Sodium in PDB 4j0n: Crystal Structure of A Manganese Dependent Isatin Hydrolase

The structure of Crystal Structure of A Manganese Dependent Isatin Hydrolase, PDB code: 4j0n was solved by K.Bjerregaard-Andersen, T.Sommer, J.K.Jensen, B.Jochimsen, M.Etzerodt, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.59 / 2.25
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	51.940, 51.940, 176.690, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 22.3

The structure of Crystal Structure of A Manganese Dependent Isatin Hydrolase also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Crystal Structure of A Manganese Dependent Isatin Hydrolase (pdb code 4j0n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Manganese Dependent Isatin Hydrolase, PDB code: 4j0n:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Manganese Dependent Isatin Hydrolase


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 A Manganese Dependent Isatin Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:51.9 occ:1.00 CD2 B:PHE62 2.7 36.8 1.0 CZ A:PHE41 2.8 44.4 1.0 CE2 B:PHE62 3.0 44.9 1.0 CE2 A:PHE209 3.2 34.4 1.0 CE1 A:PHE41 3.6 40.5 1.0 CE2 A:PHE41 3.6 41.4 1.0 CD2 A:PHE209 3.7 33.3 1.0 CG B:PHE62 3.9 36.7 1.0 CZ A:PHE209 4.2 40.2 1.0 CZ B:PHE62 4.4 47.1 1.0 CB B:PHE62 4.5 30.2 1.0 CD1 A:PHE41 4.8 36.0 1.0 CD2 A:PHE41 4.8 42.2 1.0 CE1 B:PHE63 4.9 29.8 1.0 CB A:PRO208 4.9 31.2 1.0 CZ2 A:TRP84 5.0 25.7 1.0 CG A:PHE209 5.0 29.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A Manganese Dependent Isatin Hydrolase


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 A Manganese Dependent Isatin Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:56.5 occ:1.00 CD2 A:PHE62 2.7 51.3 1.0 CZ B:PHE41 2.8 48.2 1.0 CE1 B:PHE209 3.2 38.9 1.0 CE2 A:PHE62 3.5 55.2 1.0 CE2 B:PHE41 3.5 39.0 1.0 CD1 B:PHE209 3.6 34.2 1.0 CE1 A:PHE63 3.6 31.6 1.0 CG A:PHE62 3.7 41.9 1.0 CB A:PHE62 3.8 40.5 1.0 CE1 B:PHE41 3.9 48.2 1.0 CD1 A:PHE63 4.1 34.2 1.0 CZ B:PHE209 4.1 39.5 1.0 CH2 B:TRP84 4.1 29.1 1.0 CZ2 B:TRP84 4.2 28.6 1.0 CG B:PHE209 4.7 32.4 1.0 CZ A:PHE63 4.8 33.4 1.0 CZ A:PHE62 4.8 51.3 1.0 N A:PHE62 4.9 40.0 1.0 CD2 B:PHE41 4.9 37.8 1.0 CD1 A:PHE62 4.9 43.7 1.0 CA A:PHE62 4.9 37.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Manganese Dependent Isatin Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Manganese Dependent Isatin Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:54.2 occ:1.00 O A:HOH509 2.8 37.5 1.0 CE2 B:TRP67 3.6 26.0 1.0 CZ2 B:TRP67 3.7 24.6 1.0 CB A:PRO46 3.8 26.2 1.0 NE1 B:TRP67 3.9 24.6 1.0 CG A:PRO46 4.1 25.9 1.0 CD2 B:TRP67 4.1 28.4 1.0 CH2 B:TRP67 4.2 30.0 1.0 CD1 B:TRP67 4.5 24.2 1.0 CE3 B:TRP67 4.6 26.7 1.0 CZ3 B:TRP67 4.6 27.8 1.0 CG B:TRP67 4.6 25.5 1.0 CD A:PRO46 4.8 21.6 1.0

K.Bjerregaard-Andersen, T.Sommer, J.K.Jensen, B.Jochimsen, M.Etzerodt, J.P.Morth. A Proton Wire and Water Channel Revealed in the Crystal Structure of Isatin Hydrolase. J.Biol.Chem. V. 289 21351 2014.
ISSN: ISSN 0021-9258
PubMed: 24917679
DOI: 10.1074/JBC.M114.568824