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Sodium in PDB 6ze8: Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01

Enzymatic activity of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01

All present enzymatic activity of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01:
3.2.1.14;

Protein crystallography data

The structure of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01, PDB code: 6ze8 was solved by M.Nowotny, A.Bartlomiejczak, A.Napiorkowska-Gromadzka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.34 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.325, 93.744, 281.642, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 16.8

Other elements in 6ze8:

The structure of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 (pdb code 6ze8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01, PDB code: 6ze8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ze8

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Sodium binding site 1 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:47.5
occ:1.00
 O A:HOH761 2.2 50.8 1.0
O A:HOH651 2.7 20.6 1.0
N A:GLY187 3.3 29.7 1.0
O A:HOH570 3.3 38.0 1.0
CD2 A:TYR190 3.6 38.1 1.0
N A:ALA186 3.7 20.5 1.0
CB A:PRO185 3.8 18.4 1.0
CA A:GLY187 3.8 30.4 1.0
CE2 A:TYR190 3.9 41.9 1.0
C A:ALA186 4.3 31.0 1.0
CA A:PRO185 4.3 18.3 1.0
CA A:ALA186 4.4 24.1 1.0
C A:PRO185 4.4 20.3 1.0
OH A:TYR141 4.6 28.5 1.0
O A:HOH518 4.7 51.7 1.0
CB A:ALA186 4.7 25.8 1.0
CG A:TYR190 4.8 33.7 1.0
O A:HOH513 4.9 49.6 1.0

Sodium binding site 2 out of 6 in 6ze8

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Sodium binding site 2 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:55.4
occ:1.00
 O B:HOH873 2.1 46.1 1.0
O B:HOH871 2.3 47.7 1.0
ND2 B:ASN100 3.3 15.8 0.5
O B:HOH765 3.6 46.7 1.0
CZ2 B:TRP99 4.0 19.0 1.0
O B:HOH878 4.2 48.7 1.0
CH2 B:TRP99 4.3 19.0 1.0
CG B:ASN100 4.3 17.5 0.5
O B:HOH534 4.3 30.7 1.0
CE2 B:TRP99 4.4 18.4 1.0
CB B:ASN100 4.5 21.4 1.0
O B:HOH764 4.6 44.4 1.0
CZ2 B:TRP31 4.7 15.8 1.0
CH2 B:TRP31 4.8 15.1 1.0
CE2 B:TRP31 4.8 15.6 1.0
NE1 B:TRP99 4.9 20.3 1.0
CZ3 B:TRP99 4.9 18.5 1.0

Sodium binding site 3 out of 6 in 6ze8

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Sodium binding site 3 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:43.2
occ:1.00
 N C:GLU153 3.0 18.4 1.0
CG C:GLU153 3.1 30.4 1.0
O C:ALA149 3.2 23.8 1.0
CB C:GLU153 3.4 23.5 1.0
CB C:LYS152 3.6 19.1 1.0
O C:VAL150 3.7 21.7 1.0
CA C:VAL150 3.7 24.2 1.0
CA C:GLU153 3.8 20.9 1.0
C C:VAL150 3.8 19.7 1.0
C C:LYS152 4.0 18.6 1.0
O C:HOH799 4.0 65.3 1.0
N C:LYS152 4.0 19.2 1.0
CA C:LYS152 4.0 18.8 1.0
C C:ALA149 4.1 24.0 1.0
CG C:LYS152 4.3 20.9 1.0
N C:VAL150 4.4 23.9 1.0
N C:ASP151 4.7 20.0 1.0
CD C:LYS152 4.8 22.5 1.0
CG2 C:VAL150 4.9 31.0 1.0
CB C:VAL150 4.9 27.2 1.0
C C:ASP151 4.9 20.0 1.0
C C:GLU153 5.0 19.5 1.0

Sodium binding site 4 out of 6 in 6ze8

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Sodium binding site 4 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:39.0
occ:1.00
 O D:HOH828 2.8 52.5 1.0
NZ D:LYS314 3.0 25.3 1.0
O D:HOH799 3.6 35.7 1.0
CE2 D:PHE334 3.6 15.7 1.0
CZ D:PHE334 3.7 16.3 1.0
CE D:LYS314 3.8 20.1 1.0
CD D:LYS314 4.1 22.4 1.0
OH D:TYR303 4.4 18.8 1.0
CB D:ASP336 4.5 15.3 1.0
O D:HOH607 4.6 20.0 1.0
CA D:CYS307 4.6 53.1 0.5
CE1 D:TYR303 4.7 16.5 1.0
O D:CYS307 4.9 90.3 0.5
CD2 D:PHE334 4.9 15.0 1.0
CB D:CYS307 4.9 32.3 0.5
OD2 D:ASP336 5.0 18.4 1.0
CZ D:TYR303 5.0 16.6 1.0

Sodium binding site 5 out of 6 in 6ze8

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Sodium binding site 5 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na402

b:48.3
occ:1.00
 O E:GLU74 2.9 17.2 1.0
CB E:GLN78 3.5 16.4 1.0
C E:GLU74 3.7 17.3 1.0
CD1 E:TYR130 4.0 13.2 1.0
CB E:GLU74 4.2 15.9 1.0
CE1 E:TYR130 4.2 15.2 1.0
CA E:GLU74 4.3 14.1 1.0
N E:GLN78 4.4 13.5 1.0
CG E:GLN78 4.4 40.3 1.0
CA E:GLN78 4.4 14.2 1.0
N E:THR75 4.6 13.5 1.0
O E:HOH703 4.7 44.6 1.0
CA E:THR75 4.9 15.3 1.0

Sodium binding site 6 out of 6 in 6ze8

Go back to Sodium Binding Sites List in 6ze8
Sodium binding site 6 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na402

b:42.4
occ:1.00
 O D:HOH863 2.4 43.0 1.0
O F:HOH845 2.9 64.6 1.0
O F:HOH858 3.1 44.9 1.0
O D:HOH917 3.5 32.0 1.0
CB F:LYS44 3.6 23.2 1.0
O D:HOH919 4.3 55.0 1.0
CD F:LYS44 4.3 34.1 1.0
OE1 D:GLN36 4.4 21.1 1.0
O F:HOH600 4.4 19.0 1.0
CB D:GLN36 4.5 17.5 1.0
CG F:LYS44 4.6 27.1 1.0
CA F:LYS44 4.6 16.9 1.0
O D:HOH572 4.9 47.8 1.0
CE1 D:PHE294 4.9 24.4 1.0

Reference:

R.Koralewski, B.Dymek, M.Mazur, P.Sklepkiewicz, S.Olejniczak, W.Czestkowski, K.Matyszewski, G.Andryianau, P.Niedziejko, M.Kowalski, M.Gruza, B.Borek, K.Jedrzejczak, A.Bartoszewicz, E.Pluta, A.Rymaszewska, M.Kania, T.Rejczak, S.Piasecka, M.Mlacki, M.Mazurkiewicz, M.Piotrowicz, M.Salamon, A.Zagozdzon, A.Napiorkowska-Gromadzka, A.Bartlomiejczak, W.Mozga, P.Dobrzanski, K.Dzwonek, J.Golab, M.Nowotny, J.Olczak, A.Golebiowski. Discovery of Oatd-01 , A First-in-Class Chitinase Inhibitor As Potential New Therapeutics For Idiopathic Pulmonary Fibrosis. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33078933
DOI: 10.1021/ACS.JMEDCHEM.0C01179
Page generated: Tue Oct 8 15:27:29 2024

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