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Sodium in PDB 4zg9: Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds

Enzymatic activity of Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds

All present enzymatic activity of Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds:
3.1.4.39;

Protein crystallography data

The structure of Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds, PDB code: 4zg9 was solved by A.J.Stein, G.Bain, J.H.Hutchinson, J.F.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.86 / 2.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 127.460, 209.991, 188.193, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 24.4

Other elements in 4zg9:

The structure of Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Zinc (Zn) 4 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds (pdb code 4zg9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds, PDB code: 4zg9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4zg9

Go back to Sodium Binding Sites List in 4zg9
Sodium binding site 1 out of 4 in the Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:72.5
occ:1.00
 O A:TYR670 2.4 80.9 1.0
O A:MET676 2.5 67.4 1.0
O A:ASP673 2.8 75.2 1.0
O A:HOH1018 2.8 47.6 1.0
O A:HOH1008 3.1 52.2 1.0
C A:TYR670 3.7 77.2 1.0
C A:MET676 3.7 59.1 1.0
C A:ASP673 4.0 78.8 1.0
CA A:SER677 4.2 53.2 1.0
N A:SER677 4.4 53.6 1.0
CA A:TYR670 4.5 74.7 1.0
O A:LYS671 4.6 68.3 1.0
CB A:SER677 4.6 53.0 1.0
N A:LYS671 4.6 80.3 1.0
CA A:LYS671 4.7 78.0 1.0
N A:MET676 4.7 67.2 1.0
CB A:TYR670 4.8 75.1 1.0
CA A:ASP673 4.8 77.6 1.0
CA A:MET676 4.8 61.6 1.0
C A:LYS671 4.8 71.4 1.0
N A:ASP673 4.9 79.9 1.0
N A:LYS674 4.9 79.0 1.0
CB A:ASP673 4.9 76.4 1.0
CA A:LYS674 4.9 83.8 1.0
OG A:SER677 5.0 51.1 1.0

Sodium binding site 2 out of 4 in 4zg9

Go back to Sodium Binding Sites List in 4zg9
Sodium binding site 2 out of 4 in the Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:50.7
occ:1.00
 OG A:SER808 2.1 63.7 1.0
O A:HOH1006 2.3 45.9 1.0
O A:HOH1004 2.6 43.8 1.0
O A:ASN802 2.6 62.8 1.0
O A:SER805 2.8 60.4 1.0
CB A:SER808 3.3 61.0 1.0
C A:ASN802 3.6 62.0 1.0
C A:SER805 4.0 61.0 1.0
N A:SER808 4.0 57.0 1.0
CA A:GLU803 4.2 66.3 1.0
N A:GLU803 4.2 66.5 1.0
CA A:SER808 4.2 59.0 1.0
CB A:ASN802 4.3 61.3 1.0
CA A:ASN802 4.5 60.5 1.0
O A:GLU803 4.5 56.1 1.0
O A:CYS806 4.6 54.6 1.0
OE2 A:GLU803 4.6 0.8 1.0
C A:GLU803 4.6 61.0 1.0
C A:CYS806 4.6 58.6 1.0
CA A:CYS806 4.7 68.1 1.0
N A:CYS806 4.8 65.1 1.0
N A:SER805 4.8 59.3 1.0
C A:SER808 4.8 63.9 1.0
CA A:SER805 4.9 58.7 1.0
N A:SER809 5.0 65.7 1.0

Sodium binding site 3 out of 4 in 4zg9

Go back to Sodium Binding Sites List in 4zg9
Sodium binding site 3 out of 4 in the Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na907

b:56.3
occ:1.00
 O B:TYR670 2.3 61.9 1.0
O B:HOH1006 2.6 54.1 1.0
O B:ASP673 2.8 64.7 1.0
O B:MET676 2.9 53.2 1.0
C B:TYR670 3.5 60.4 1.0
C B:ASP673 3.9 68.7 1.0
O B:LYS671 4.1 73.0 1.0
CA B:LYS671 4.1 63.6 1.0
C B:MET676 4.1 54.8 1.0
N B:LYS671 4.2 63.2 1.0
C B:LYS671 4.3 67.4 1.0
CA B:TYR670 4.5 57.7 1.0
CA B:LYS674 4.5 75.1 1.0
O B:LYS674 4.6 75.5 1.0
N B:LYS674 4.6 68.4 1.0
C B:LYS674 4.7 73.9 1.0
N B:ASP673 4.8 78.2 1.0
N B:MET676 4.9 56.8 1.0
CB B:TYR670 4.9 55.5 1.0
CA B:ASP673 4.9 71.3 1.0
CA B:SER677 4.9 51.0 1.0
N B:SER677 5.0 53.1 1.0

Sodium binding site 4 out of 4 in 4zg9

Go back to Sodium Binding Sites List in 4zg9
Sodium binding site 4 out of 4 in the Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na908

b:56.9
occ:1.00
 O B:HOH1008 2.2 51.4 1.0
OG B:SER808 2.3 59.1 1.0
O B:SER805 2.4 55.0 1.0
O B:ASN802 2.7 52.0 1.0
CB B:SER808 3.4 60.5 1.0
C B:SER805 3.6 56.1 1.0
C B:ASN802 3.7 55.6 1.0
N B:SER808 4.1 60.6 1.0
O B:CYS806 4.1 48.5 1.0
CA B:GLU803 4.2 55.7 1.0
CA B:SER808 4.3 60.2 1.0
C B:CYS806 4.3 57.6 1.0
CA B:CYS806 4.3 65.8 1.0
N B:GLU803 4.3 53.9 1.0
N B:CYS806 4.4 61.0 1.0
CB B:ASN802 4.4 48.3 1.0
C B:GLU803 4.6 53.3 1.0
O B:GLU803 4.6 50.4 1.0
N B:SER805 4.6 52.8 1.0
CA B:ASN802 4.6 53.0 1.0
CA B:SER805 4.7 54.5 1.0
OE2 B:GLU803 4.8 83.3 1.0
N B:SER809 4.9 63.3 1.0
C B:SER808 4.9 59.1 1.0
N B:ASN807 5.0 54.4 1.0

Reference:

A.J.Stein, G.Bain, P.Prodanovich, A.M.Santini, J.Darlington, N.M.Stelzer, R.S.Sidhu, J.Schaub, L.Goulet, D.Lonergan, I.Calderon, J.F.Evans, J.H.Hutchinson. Structural Basis For Inhibition of Human Autotaxin By Four Potent Compounds with Distinct Modes of Binding. Mol.Pharmacol. V. 88 982 2015.
ISSN: ESSN 1521-0111
PubMed: 26371182
DOI: 10.1124/MOL.115.100404
Page generated: Mon Oct 7 19:40:40 2024

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