Sodium in PDB 5faw: T502A Mutant of Choline Tma-Lyase

All present enzymatic activity of T502A Mutant of Choline Tma-Lyase:
4.3.99.4;

The structure of T502A Mutant of Choline Tma-Lyase, PDB code: 5faw was solved by M.A.Funk, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.48 / 1.85
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	229.569, 229.569, 78.632, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.8

The binding sites of Sodium atom in the T502A Mutant of Choline Tma-Lyase (pdb code 5faw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the T502A Mutant of Choline Tma-Lyase, PDB code: 5faw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the T502A Mutant of Choline Tma-Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of T502A Mutant of Choline Tma-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:24.3 occ:1.00 O A:MET748 2.3 13.8 1.0 O A:SER746 2.4 15.1 1.0 O A:HOH1646 2.4 18.4 1.0 O A:HOH1231 2.4 14.9 1.0 O A:HOH1489 2.5 13.2 1.0 O B:HOH1604 2.5 21.3 1.0 HA A:ALA749 3.2 15.5 1.0 C A:SER746 3.3 15.3 1.0 HD22 A:ASN750 3.3 17.0 1.0 HA A:SER746 3.3 18.9 1.0 C A:MET748 3.5 13.4 1.0 H A:ASN750 3.5 15.8 1.0 CA A:SER746 3.9 15.7 1.0 O A:HOH1510 3.9 22.5 1.0 ND2 A:ASN750 4.0 14.2 1.0 CA A:ALA749 4.1 12.9 1.0 HB2 A:SER746 4.1 19.7 1.0 HD21 A:ASN750 4.2 17.0 1.0 N A:ALA749 4.2 13.0 1.0 O A:HOH1933 4.3 60.5 1.0 N A:ASN750 4.3 13.2 1.0 N A:MET748 4.3 14.8 1.0 HZ2 B:LYS439 4.3 46.2 1.0 O A:LEU787 4.3 16.3 1.0 N A:LYS747 4.4 15.3 1.0 C A:LYS747 4.4 14.3 1.0 H A:MET748 4.4 17.7 1.0 O B:HOH1493 4.4 20.5 1.0 CA A:MET748 4.5 14.3 1.0 O B:HOH1302 4.5 44.8 1.0 HA A:LYS747 4.5 18.0 1.0 O A:VAL745 4.6 14.9 1.0 CB A:SER746 4.6 16.4 1.0 HE3 B:LYS439 4.6 48.4 1.0 CA A:LYS747 4.7 15.0 1.0 O A:GLY788 4.7 15.1 1.0 C A:ALA749 4.7 12.8 1.0 O A:LYS747 4.8 14.0 1.0 HB2 A:ASN750 4.8 16.5 1.0 OD1 A:ASN789 4.9 16.1 1.0 HZ3 B:LYS439 4.9 46.2 1.0 NZ B:LYS439 4.9 38.5 1.0 O A:HOH1957 5.0 30.9 1.0

Sodium binding site 2 out of 2 in the T502A Mutant of Choline Tma-Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of T502A Mutant of Choline Tma-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na907 b:57.5 occ:1.00 O A:HOH1260 2.3 43.2 1.0 O A:HOH1665 2.4 28.0 1.0 O A:HOH1786 2.5 44.6 1.0 O A:HOH1013 2.6 44.7 1.0 O A:LEU244 2.7 16.1 1.0 O A:GLU242 2.8 20.5 1.0 O A:HOH1730 3.2 56.7 1.0 HA A:GLU242 3.6 26.8 1.0 C A:GLU242 3.7 19.1 1.0 O A:HOH1688 3.8 62.0 1.0 C A:LEU244 3.8 15.6 1.0 O A:LEU241 3.9 17.0 1.0 H A:LEU244 4.0 18.8 1.0 CA A:GLU242 4.2 22.3 1.0 HA A:ASP245 4.2 18.9 1.0 HB2 A:ASP245 4.2 19.8 1.0 O A:HOH1777 4.2 32.8 1.0 N A:LEU244 4.3 15.6 1.0 OE1 A:GLU242 4.3 53.7 1.0 N A:GLN243 4.6 16.7 1.0 CA A:LEU244 4.7 15.2 1.0 HG3 A:GLU242 4.7 49.9 1.0 N A:ASP245 4.7 15.4 1.0 O A:HOH1673 4.7 24.1 1.0 C A:GLN243 4.8 17.8 1.0 HA A:GLN243 4.8 22.4 1.0 CA A:ASP245 4.8 15.8 1.0 C A:LEU241 4.8 16.5 1.0 CB A:ASP245 4.9 16.5 1.0 CD A:GLU242 4.9 50.3 1.0 OD2 A:ASP245 4.9 20.2 1.0 CA A:GLN243 5.0 18.7 1.0

S.Bodea, M.A.Funk, E.P.Balskus, C.L.Drennan. Molecular Basis of C-N Bond Cleavage By the Glycyl Radical Enzyme Choline Trimethylamine-Lyase. Cell Chem Biol V. 23 1206 2016.
ISSN: ESSN 2451-9456
PubMed: 27642068
DOI: 10.1016/J.CHEMBIOL.2016.07.020