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Sodium in PDB 5fav: E491Q Mutant of Choline Tma-Lyase

Enzymatic activity of E491Q Mutant of Choline Tma-Lyase

All present enzymatic activity of E491Q Mutant of Choline Tma-Lyase:
4.3.99.4;

Protein crystallography data

The structure of E491Q Mutant of Choline Tma-Lyase, PDB code: 5fav 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) 49.47 / 1.60
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 228.922, 228.922, 78.924, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.8

Sodium Binding Sites:

The binding sites of Sodium atom in the E491Q Mutant of Choline Tma-Lyase (pdb code 5fav). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the E491Q Mutant of Choline Tma-Lyase, PDB code: 5fav:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5fav

Go back to Sodium Binding Sites List in 5fav
Sodium binding site 1 out of 3 in the E491Q 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 E491Q Mutant of Choline Tma-Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na901

b:19.5
occ:1.00
 O A:MET748 2.3 14.2 1.0
O A:SER746 2.4 15.1 1.0
O A:HOH1750 2.4 24.1 1.0
O A:HOH1321 2.4 15.0 1.0
O A:HOH1552 2.5 17.1 1.0
O B:HOH1731 2.5 29.2 1.0
HA A:ALA749 3.1 16.6 1.0
C A:SER746 3.3 15.3 1.0
HA A:SER746 3.3 16.1 1.0
C A:MET748 3.4 11.8 1.0
HD22 A:ASN750 3.4 17.2 1.0
H A:ASN750 3.6 16.7 1.0
O A:HOH1371 3.8 29.9 1.0
CA A:SER746 3.8 13.4 1.0
CA A:ALA749 4.0 13.8 1.0
ND2 A:ASN750 4.0 14.4 1.0
N A:ALA749 4.1 11.6 1.0
O A:HOH2000 4.1 55.1 1.0
HB2 A:SER746 4.1 16.9 1.0
HD21 A:ASN750 4.1 17.2 1.0
N A:MET748 4.2 14.0 1.0
N A:ASN750 4.3 13.9 1.0
O A:LEU787 4.3 17.5 1.0
C A:LYS747 4.4 13.4 1.0
N A:LYS747 4.4 15.5 1.0
H A:MET748 4.4 16.8 1.0
HZ3 B:LYS439 4.5 68.7 1.0
CA A:MET748 4.5 14.0 1.0
O B:HOH1352 4.5 44.5 1.0
O B:HOH1477 4.5 19.4 1.0
HA A:LYS747 4.5 17.1 1.0
HE3 B:LYS439 4.5 73.6 1.0
O A:VAL745 4.6 13.6 1.0
CB A:SER746 4.6 14.1 1.0
C A:ALA749 4.7 11.6 1.0
CA A:LYS747 4.7 14.2 1.0
O A:LYS747 4.7 15.0 1.0
O A:GLY788 4.8 16.2 1.0
OD1 A:ASN789 4.8 16.1 1.0
H A:ALA749 4.8 13.9 1.0
O A:HOH1965 4.9 37.0 1.0
HB2 A:ALA749 4.9 16.6 1.0

Sodium binding site 2 out of 3 in 5fav

Go back to Sodium Binding Sites List in 5fav
Sodium binding site 2 out of 3 in the E491Q 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 E491Q Mutant of Choline Tma-Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:43.9
occ:1.00
 O A:HOH1110 2.3 36.6 1.0
O A:HOH1721 2.4 34.6 1.0
O A:HOH1011 2.6 52.8 1.0
O A:LEU244 2.6 14.4 1.0
O A:HOH1614 2.7 45.6 1.0
O A:GLU242 2.9 22.6 1.0
O A:HOH1823 3.1 65.4 1.0
O A:HOH1204 3.2 62.9 1.0
HA A:GLU242 3.5 19.2 1.0
C A:GLU242 3.6 19.0 1.0
O A:LEU241 3.8 19.1 1.0
C A:LEU244 3.8 12.7 1.0
H A:LEU244 3.8 15.9 1.0
O A:HOH1751 4.0 36.4 1.0
CA A:GLU242 4.1 16.0 1.0
N A:LEU244 4.2 13.2 1.0
OE1 A:GLU242 4.2 53.5 1.0
HB2 A:ASP245 4.2 19.8 1.0
HA A:ASP245 4.3 16.5 1.0
N A:GLN243 4.5 14.5 1.0
CA A:LEU244 4.7 12.5 1.0
HA A:GLN243 4.7 16.9 1.0
HG3 A:GLU242 4.7 52.6 1.0
OD2 A:ASP245 4.7 25.3 1.0
N A:ASP245 4.8 12.8 1.0
C A:GLN243 4.8 16.3 1.0
C A:LEU241 4.8 21.4 1.0
CD A:GLU242 4.8 51.7 1.0
CA A:ASP245 4.8 13.7 1.0
O A:HOH1679 4.9 26.9 1.0
CB A:ASP245 4.9 16.5 1.0
CA A:GLN243 4.9 14.1 1.0
N A:GLU242 4.9 16.0 1.0

Sodium binding site 3 out of 3 in 5fav

Go back to Sodium Binding Sites List in 5fav
Sodium binding site 3 out of 3 in the E491Q 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 3 of E491Q Mutant of Choline Tma-Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na901

b:23.5
occ:1.00
 O B:MET748 2.3 17.6 1.0
O A:HOH1719 2.4 26.9 1.0
O B:SER746 2.4 18.4 1.0
O B:HOH1448 2.4 21.2 1.0
O B:HOH1668 2.5 34.2 1.0
O B:HOH1587 2.6 23.1 1.0
HA B:ALA749 3.2 20.1 1.0
C B:SER746 3.3 20.9 1.0
HA B:SER746 3.3 22.4 1.0
C B:MET748 3.3 17.3 1.0
HD22 B:ASN750 3.3 24.1 1.0
H B:ASN750 3.7 19.8 1.0
CA B:SER746 3.8 18.7 1.0
CA B:ALA749 4.0 16.7 1.0
N B:ALA749 4.0 17.1 1.0
ND2 B:ASN750 4.0 20.0 1.0
HB2 B:SER746 4.1 22.9 1.0
HD21 B:ASN750 4.2 24.1 1.0
N B:MET748 4.2 18.1 1.0
O A:HOH1768 4.2 35.9 1.0
H B:MET748 4.3 21.7 1.0
N B:LYS747 4.3 18.9 1.0
C B:LYS747 4.3 18.4 1.0
HZ3 A:LYS439 4.4 58.9 1.0
O B:LEU787 4.4 19.4 1.0
CA B:MET748 4.4 17.6 1.0
N B:ASN750 4.4 16.5 1.0
HA B:LYS747 4.5 22.6 1.0
CB B:SER746 4.5 19.1 1.0
O B:HOH1512 4.6 26.4 1.0
O B:VAL745 4.6 18.4 1.0
HZ2 A:LYS439 4.7 58.9 1.0
CA B:LYS747 4.7 18.9 1.0
C B:ALA749 4.8 16.4 1.0
O B:LYS747 4.8 21.0 1.0
H B:ALA749 4.8 20.4 1.0
O B:HOH1496 4.8 28.6 1.0
O B:GLY788 4.8 17.1 1.0
OD1 B:ASN789 4.9 20.2 1.0
NZ A:LYS439 5.0 49.1 1.0
HB2 B:ALA749 5.0 24.7 1.0

Reference:

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
Page generated: Sun Aug 17 23:46:30 2025

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