Sodium in PDB 4rzm: Crystal Structure of the LSD19-Lasalocid A Complex

The structure of Crystal Structure of the LSD19-Lasalocid A Complex, PDB code: 4rzm was solved by I.I.Mathews, K.Hotta, X.Chen, C.-Y.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.16 / 2.33
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	140.140, 140.140, 198.480, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.7

The structure of Crystal Structure of the LSD19-Lasalocid A Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the LSD19-Lasalocid A Complex (pdb code 4rzm). 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 the LSD19-Lasalocid A Complex, PDB code: 4rzm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the LSD19-Lasalocid A Complex


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 the LSD19-Lasalocid A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:64.4 occ:1.00 O A:VAL123 2.3 67.2 1.0 O A:HOH449 2.3 70.7 1.0 O A:THR129 2.3 71.2 1.0 O A:SER126 2.3 68.1 1.0 O A:HOH451 2.4 62.7 1.0 C A:VAL123 3.3 64.2 1.0 C A:SER126 3.4 69.5 1.0 C A:THR129 3.5 64.2 1.0 CA A:THR124 3.8 56.3 1.0 N A:SER126 3.9 60.6 1.0 N A:THR124 4.0 66.4 1.0 CG2 A:THR129 4.0 70.1 1.0 CA A:SER126 4.1 68.7 1.0 C A:THR124 4.2 61.6 1.0 N A:ALA130 4.3 68.8 1.0 CA A:ALA130 4.4 75.5 1.0 CA A:VAL123 4.4 63.4 1.0 N A:THR129 4.4 70.2 1.0 CA A:THR129 4.4 70.5 1.0 CB A:SER126 4.5 61.8 1.0 N A:SER127 4.6 63.6 1.0 N A:ASP125 4.6 61.7 1.0 O A:THR124 4.7 57.5 1.0 CB A:THR129 4.8 75.3 1.0 CB A:VAL123 4.8 69.8 1.0 CA A:SER127 4.9 64.3 1.0 O A:ARG131 5.0 70.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the LSD19-Lasalocid A Complex


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 the LSD19-Lasalocid A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na308 b:59.9 occ:1.00 O B:HIS232 2.6 51.1 1.0 O1 B:FMT306 2.6 56.1 1.0 O2 B:FMT306 2.6 60.0 1.0 O2 B:FMT307 2.7 71.1 1.0 O1 B:FMT307 2.8 56.0 1.0 C B:FMT306 2.9 83.4 1.0 C B:FMT307 3.1 90.7 1.0 C B:HIS232 3.7 49.5 1.0 CB B:HIS232 3.9 50.7 1.0 CA B:HIS232 4.4 45.5 1.0 ND1 B:HIS74 4.5 55.7 1.0 O B:HOH420 4.7 53.3 1.0 CE1 B:HIS74 4.7 53.5 1.0 O B:HOH419 4.7 51.1 1.0 N B:LEU233 4.7 56.6 1.0 CA B:LEU233 5.0 54.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the LSD19-Lasalocid A Complex


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 the LSD19-Lasalocid A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na309 b:83.3 occ:1.00 O B:THR129 2.3 0.8 1.0 O B:SER126 2.3 79.7 1.0 O B:HOH466 2.4 90.4 1.0 O B:VAL123 2.4 83.4 1.0 O B:HOH465 2.5 78.4 1.0 C B:SER126 3.5 75.2 1.0 C B:THR129 3.5 0.6 1.0 C B:VAL123 3.5 75.5 1.0 CA B:THR124 3.9 74.2 1.0 N B:SER126 4.0 76.2 1.0 N B:THR124 4.1 73.1 1.0 CA B:SER126 4.2 88.2 1.0 C B:THR124 4.2 78.5 1.0 CG2 B:THR129 4.3 86.4 1.0 N B:ALA130 4.3 0.2 1.0 CA B:ALA130 4.4 0.6 1.0 N B:THR129 4.5 0.8 1.0 CA B:THR129 4.5 95.2 1.0 N B:SER127 4.5 83.3 1.0 O B:THR124 4.6 71.3 1.0 CB B:SER126 4.7 82.5 1.0 CA B:VAL123 4.7 83.3 1.0 N B:ASP125 4.7 72.2 1.0 CA B:SER127 4.7 86.2 1.0 CB B:THR129 4.9 0.1 1.0 O B:ARG131 5.0 87.5 1.0

F.T.Wong, K.Hotta, X.Chen, M.Fang, K.Watanabe, C.Y.Kim. Epoxide Hydrolase-Lasalocid A Structure Provides Mechanistic Insight Into Polyether Natural Product Biosynthesis. J.Am.Chem.Soc. V. 137 86 2015.
ISSN: ISSN 0002-7863
PubMed: 25535803
DOI: 10.1021/JA511374K