Sodium in PDB 5mlx: Open Loop Conformation of PHAZ7 Y105E Mutant

The structure of Open Loop Conformation of PHAZ7 Y105E Mutant, PDB code: 5mlx was solved by T.Kellici, T.Mavromoustakos, D.Jendrossek, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.08 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.300, 199.500, 44.400, 90.00, 114.20, 90.00
R / Rfree (%)	12.6 / 15.2

The structure of Open Loop Conformation of PHAZ7 Y105E Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Open Loop Conformation of PHAZ7 Y105E Mutant (pdb code 5mlx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Open Loop Conformation of PHAZ7 Y105E Mutant, PDB code: 5mlx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Open Loop Conformation of PHAZ7 Y105E Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Open Loop Conformation of PHAZ7 Y105E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:19.4 occ:1.00 O A:HOH1130 2.0 37.1 1.0 OG1 A:THR41 3.0 12.9 1.0 O A:HOH893 3.2 19.8 1.0 O A:HOH1088 3.4 23.2 1.0 O A:GLN129 3.5 9.1 1.0 O A:HOH1154 3.6 33.2 1.0 N A:GLN129 3.7 8.7 1.0 CB A:THR41 3.8 10.6 1.0 CB A:GLN129 3.9 11.0 1.0 CG2 A:THR41 3.9 6.8 1.0 CA A:THR41 4.0 8.9 1.0 CD A:LYS127 4.0 15.1 1.0 CB A:LYS127 4.0 7.7 1.0 C A:GLN129 4.1 9.4 1.0 CA A:GLN129 4.1 7.4 1.0 N A:SER128 4.3 8.7 1.0 O A:HOH874 4.3 23.9 1.0 CG A:LYS127 4.4 9.5 1.0 OG A:SER128 4.6 17.4 1.0 N A:THR41 4.6 8.8 1.0 CD A:PRO42 4.7 8.4 1.0 C A:SER128 4.7 9.4 1.0 O A:HOH1341 4.7 29.7 1.0 CG A:GLN129 4.7 7.2 1.0 CA A:LYS127 4.8 9.1 1.0 C A:LYS127 4.8 10.3 1.0 CE A:LYS127 4.8 18.4 1.0 NZ A:LYS127 5.0 25.4 1.0 OE1 A:GLN129 5.0 11.9 1.0

Sodium binding site 2 out of 5 in the Open Loop Conformation of PHAZ7 Y105E Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Open Loop Conformation of PHAZ7 Y105E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:21.1 occ:1.00 O A:HOH968 2.7 9.2 1.0 O A:HOH921 2.8 13.7 1.0 O A:HOH1076 2.8 15.8 1.0 O A:HOH1374 3.0 28.2 1.0 CE2 A:PHE197 3.5 7.8 1.0 OG A:SER136 4.0 14.8 1.0 CZ A:PHE197 4.0 7.4 1.0 CB A:ASN49 4.0 6.2 1.0 CB A:MET137 4.1 7.1 1.0 CD2 A:PHE197 4.3 7.9 1.0 N A:MET137 4.4 6.0 1.0 O A:HOH885 4.4 11.4 1.0 ND2 A:ASN49 4.5 9.9 1.0 CD1 A:LEU168 4.5 12.8 1.0 CA A:MET137 4.6 5.4 1.0 O A:HOH1248 4.6 33.2 1.0 CG A:MET137 4.7 9.0 1.0 SD A:MET137 4.7 14.9 1.0 CG A:ASN49 4.9 8.4 1.0 O A:HOH1027 5.0 13.6 1.0 CB A:SER136 5.0 8.3 1.0 CG1 A:VAL244 5.0 8.2 1.0 N A:ASN49 5.0 7.5 1.0 CE1 A:PHE197 5.0 7.8 1.0

Sodium binding site 3 out of 5 in the Open Loop Conformation of PHAZ7 Y105E Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Open Loop Conformation of PHAZ7 Y105E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:23.0 occ:1.00 N A:ASP84 3.1 6.9 1.0 O A:HOH1308 3.4 25.4 1.0 CB A:ASN83 3.5 8.2 1.0 O A:HOH857 3.5 28.5 1.0 O A:HOH1091 3.8 25.3 1.0 CB A:ASP84 3.8 10.0 1.0 CA A:ASN83 3.8 8.9 1.0 C A:ASN83 4.0 7.2 1.0 OD2 A:ASP84 4.1 15.7 1.0 SG A:CYS36 4.1 10.1 1.0 CA A:ASP84 4.1 7.5 1.0 CG A:ASP84 4.1 11.3 1.0 CB A:CYS36 4.3 11.7 1.0 CE A:LYS78 4.5 17.6 1.0 CG A:ASN83 4.6 8.4 1.0 O A:HOH1320 4.6 31.4 1.0 OD1 A:ASP84 4.8 6.9 1.0 NZ A:LYS78 4.9 23.3 1.0 OD1 A:ASN83 5.0 8.3 1.0 O A:SER35 5.0 13.2 1.0 C A:ASP84 5.0 7.2 1.0

Sodium binding site 4 out of 5 in the Open Loop Conformation of PHAZ7 Y105E Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Open Loop Conformation of PHAZ7 Y105E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:13.8 occ:1.00 O B:HOH932 3.1 32.6 1.0 N B:GLY25 3.1 10.6 1.0 O B:HOH956 3.4 16.5 1.0 N B:PRO24 3.5 7.8 1.0 CD B:PRO24 3.6 8.1 1.0 C B:ALA23 3.6 10.2 1.0 CA B:ALA23 3.6 9.6 1.0 O B:HOH906 3.7 28.2 1.0 CA B:GLY25 3.8 12.2 1.0 CB B:ALA23 3.9 12.7 1.0 CG B:PRO24 4.1 7.7 1.0 C B:PRO24 4.2 7.8 1.0 CE2 B:TYR18 4.2 6.0 1.0 O B:ALA23 4.2 13.3 1.0 CD2 B:TYR18 4.3 7.7 1.0 CA B:PRO24 4.4 6.8 1.0 O B:HOH1030 4.7 33.4 1.0 C B:GLY25 4.8 12.3 1.0 O B:HOH703 4.9 25.7 1.0 CB B:PRO24 5.0 7.7 1.0 N B:ALA23 5.0 8.6 1.0

Sodium binding site 5 out of 5 in the Open Loop Conformation of PHAZ7 Y105E Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Open Loop Conformation of PHAZ7 Y105E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:22.3 occ:1.00 O B:HOH686 3.0 22.1 1.0 O B:HOH826 3.0 28.9 1.0 O B:HOH834 3.1 13.0 1.0 N B:ASP329 3.3 8.8 1.0 O B:HOH857 3.5 23.2 1.0 N B:LEU328 3.6 10.0 1.0 O B:THR326 3.7 9.8 1.0 CB B:ASP329 3.7 8.8 1.0 CA B:ASP329 4.1 7.4 1.0 C B:LEU328 4.1 9.3 1.0 CA B:LEU328 4.2 10.1 1.0 C B:GLY327 4.2 10.2 1.0 CB B:LEU328 4.2 10.0 1.0 CA B:GLY327 4.3 9.6 1.0 C B:THR326 4.6 8.0 1.0 N B:GLY327 5.0 8.0 1.0

T.F.Kellici, T.Mavromoustakos, D.Jendrossek, A.C.Papageorgiou. Crystal Structure Analysis, Covalent Docking, and Molecular Dynamics Calculations Reveal A Conformational Switch in PHAZ7 Phb Depolymerase. Proteins V. 85 1351 2017.
ISSN: ESSN 1097-0134
PubMed: 28370478
DOI: 10.1002/PROT.25296