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Sodium in PDB 5fay: Y208F Mutant of Choline Tma-Lyase

Enzymatic activity of Y208F Mutant of Choline Tma-Lyase

All present enzymatic activity of Y208F Mutant of Choline Tma-Lyase:
4.3.99.4;

Protein crystallography data

The structure of Y208F Mutant of Choline Tma-Lyase, PDB code: 5fay 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 / 1.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 228.941, 228.941, 78.952, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Y208F Mutant of Choline Tma-Lyase (pdb code 5fay). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Y208F Mutant of Choline Tma-Lyase, PDB code: 5fay:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5fay

Go back to Sodium Binding Sites List in 5fay
Sodium binding site 1 out of 3 in the Y208F 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 Y208F Mutant of Choline Tma-Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na901

b:27.8
occ:1.00
 O A:HOH1757 2.3 24.4 1.0
O A:MET748 2.4 18.6 1.0
O A:HOH1415 2.4 17.1 1.0
O A:SER746 2.4 17.2 1.0
O B:HOH1672 2.5 27.6 1.0
O A:HOH1572 2.5 14.8 1.0
HA A:ALA749 3.2 20.4 1.0
C A:SER746 3.3 17.3 1.0
HA A:SER746 3.4 20.6 1.0
C A:MET748 3.4 19.9 1.0
HD22 A:ASN750 3.5 22.7 1.0
H A:ASN750 3.6 21.2 1.0
CA A:SER746 3.9 17.2 1.0
O A:HOH1603 3.9 39.9 1.0
CA A:ALA749 4.0 17.0 1.0
ND2 A:ASN750 4.1 18.9 1.0
N A:ALA749 4.1 15.7 1.0
HB2 A:SER746 4.2 21.6 1.0
HD21 A:ASN750 4.3 22.7 1.0
O A:HOH1933 4.3 71.2 1.0
O A:LEU787 4.3 18.4 1.0
O B:HOH1413 4.3 55.4 1.0
N A:ASN750 4.4 17.6 1.0
N A:MET748 4.4 19.4 1.0
N A:LYS747 4.4 17.0 1.0
O B:HOH1533 4.4 20.9 1.0
HZ3 B:LYS439 4.4 56.3 1.0
C A:LYS747 4.4 16.5 1.0
HE3 B:LYS439 4.5 61.4 1.0
H A:MET748 4.5 23.3 1.0
CA A:MET748 4.5 20.4 1.0
HA A:LYS747 4.6 20.5 1.0
CB A:SER746 4.6 18.0 1.0
O A:VAL745 4.6 17.7 1.0
O A:GLY788 4.7 19.8 1.0
CA A:LYS747 4.7 17.1 1.0
C A:ALA749 4.8 16.8 1.0
O A:LYS747 4.8 16.6 1.0
OD1 A:ASN789 4.8 19.9 1.0
HB2 A:ASN750 4.9 23.9 1.0
H A:ALA749 4.9 18.8 1.0
O A:HOH2004 4.9 44.8 1.0

Sodium binding site 2 out of 3 in 5fay

Go back to Sodium Binding Sites List in 5fay
Sodium binding site 2 out of 3 in the Y208F 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 Y208F Mutant of Choline Tma-Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:52.8
occ:1.00
 O A:HOH1225 2.4 43.2 1.0
O A:HOH1018 2.4 61.4 1.0
O A:HOH1702 2.5 62.4 1.0
O A:HOH1617 2.8 40.9 1.0
O A:LEU244 2.9 16.0 1.0
O A:GLU242 3.0 21.1 1.0
O A:HOH1810 3.1 71.0 1.0
HA A:GLU242 3.4 26.7 1.0
O A:HOH1507 3.7 66.8 1.0
C A:GLU242 3.7 20.4 1.0
O A:HOH1786 4.0 37.6 1.0
O A:LEU241 4.0 20.3 1.0
OE1 A:GLU242 4.1 55.9 1.0
CA A:GLU242 4.1 22.3 1.0
C A:LEU244 4.1 15.5 1.0
H A:LEU244 4.2 18.6 1.0
HA A:ASP245 4.4 19.9 1.0
HB2 A:ASP245 4.5 23.6 1.0
HG3 A:GLU242 4.5 50.7 1.0
N A:LEU244 4.6 15.5 1.0
CD A:GLU242 4.6 51.9 1.0
N A:GLN243 4.8 18.1 1.0
O A:HOH1657 4.8 28.1 1.0
C A:LEU241 4.9 20.6 1.0
OD2 A:ASP245 4.9 26.4 1.0
CG A:GLU242 5.0 42.3 1.0
N A:GLU242 5.0 19.8 1.0
CA A:LEU244 5.0 15.1 1.0

Sodium binding site 3 out of 3 in 5fay

Go back to Sodium Binding Sites List in 5fay
Sodium binding site 3 out of 3 in the Y208F 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 Y208F Mutant of Choline Tma-Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na901

b:27.1
occ:1.00
 O B:MET748 2.3 21.6 1.0
O A:HOH1656 2.4 26.5 1.0
O B:SER746 2.4 23.3 1.0
O B:HOH1645 2.4 46.0 1.0
O B:HOH1427 2.5 21.4 1.0
O B:HOH1527 2.6 22.2 1.0
HA B:SER746 3.2 28.0 1.0
HD22 B:ASN750 3.2 28.9 1.0
C B:SER746 3.2 23.5 1.0
HA B:ALA749 3.2 24.9 1.0
C B:MET748 3.4 21.6 1.0
H B:ASN750 3.7 24.1 1.0
CA B:SER746 3.7 23.4 1.0
ND2 B:ASN750 3.9 24.0 1.0
HB2 B:SER746 3.9 28.7 1.0
HD21 B:ASN750 3.9 28.9 1.0
CA B:ALA749 4.0 20.7 1.0
N B:ALA749 4.1 21.3 1.0
N B:MET748 4.2 22.8 1.0
N B:LYS747 4.3 23.9 1.0
O A:HOH1777 4.3 37.4 1.0
C B:LYS747 4.3 23.4 1.0
O B:LEU787 4.4 22.8 1.0
CB B:SER746 4.4 23.9 1.0
N B:ASN750 4.4 20.1 1.0
H B:MET748 4.4 27.4 1.0
HZ3 A:LYS439 4.4 53.0 1.0
CA B:MET748 4.4 22.1 1.0
HA B:LYS747 4.5 29.0 1.0
O B:VAL745 4.5 22.5 1.0
O B:HOH1515 4.6 29.3 1.0
CA B:LYS747 4.7 24.1 1.0
HZ2 A:LYS439 4.7 53.0 1.0
O A:HOH1361 4.7 44.6 1.0
O B:LYS747 4.7 23.4 1.0
C B:ALA749 4.8 20.2 1.0
H B:ALA749 4.8 25.5 1.0
OD1 B:ASN789 4.9 22.4 1.0
O B:GLY788 4.9 20.6 1.0
N B:SER746 4.9 23.6 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 23:47:44 2025

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