Sodium in PDB 5tl4: Crystal Structure of Sphingomonas Paucimobilis Aryl O-Demethylase Ligm

The structure of Crystal Structure of Sphingomonas Paucimobilis Aryl O-Demethylase Ligm, PDB code: 5tl4 was solved by A.C.Kohler, P.D.Adams, B.A.Simmons, K.L.Sale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.01 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	112.837, 126.184, 155.646, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.2

The structure of Crystal Structure of Sphingomonas Paucimobilis Aryl O-Demethylase Ligm also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of Sphingomonas Paucimobilis Aryl O-Demethylase Ligm (pdb code 5tl4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Sphingomonas Paucimobilis Aryl O-Demethylase Ligm, PDB code: 5tl4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Sphingomonas Paucimobilis Aryl O-Demethylase Ligm


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 Sphingomonas Paucimobilis Aryl O-Demethylase Ligm within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:16.5 occ:1.00 O A:HOH789 3.1 19.7 1.0 O A:HOH1002 3.2 20.5 1.0 ND2 A:ASN81 3.3 14.0 1.0 NZ A:LYS92 3.5 17.1 1.0 CB A:ASN81 3.6 11.2 1.0 CG A:ASN81 3.9 13.8 1.0 CD A:LYS92 4.0 14.6 1.0 CG A:LYS92 4.1 15.9 1.0 O A:HOH758 4.2 40.8 1.0 O A:HOH1032 4.2 36.6 1.0 CE A:LYS92 4.4 15.9 1.0 CB A:LYS92 4.4 12.4 1.0 O A:HOH1253 4.4 25.1 1.0 O A:HOH911 4.5 28.6 1.0 CA A:ASN81 4.5 14.0 1.0 N A:SER82 4.7 15.2 1.0 CD1 A:PHE312 4.8 33.2 1.0 O A:SER82 4.8 16.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Sphingomonas Paucimobilis Aryl O-Demethylase Ligm


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 Sphingomonas Paucimobilis Aryl O-Demethylase Ligm within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:51.7 occ:1.00 O C:HOH882 2.3 17.9 1.0 O C:HOH843 3.1 31.1 1.0 O C:HOH1231 3.7 44.6 1.0 O C:HOH788 3.9 32.9 1.0 CD2 C:PHE189 4.0 31.2 1.0 CZ C:PHE312 4.1 31.9 1.0 CE2 C:PHE189 4.1 34.1 1.0 CE1 C:PHE312 4.1 39.2 1.0 N C:GLN93 4.2 14.2 1.0 CB C:GLN93 4.3 11.2 1.0 CE2 C:PHE188 4.3 43.4 1.0 CG C:PHE189 4.7 25.8 1.0 CE2 C:PHE312 4.8 26.6 1.0 CA C:GLN93 4.9 16.2 1.0 CZ C:PHE189 4.9 34.9 1.0 CD2 C:PHE188 4.9 47.5 1.0 O C:HOH1263 4.9 52.1 1.0 O C:HOH1185 4.9 54.8 1.0 CD1 C:PHE312 4.9 30.7 1.0 OE1 C:GLN93 4.9 20.1 1.0 CL C:CL502 5.0 28.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Sphingomonas Paucimobilis Aryl O-Demethylase Ligm


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 Sphingomonas Paucimobilis Aryl O-Demethylase Ligm within 5.0Å range: probe atom residue distance (Å) B Occ D:Na502 b:28.9 occ:1.00 O D:HOH1016 2.9 31.5 1.0 O D:HOH997 3.0 24.3 1.0 NH1 D:ARG22 3.2 15.7 1.0 CD D:ARG22 3.6 16.7 1.0 CA D:GLU19 3.7 21.9 1.0 N D:GLU19 4.1 17.1 1.0 CG1 D:VAL18 4.1 15.2 1.0 CB D:GLU19 4.1 26.6 1.0 CB D:ARG22 4.2 16.3 1.0 CZ D:ARG22 4.2 16.2 1.0 CG D:ARG22 4.3 14.1 1.0 C D:VAL18 4.3 18.1 1.0 O D:VAL18 4.3 16.9 1.0 NE D:ARG22 4.4 14.4 1.0 CG D:GLU19 4.5 37.5 1.0 O D:HOH782 4.5 38.9 1.0 ND2 D:ASN23 4.6 18.2 1.0 OE2 D:GLU426 4.9 22.3 1.0 C D:GLU19 4.9 21.3 1.0 CB D:VAL18 4.9 21.6 1.0 O D:HOH1044 5.0 36.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Sphingomonas Paucimobilis Aryl O-Demethylase Ligm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Sphingomonas Paucimobilis Aryl O-Demethylase Ligm within 5.0Å range: probe atom residue distance (Å) B Occ D:Na503 b:20.5 occ:1.00 O D:HOH795 3.1 18.0 1.0 O D:HOH957 3.1 20.7 1.0 NZ D:LYS92 3.3 19.6 1.0 ND2 D:ASN81 3.4 14.2 1.0 CB D:ASN81 3.7 11.9 1.0 CG D:LYS92 3.8 18.0 1.0 CD D:LYS92 3.9 13.8 1.0 CG D:ASN81 4.0 15.7 1.0 CE D:LYS92 4.2 16.4 1.0 CB D:LYS92 4.2 17.6 1.0 O D:HOH1222 4.4 35.4 1.0 O D:HOH1055 4.4 43.9 1.0 CA D:ASN81 4.5 15.2 1.0 O D:HOH775 4.5 27.4 1.0 N D:SER82 4.7 13.5 1.0 O D:SER82 4.8 16.3 1.0 O D:HOH1174 4.9 44.8 1.0

A.C.Kohler, M.J.L.Mills, P.D.Adams, B.A.Simmons, K.L.Sale. Structure of Aryl O-Demethylase Offers Molecular Insight Into A Catalytic Tyrosine-Dependent Mechanism. Proc. Natl. Acad. Sci. V. 114 E3205 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28373573
DOI: 10.1073/PNAS.1619263114