Sodium 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:

Manganese

(Mn)

2 atoms

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

Sodium 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 Sodium with other atoms in the Na 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:Na502 b:46.4 occ:1.00 OG1 A:THR168 2.2 65.0 1.0 O A:HOH607 2.2 40.1 1.0 O2P A:4LU508 2.2 30.0 1.0 O A:VAL167 2.2 56.4 1.0 OE2 A:GLU233 2.3 75.1 1.0 OD1 A:ASP166 2.3 49.0 1.0 C A:VAL167 3.0 50.5 1.0 CD A:GLU233 3.1 64.8 1.0 MN A:MN501 3.2 61.3 1.0 P A:4LU508 3.2 30.0 1.0 CB A:THR168 3.2 48.7 1.0 O5' A:4LU508 3.3 30.0 1.0 CG A:ASP166 3.3 50.9 1.0 CA A:THR168 3.5 46.8 1.0 OE1 A:GLU233 3.5 68.4 1.0 N A:THR168 3.6 47.2 1.0 OD2 A:ASP166 3.7 52.7 1.0 CG2 A:THR168 3.8 43.2 1.0 N A:VAL167 3.8 51.9 1.0 O3P A:4LU508 4.0 30.0 1.0 O A:ALA220 4.0 51.4 1.0 CA A:VAL167 4.0 52.9 1.0 CG A:GLU233 4.2 53.1 1.0 O A:HOH665 4.2 40.5 1.0 O A:HOH678 4.4 47.0 1.0 O1P A:4LU508 4.4 30.0 1.0 C5' A:4LU508 4.5 30.0 1.0 CB A:ASP166 4.7 50.3 1.0 C A:ASP166 4.8 54.4 1.0 CG1 A:VAL167 4.9 47.2 1.0 C4' A:4LU508 4.9 30.0 1.0 O A:PHE222 5.0 50.4 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na502 b:66.0 occ:1.00 O2P B:4LU504 2.3 20.0 1.0 O B:HOH606 2.3 69.2 1.0 OG1 B:THR168 2.4 85.8 1.0 O B:VAL167 2.4 84.3 1.0 OD1 B:ASP166 2.4 75.0 1.0 OE2 B:GLU233 2.4 0.0 1.0 CD B:GLU233 2.8 0.4 1.0 OE1 B:GLU233 3.1 0.1 1.0 MN B:MN501 3.2 81.3 1.0 C B:VAL167 3.3 79.0 1.0 P B:4LU504 3.3 20.0 1.0 O5' B:4LU504 3.3 20.0 1.0 CG B:ASP166 3.4 79.3 1.0 CB B:THR168 3.4 82.8 1.0 OD2 B:ASP166 3.7 81.8 1.0 CG2 B:THR168 3.7 80.7 1.0 CA B:THR168 3.8 79.9 1.0 CG B:GLU233 3.8 96.2 1.0 N B:THR168 3.9 78.6 1.0 N B:VAL167 4.0 78.4 1.0 O B:ALA220 4.0 79.4 1.0 O3P B:4LU504 4.1 20.0 1.0 CA B:VAL167 4.3 76.6 1.0 O B:HOH607 4.5 68.9 1.0 O1P B:4LU504 4.6 20.0 1.0 O B:HOH681 4.6 66.0 1.0 C5' B:4LU504 4.7 20.0 1.0 CB B:ASP166 4.7 80.5 1.0 CB B:GLU233 4.8 87.2 1.0 C B:ASP166 4.8 78.5 1.0 CG2 B:VAL167 5.0 77.3 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