Sodium in PDB 5g4j: Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine

All present enzymatic activity of Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine:
4.2.3.2;

The structure of Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine, PDB code: 5g4j was solved by A.Cuetos, A.N.Tuan, J.Mangas Sanchez, G.Grogan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.60 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.166, 96.371, 121.897, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.9

The binding sites of Sodium atom in the Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine (pdb code 5g4j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine, PDB code: 5g4j:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1442 b:15.5 occ:1.00 N A:GLU235 3.3 15.3 1.0 O A:HOH2221 3.4 16.2 1.0 N A:ASN271 3.4 20.8 1.0 N A:GLY232 3.6 19.4 1.0 CB A:GLU235 3.7 20.9 1.0 CA A:GLY232 3.8 19.1 1.0 CB A:PHE270 3.9 17.0 1.0 CA A:GLU235 4.0 16.6 1.0 N A:ILE234 4.1 17.5 1.0 CA A:PHE270 4.1 18.2 1.0 CB A:ILE234 4.1 16.1 1.0 C A:GLY232 4.1 19.1 1.0 CD1 A:PHE270 4.1 18.3 1.0 C A:PHE270 4.3 20.1 1.0 C A:ILE234 4.3 16.5 1.0 CA A:ILE234 4.3 16.2 1.0 CA A:ASN271 4.3 23.5 1.0 CB A:ASN271 4.3 28.8 1.0 N A:TYR233 4.4 18.4 1.0 CG A:PHE270 4.4 16.1 1.0 O A:ASN271 4.6 23.1 1.0 O A:GLY232 4.7 18.4 1.0 C A:SER231 4.7 24.7 1.0 C A:ASN271 4.7 21.8 1.0 OE1 A:GLU235 4.8 32.9 1.0 C A:TYR233 4.9 17.6 1.0 CG2 A:ILE234 4.9 16.7 1.0 CG A:GLU235 5.0 24.3 1.0

Sodium binding site 2 out of 3 in the Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1443 b:30.8 occ:1.00 O A:SER356 2.2 30.5 1.0 O A:VAL359 2.2 24.6 1.0 O A:HOH2285 2.2 32.0 1.0 O A:ALA353 2.3 32.6 1.0 C A:VAL359 3.4 23.8 1.0 C A:SER356 3.4 32.2 1.0 C A:ALA353 3.5 32.0 1.0 N A:VAL359 4.0 25.2 1.0 CA A:VAL359 4.1 23.2 1.0 CA A:ALA353 4.1 28.2 1.0 CB A:VAL359 4.2 22.8 1.0 CA A:GLY357 4.3 28.5 1.0 N A:GLY357 4.3 28.4 1.0 N A:SER356 4.3 33.9 1.0 O A:GLY360 4.4 26.9 1.0 CA A:SER356 4.4 30.6 1.0 N A:GLY360 4.5 24.7 1.0 N A:GLN354 4.5 34.5 1.0 O A:GLN354 4.6 40.6 1.0 CB A:ALA353 4.6 27.4 1.0 C A:GLY357 4.6 26.1 1.0 C A:GLN354 4.7 40.5 1.0 CA A:GLY360 4.7 24.4 1.0 CA A:GLN354 4.8 39.8 1.0 CG1 A:VAL359 4.9 23.0 1.0 CB A:SER356 5.0 33.4 1.0

Sodium binding site 3 out of 3 in the Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Phospholyase A1RDF1 From Arthrobacter in Complex with Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1441 b:27.3 occ:1.00 N B:GLU235 3.3 26.4 1.0 O B:HOH2125 3.5 26.8 1.0 N B:ASN271 3.5 29.9 1.0 N B:GLY232 3.6 29.9 1.0 CB B:GLU235 3.6 29.6 1.0 CA B:GLY232 3.8 29.1 1.0 CB B:PHE270 3.9 27.8 1.0 N B:ILE234 4.0 23.3 1.0 CA B:GLU235 4.0 24.9 1.0 CB B:ILE234 4.0 24.7 1.0 C B:GLY232 4.1 27.7 1.0 CD1 B:PHE270 4.1 24.9 1.0 CA B:PHE270 4.1 28.4 1.0 C B:ILE234 4.2 25.6 1.0 CA B:ILE234 4.3 25.9 1.0 C B:PHE270 4.3 27.3 1.0 N B:TYR233 4.4 25.1 1.0 CB B:ASN271 4.4 36.6 1.0 CG B:PHE270 4.4 23.7 1.0 CA B:ASN271 4.4 33.0 1.0 O B:ASN271 4.6 31.9 1.0 O B:GLY232 4.6 27.1 1.0 C B:SER231 4.7 33.2 1.0 C B:ASN271 4.8 33.1 1.0 C B:TYR233 4.8 24.7 1.0 CG2 B:ILE234 4.8 25.7 1.0 CG B:GLU235 5.0 38.1 1.0 CG1 B:ILE234 5.0 25.1 1.0

A.Cuetos, F.Steffen-Munsberg, J.Mangas Sanchez, A.Frese, U.T.Bornscheuer, M.Hohne, G.Grogan. Structural Basis For Phospholyase Activity of A Class III Transaminase Homologue. Chembiochem V. 17 2308 2016.
ISSN: ESSN 1439-7633
PubMed: 27709756
DOI: 10.1002/CBIC.201600482