Chlorine in PDB 6dy1: Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100

Enzymatic activity of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100

All present enzymatic activity of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100:
3.5.1.60;

Protein crystallography data

The structure of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100, PDB code: 6dy1 was solved by A.Gorelik, A.Gebai, K.Illes, D.Piomelli, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 3.00
Space group P 43 3 2
Cell size a, b, c (Å), α, β, γ (°) 159.351, 159.351, 159.351, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.3

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 (pdb code 6dy1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100, PDB code: 6dy1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 6dy1

Go back to Chlorine Binding Sites List in 6dy1
Chlorine binding site 1 out of 12 in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:64.4
occ:1.00
 HH21 A:ARG55 3.2 71.6 1.0
HE1 A:HIS56 3.9 62.3 1.0
NH2 A:ARG55 3.9 59.6 1.0
HH22 A:ARG55 4.0 71.6 1.0
CE1 A:HIS56 4.3 51.9 1.0
ND1 A:HIS56 4.5 27.7 1.0
HE A:ARG55 4.8 53.1 1.0

Chlorine binding site 2 out of 12 in 6dy1

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Chlorine binding site 2 out of 12 in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:64.0
occ:1.00
 HG1 B:THR288 2.0 41.9 1.0
H B:THR288 2.5 39.4 1.0
OG1 B:THR288 2.7 34.9 1.0
HE B:ARG303 2.8 63.2 1.0
HH21 B:ARG303 3.2 53.7 1.0
H B:TYR290 3.2 62.0 1.0
O B:TYR290 3.2 49.3 1.0
N B:THR288 3.3 32.9 1.0
OE2 B:GLU287 3.4 28.4 1.0
HA B:GLU287 3.4 45.8 1.0
NE B:ARG303 3.4 52.7 1.0
HB2 B:TYR290 3.6 66.8 1.0
HG23 B:THR288 3.7 40.2 1.0
HG3 B:ARG303 3.8 65.5 1.0
NH2 B:ARG303 3.8 44.7 1.0
HB2 B:ARG303 3.8 60.1 1.0
CB B:THR288 3.8 32.6 1.0
H B:ASN289 3.9 44.8 1.0
N B:TYR290 4.0 51.7 1.0
CZ B:ARG303 4.0 49.6 1.0
HD2 B:TYR290 4.0 61.7 1.0
CA B:THR288 4.0 37.0 1.0
C B:TYR290 4.1 56.2 1.0
HA B:HIS292 4.1 51.9 1.0
CD B:GLU287 4.1 20.2 1.0
CG2 B:THR288 4.2 33.5 1.0
C B:GLU287 4.2 40.4 1.0
CA B:GLU287 4.2 38.2 1.0
N B:ASN289 4.3 37.4 1.0
O B:VAL286 4.3 27.3 1.0
CA B:TYR290 4.4 52.9 1.0
CB B:TYR290 4.4 55.6 1.0
CG B:ARG303 4.4 54.5 1.0
CD B:ARG303 4.4 53.3 1.0
HG21 B:THR288 4.5 40.2 1.0
C B:THR288 4.5 33.9 1.0
HH22 B:ARG303 4.5 53.7 1.0
CB B:ARG303 4.5 50.1 1.0
OE1 B:GLU287 4.6 26.4 1.0
HB B:THR288 4.6 39.1 1.0
HD3 B:ARG303 4.6 63.9 1.0
HB3 B:HIS292 4.8 55.8 1.0
CD2 B:TYR290 4.8 51.4 1.0
HG12 B:VAL286 4.9 46.2 1.0
O B:ASP291 4.9 54.8 1.0
HA B:THR288 4.9 44.4 1.0
CA B:HIS292 4.9 43.3 1.0
C B:ASP291 5.0 38.5 1.0

Chlorine binding site 3 out of 12 in 6dy1

Go back to Chlorine Binding Sites List in 6dy1
Chlorine binding site 3 out of 12 in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:69.7
occ:1.00
 HB1 B:ALA234 2.7 45.2 1.0
O B:HOH544 3.0 27.6 1.0
HE B:ARG238 3.1 42.6 1.0
H B:GLU230 3.3 39.9 1.0
HH21 B:ARG238 3.3 60.8 1.0
HA B:ALA229 3.4 26.2 1.0
CB B:ALA234 3.4 37.6 1.0
HB2 B:ALA234 3.5 45.2 1.0
HB3 B:ALA234 3.6 45.2 1.0
NE B:ARG238 3.9 35.5 1.0
HB2 B:GLU230 3.9 47.9 1.0
NH2 B:ARG238 4.1 50.7 1.0
N B:GLU230 4.1 33.2 1.0
HG2 B:GLU230 4.3 89.8 1.0
O B:GLU228 4.3 44.4 1.0
CA B:ALA229 4.4 21.9 1.0
CZ B:ARG238 4.5 43.4 1.0
HG3 B:GLU230 4.6 89.8 1.0
CB B:GLU230 4.7 39.9 1.0
HD2 B:ARG238 4.7 39.5 1.0
CG B:GLU230 4.7 74.8 1.0
C B:ALA229 4.8 27.5 1.0
CA B:ALA234 4.8 18.0 1.0
HH22 B:ARG238 4.8 60.8 1.0
CD B:ARG238 4.9 32.9 1.0
HA B:ALA234 4.9 21.6 1.0
HB1 B:ALA229 5.0 24.4 1.0

Chlorine binding site 4 out of 12 in 6dy1

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Chlorine binding site 4 out of 12 in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl408

b:77.7
occ:1.00
 HH21 B:ARG354 2.6 0.2 1.0
HE B:ARG354 3.0 0.8 1.0
NH2 B:ARG354 3.3 0.5 1.0
NE B:ARG354 3.6 93.2 1.0
HH22 B:ARG354 3.8 0.2 1.0
CZ B:ARG354 3.9 0.1 1.0
HG2 B:ARG354 4.5 65.3 1.0
CD B:ARG354 4.9 69.2 1.0

Chlorine binding site 5 out of 12 in 6dy1

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Chlorine binding site 5 out of 12 in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl409

b:62.2
occ:1.00
 HD21 B:ASN334 2.9 67.2 1.0
HD22 B:ASN334 3.3 67.2 1.0
O B:HOH551 3.4 39.0 1.0
ND2 B:ASN334 3.5 56.0 1.0
HE B:ARG302 3.8 60.5 1.0
HH21 B:ARG302 3.9 58.0 1.0
HB3 B:ASP147 3.9 68.9 1.0
HB2 B:TYR336 4.1 57.6 1.0
NH2 B:ARG302 4.1 48.3 1.0
NE B:ARG302 4.1 50.4 1.0
HB2 B:ASP147 4.2 68.9 1.0
CZ B:ARG302 4.3 50.1 1.0
OD2 B:ASP147 4.4 43.5 1.0
CB B:ASP147 4.4 57.4 1.0
O B:HOH547 4.5 41.4 1.0
HH22 B:ARG302 4.6 58.0 1.0
HD3 B:ARG302 4.6 75.5 1.0
OD2 B:ASP300 4.7 58.1 1.0
CG B:ASN334 4.8 55.4 1.0
CB B:TYR336 4.8 48.0 1.0
CG B:TYR336 4.8 56.1 1.0
HB3 B:TYR336 4.9 57.6 1.0
OD1 B:ASP300 4.9 87.0 1.0
CG B:ASP147 4.9 42.5 1.0
CD B:ARG302 5.0 62.9 1.0

Chlorine binding site 6 out of 12 in 6dy1

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Chlorine binding site 6 out of 12 in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl410

b:54.9
occ:1.00
 O B:HOH501 3.5 39.3 1.0
HH11 B:ARG200 3.7 0.7 1.0
HB2 B:ARG200 3.8 70.3 1.0
HA B:TYR290 3.8 63.5 1.0
HG3 B:ARG198 3.9 37.5 1.0
O B:ASP199 4.0 34.6 1.0
H B:ASP291 4.0 62.6 1.0
HD2 B:ARG200 4.1 94.5 1.0
OD1 B:ASP291 4.1 36.1 1.0
HD1 B:TYR290 4.1 89.5 1.0
OH B:TYR249 4.2 39.8 1.0
HH B:TYR249 4.3 47.7 1.0
OD2 B:ASP291 4.4 43.2 1.0
HE B:ARG198 4.4 30.6 1.0
CG B:ASP291 4.4 36.6 1.0
NH1 B:ARG200 4.4 0.5 1.0
HG2 B:ARG198 4.5 37.5 1.0
HH12 B:ARG200 4.6 0.7 1.0
O B:ASN289 4.7 40.7 1.0
CG B:ARG198 4.7 31.3 1.0
N B:ASP291 4.7 52.2 1.0
CB B:ARG200 4.7 58.5 1.0
CA B:TYR290 4.8 52.9 1.0
HG3 B:ARG200 4.8 89.9 1.0
NE B:ARG198 4.9 25.5 1.0
C B:ASP199 4.9 31.3 1.0
HB3 B:TYR290 4.9 66.8 1.0
H B:ASP199 4.9 38.1 1.0
CD1 B:TYR290 4.9 74.6 1.0
CD B:ARG200 5.0 78.7 1.0
HH21 B:ARG198 5.0 36.6 1.0

Chlorine binding site 7 out of 12 in 6dy1

Go back to Chlorine Binding Sites List in 6dy1
Chlorine binding site 7 out of 12 in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl411

b:73.0
occ:1.00
 HA2 B:GLY201 3.3 64.0 1.0
HG2 B:ARG200 3.7 89.9 1.0
HE B:ARG200 3.9 0.4 1.0
O B:HOH552 3.9 55.4 1.0
O4 B:SO4404 3.9 89.3 1.0
CA B:GLY201 4.2 53.4 1.0
HA3 B:GLY201 4.4 64.0 1.0
OE1 B:GLU205 4.5 68.1 1.0
NE B:ARG200 4.5 97.0 1.0
N B:GLY201 4.5 49.6 1.0
H B:GLY201 4.5 59.6 1.0
CG B:ARG200 4.6 75.0 1.0
HD3 B:ARG200 4.9 94.5 1.0
HG3 B:ARG200 4.9 89.9 1.0
HH21 B:ARG200 4.9 0.6 1.0
CD B:ARG200 4.9 78.7 1.0
OE2 B:GLU205 5.0 74.3 1.0

Chlorine binding site 8 out of 12 in 6dy1

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Chlorine binding site 8 out of 12 in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl412

b:49.0
occ:1.00
 O B:HOH545 2.9 25.2 1.0
HA3 B:GLY269 3.4 24.2 1.0
O B:HOH532 3.5 29.6 1.0
HD2 B:PRO270 3.7 13.0 1.0
CA B:GLY269 4.3 20.2 1.0
HB3 B:ASP268 4.5 65.9 1.0
N B:GLY269 4.6 20.1 1.0
CD B:PRO270 4.6 10.8 1.0
O B:ASP268 4.8 23.3 1.0
C B:ASP268 4.8 23.3 1.0
HB2 B:ASP268 4.8 65.9 1.0
HA2 B:GLY269 4.9 24.2 1.0
H B:GLY269 4.9 24.2 1.0
C B:GLY269 5.0 14.7 1.0

Chlorine binding site 9 out of 12 in 6dy1

Go back to Chlorine Binding Sites List in 6dy1
Chlorine binding site 9 out of 12 in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl413

b:67.7
occ:1.00
 HE B:ARG223 2.9 13.7 1.0
O A:HOH325 3.0 36.1 1.0
HH21 B:ARG223 3.4 30.0 1.0
NE B:ARG223 3.5 11.4 1.0
HG2 B:ARG223 3.5 18.5 1.0
HG B:SER227 3.8 40.3 1.0
NH2 B:ARG223 3.9 25.0 1.0
CZ B:ARG223 3.9 18.4 1.0
HA B:THR224 4.0 20.1 1.0
HD13 A:LEU42 4.0 24.5 1.0
HB2 B:SER227 4.1 37.0 1.0
HB3 B:SER227 4.2 37.0 1.0
HH2 B:TRP220 4.2 32.2 1.0
HZ B:PHE171 4.3 15.6 1.0
CD B:ARG223 4.3 16.2 1.0
CG B:ARG223 4.3 15.4 1.0
HD3 B:ARG223 4.3 19.4 1.0
CH2 B:TRP220 4.4 26.9 1.0
CB B:SER227 4.4 30.8 1.0
OG B:SER227 4.5 33.6 1.0
HH22 B:ARG223 4.5 30.0 1.0
HZ2 B:TRP220 4.5 24.6 1.0
HD22 A:LEU42 4.5 24.6 1.0
CZ2 B:TRP220 4.6 20.5 1.0
HD11 A:LEU42 4.7 24.5 1.0
CD1 A:LEU42 4.8 20.4 1.0
HG3 B:ARG223 4.8 18.5 1.0
CA B:THR224 4.9 16.8 1.0
O B:ARG223 4.9 14.2 1.0

Chlorine binding site 10 out of 12 in 6dy1

Go back to Chlorine Binding Sites List in 6dy1
Chlorine binding site 10 out of 12 in the Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Rabbit N-Acylethanolamine-Hydrolyzing Acid Amidase (Naaa) with Fatty Acid (Myristate), in Presence of Triton X-100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl414

b:80.1
occ:1.00
 HB B:THR255 3.2 41.1 1.0
HG21 B:THR255 3.3 69.5 1.0
HB3 B:HIS189 3.4 58.8 1.0
HA B:HIS189 3.5 39.8 1.0
HA B:ALA346 3.7 55.6 1.0
CG2 B:THR255 3.9 58.0 1.0
CB B:THR255 3.9 34.3 1.0
HG22 B:THR255 3.9 69.5 1.0
ND1 B:HIS189 4.0 43.5 1.0
CB B:HIS189 4.0 49.0 1.0
CG B:HIS189 4.1 38.6 1.0
CA B:HIS189 4.2 33.2 1.0
OG1 B:THR255 4.3 25.0 1.0
HB1 B:ALA346 4.4 71.2 1.0
CA B:ALA346 4.6 46.3 1.0
O B:HIS189 4.6 25.5 1.0
C B:HIS189 4.6 29.7 1.0
HB2 B:ALA346 4.6 71.2 1.0
HG1 B:THR255 4.6 30.0 1.0
HG23 B:THR255 4.7 69.5 1.0
CB B:ALA346 4.8 59.4 1.0
CE1 B:HIS189 4.8 52.1 1.0
O B:ALA346 4.9 48.8 1.0
HB2 B:HIS189 4.9 58.8 1.0
CD2 B:HIS189 5.0 42.2 1.0

Reference:

A.Gorelik, A.Gebai, K.Illes, D.Piomelli, B.Nagar. Molecular Mechanism of Activation of the Immunoregulatory Amidase Naaa. Proc. Natl. Acad. Sci. V. 115 10032 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30301806
DOI: 10.1073/PNAS.1811759115
Page generated: Sat Jul 27 21:59:19 2024

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