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Zinc in PDB 4zg6: 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: 4zg6 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) 34.69 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.616, 70.488, 107.374, 104.65, 99.27, 99.86
R / Rfree (%) 22 / 26.5

Other elements in 4zg6:

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

Fluorine (F) 2 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds (pdb code 4zg6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Basis For Inhibition of Human Autotaxin By Four Novel Compounds, PDB code: 4zg6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4zg6

Go back to Zinc Binding Sites List in 4zg6
Zinc 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 Zinc with other atoms in the Zn 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:Zn904

b:39.3
occ:1.00
 OG1 A:THR210 1.7 27.8 1.0
OD1 A:ASP172 2.0 33.2 1.0
NE2 A:HIS360 2.1 27.1 1.0
OD2 A:ASP359 2.2 27.8 1.0
CG A:ASP172 2.6 32.3 1.0
OD2 A:ASP172 2.8 34.6 1.0
CB A:THR210 2.9 27.8 1.0
CG A:ASP359 2.9 27.3 1.0
CD2 A:HIS360 2.9 24.1 1.0
CE1 A:HIS360 3.0 26.9 1.0
OD1 A:ASP359 3.0 29.7 1.0
CA A:THR210 3.3 27.0 1.0
CG2 A:THR210 3.5 30.0 1.0
N A:THR210 3.8 26.5 1.0
CB A:ASP172 4.0 31.6 1.0
CG A:HIS360 4.0 27.6 1.0
ND1 A:HIS360 4.0 27.8 1.0
N A:GLY173 4.0 27.9 1.0
C1 A:GOL909 4.1 35.9 1.0
OD1 A:ASP312 4.2 31.4 1.0
CA A:ASP172 4.3 28.2 1.0
CB A:ASP359 4.3 27.4 1.0
CG A:ASP312 4.5 32.5 1.0
C A:ASP172 4.5 31.6 1.0
CE1 A:HIS475 4.5 29.8 1.0
C A:LYS209 4.6 27.7 1.0
C A:THR210 4.6 23.5 1.0
ZN A:ZN905 4.7 34.1 1.0
O1 A:GOL909 4.7 38.1 1.0
NE2 A:HIS475 4.7 30.4 1.0
O3 A:GOL909 4.8 29.7 1.0
CA A:GLY173 4.8 29.3 1.0
OD2 A:ASP312 4.8 34.6 1.0
CB A:ASP312 4.9 33.6 1.0

Zinc binding site 2 out of 4 in 4zg6

Go back to Zinc Binding Sites List in 4zg6
Zinc 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 Zinc with other atoms in the Zn 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:Zn905

b:34.1
occ:1.00
 O A:HOH1001 1.5 33.3 1.0
O3 A:GOL909 1.6 29.7 1.0
OD1 A:ASP312 2.1 31.4 1.0
NE2 A:HIS316 2.1 47.3 1.0
NE2 A:HIS475 2.2 30.4 1.0
OD2 A:ASP312 2.5 34.6 1.0
CG A:ASP312 2.6 32.5 1.0
C3 A:GOL909 3.0 35.4 1.0
CE1 A:HIS316 3.1 48.7 1.0
CD2 A:HIS316 3.1 48.5 1.0
CE1 A:HIS475 3.2 29.8 1.0
CD2 A:HIS475 3.2 28.9 1.0
O2 A:GOL909 3.4 36.2 1.0
C1 A:GOL909 3.6 35.9 1.0
C2 A:GOL909 3.6 34.3 1.0
CB A:ASP312 4.1 33.6 1.0
CE1 A:HIS360 4.1 26.9 1.0
ND1 A:HIS316 4.2 50.2 1.0
CG A:HIS316 4.2 49.9 1.0
ND1 A:HIS475 4.3 27.4 1.0
CG A:HIS475 4.4 28.4 1.0
NE2 A:HIS360 4.4 27.1 1.0
CE A:MET362 4.5 34.1 1.0
OD1 A:ASP172 4.6 33.2 1.0
OG1 A:THR210 4.7 27.8 1.0
O A:HOH1022 4.7 42.4 1.0
ZN A:ZN904 4.7 39.3 1.0
O1 A:GOL909 4.9 38.1 1.0
CA A:ASP312 4.9 37.1 1.0

Zinc binding site 3 out of 4 in 4zg6

Go back to Zinc Binding Sites List in 4zg6
Zinc 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 Zinc with other atoms in the Zn 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:Zn904

b:40.5
occ:1.00
 OG1 B:THR210 1.8 28.1 1.0
OD1 B:ASP172 1.9 34.4 1.0
OD2 B:ASP359 2.1 25.4 1.0
NE2 B:HIS360 2.2 27.0 1.0
CG B:ASP172 2.6 32.8 1.0
OD2 B:ASP172 2.8 38.4 1.0
CB B:THR210 2.9 28.3 1.0
CG B:ASP359 2.9 27.1 1.0
CD2 B:HIS360 3.0 26.0 1.0
OD1 B:ASP359 3.1 24.5 1.0
CE1 B:HIS360 3.1 26.1 1.0
CA B:THR210 3.3 26.2 1.0
CG2 B:THR210 3.5 29.2 1.0
N B:THR210 3.8 25.8 1.0
CB B:ASP172 3.9 33.3 1.0
C1 B:GOL909 4.1 39.1 1.0
N B:GLY173 4.1 31.0 1.0
CG B:HIS360 4.1 25.7 1.0
O B:HOH1266 4.1 39.9 1.0
ND1 B:HIS360 4.1 25.8 1.0
CA B:ASP172 4.2 31.4 1.0
CB B:ASP359 4.3 24.5 1.0
OD1 B:ASP312 4.4 35.8 1.0
CE1 B:HIS475 4.5 29.7 1.0
C B:ASP172 4.5 34.3 1.0
CG B:ASP312 4.5 32.2 1.0
C B:LYS209 4.6 27.4 1.0
NE2 B:HIS475 4.6 28.2 1.0
C B:THR210 4.7 24.9 1.0
ZN B:ZN905 4.7 31.4 1.0
C3 B:GOL909 4.7 38.3 1.0
OD2 B:ASP312 4.8 35.8 1.0
O1 B:GOL909 4.8 48.0 1.0
CA B:GLY173 4.9 28.5 1.0
CB B:ASP312 4.9 32.6 1.0

Zinc binding site 4 out of 4 in 4zg6

Go back to Zinc Binding Sites List in 4zg6
Zinc 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 Zinc with other atoms in the Zn 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:Zn905

b:31.4
occ:1.00
 O3 B:GOL909 1.5 29.6 1.0
NE2 B:HIS475 2.1 28.2 1.0
NE2 B:HIS316 2.2 37.0 1.0
OD1 B:ASP312 2.2 35.8 1.0
OD2 B:ASP312 2.3 35.8 1.0
CG B:ASP312 2.6 32.2 1.0
C3 B:GOL909 2.6 38.3 1.0
CD2 B:HIS475 3.0 27.4 1.0
CE1 B:HIS316 3.1 38.5 1.0
CD2 B:HIS316 3.1 38.0 1.0
CE1 B:HIS475 3.2 29.7 1.0
C2 B:GOL909 3.7 35.9 1.0
O2 B:GOL909 3.9 39.3 1.0
C1 B:GOL909 3.9 39.1 1.0
CB B:ASP312 4.1 32.6 1.0
CE1 B:HIS360 4.1 26.1 1.0
CG B:HIS475 4.2 27.4 1.0
ND1 B:HIS316 4.2 38.6 1.0
ND1 B:HIS475 4.2 28.4 1.0
CG B:HIS316 4.2 39.6 1.0
CE B:MET362 4.4 29.2 1.0
NE2 B:HIS360 4.4 27.0 1.0
O B:HOH1266 4.5 39.9 1.0
OD1 B:ASP172 4.6 34.4 1.0
ZN B:ZN904 4.7 40.5 1.0
OG1 B:THR210 4.7 28.1 1.0
O B:ASP312 4.8 32.0 1.0
O1 B:GOL909 4.9 48.0 1.0
CA B:ASP312 4.9 32.9 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: Sun Oct 27 11:44:35 2024

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