0 OG1 A:THR227 4.6 43.8 1.0 O A:PHE222 4.7 50.4 1.0 OG1 A:THR168 4.8 65.0 1.0 O A:PRO228 4.8 56.2 1.0 O A:VAL167 5.0 56.4 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of E. Cloacae 3,4-Dihydroxybenzoic Acid Decarboxylase (Aroy) Reconstituted with Prfmn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of E. Cloacae 3,4-Dihydroxybenzoic Acid Decarboxylase (Aroy) Reconstituted with Prfmn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:81.3 occ:1.00 OE2 B:GLU233 2.0 0.0 1.0 O2P B:4LU504 2.1 20.0 1.0 ND1 B:HIS189 2.5 78.1 1.0 O B:HOH604 2.5 64.4 1.0 OD2 B:ASP166 2.6 81.8 1.0 O B:HOH681 2.6 66.0 1.0 NA B:NA502 3.2 66.0 1.0 CD B:GLU233 3.2 0.4 1.0 P B:4LU504 3.3 20.0 1.0 CE1 B:HIS189 3.3 81.3 1.0 CG B:ASP166 3.5 79.3 1.0 O1P B:4LU504 3.5 20.0 1.0 CG B:HIS189 3.5 79.7 1.0 OD1 B:ASP166 3.6 75.0 1.0 CB B:HIS189 3.8 80.2 1.0 CG B:GLU233 4.0 96.2 1.0 OE1 B:GLU233 4.1 0.1 1.0 O B:HOH635 4.2 65.1 1.0 O B:THR227 4.2 67.4 1.0 O5' B:4LU504 4.3 20.0 1.0 O B:TYR231 4.4 88.2 1.0 O3P B:4LU504 4.4 20.0 1.0 O B:PRO228 4.4 76.8 1.0 NE2 B:HIS189 4.5 84.0 1.0 OG1 B:THR227 4.5 70.8 1.0 CD2 B:HIS189 4.6 82.6 1.0 O B:HOH606 4.6 69.2 1.0 O B:PHE222 4.7 81.9 1.0 CB B:ASP166 4.9 80.5 1.0

S.E.Payer, S.A.Marshall, N.Barland, X.Sheng, T.Reiter, A.Dordic, G.Steinkellner, C.Wuensch, S.Kaltwasser, K.Fisher, S.E.J.Rigby, P.Macheroux, J.Vonck, K.Gruber, K.Faber, F.Himo, D.Leys, T.Pavkov-Keller, S.M.Glueck. Regioselective Para-Carboxylation of Catechols with A Prenylated Flavin Dependent Decarboxylase. Angew. Chem. Int. Ed. Engl. V. 56 13893 2017.
ISSN: ESSN 1521-3773
PubMed: 28857436
DOI: 10.1002/ANIE.201708091