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Arsenic in PDB 5jh9: Crystal Structure of PRAPE1

Enzymatic activity of Crystal Structure of PRAPE1

All present enzymatic activity of Crystal Structure of PRAPE1:
3.4.11.22;

Protein crystallography data

The structure of Crystal Structure of PRAPE1, PDB code: 5jh9 was solved by N.N.Noda, W.Adachi, F.Inagaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.79 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 140.428, 140.428, 348.922, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 20.7

Other elements in 5jh9:

The structure of Crystal Structure of PRAPE1 also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of PRAPE1 (pdb code 5jh9). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 8 binding sites of Arsenic where determined in the Crystal Structure of PRAPE1, PDB code: 5jh9:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Arsenic binding site 1 out of 8 in 5jh9

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Arsenic binding site 1 out of 8 in the Crystal Structure of PRAPE1


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of PRAPE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As603

b:31.7
occ:1.00
 AS A:CAC603 0.0 31.7 1.0
O1 A:CAC603 1.7 30.6 1.0
O2 A:CAC603 1.7 30.1 1.0
C2 A:CAC603 2.0 31.1 1.0
C1 A:CAC603 2.0 30.5 1.0
ZN A:ZN602 2.9 32.8 1.0
OE2 A:GLU339 3.3 29.8 1.0
ZN A:ZN601 3.3 57.6 1.0
OE1 A:GLU340 3.5 29.6 1.0
OE1 A:GLU339 3.6 29.6 1.0
O A:HOH765 3.6 20.4 1.0
CD A:GLU339 3.9 29.4 1.0
NE2 B:HIS210 4.0 30.4 1.0
OD2 A:ASP385 4.0 28.7 1.0
O A:GLY454 4.0 41.5 1.0
OD2 A:ASP303 4.1 27.7 1.0
CD A:GLU340 4.2 29.9 1.0
OE2 A:GLU340 4.4 30.2 1.0
O A:HOH861 4.4 37.6 1.0
NE2 A:HIS479 4.5 27.8 1.0
OD1 A:ASP303 4.7 28.4 1.0
CD2 B:HIS210 4.7 29.9 1.0
CG A:ASP303 4.8 28.2 1.0
NE2 A:HIS132 4.9 26.9 1.0
O A:HOH740 4.9 29.6 1.0
CE1 B:HIS210 5.0 29.9 1.0

Arsenic binding site 2 out of 8 in 5jh9

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Arsenic binding site 2 out of 8 in the Crystal Structure of PRAPE1


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of PRAPE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As604

b:86.6
occ:1.00
 AS A:CAC604 0.0 86.6 1.0
O2 A:CAC604 1.7 79.5 1.0
O1 A:CAC604 1.7 76.8 1.0
C1 A:CAC604 2.0 82.7 1.0
C2 A:CAC604 2.0 81.6 1.0
OE1 A:GLN224 3.8 31.6 1.0
NE2 A:GLN224 3.9 31.8 1.0
O A:GLU216 4.0 33.3 1.0
O A:PRO214 4.2 30.4 1.0
O A:PRO218 4.2 32.9 1.0
CD A:GLN224 4.3 31.5 1.0
O B:HOH747 4.3 36.6 1.0
CD1 A:PHE219 4.7 29.0 1.0
C A:PRO214 4.9 30.6 1.0
CA A:PRO214 5.0 31.4 1.0

Arsenic binding site 3 out of 8 in 5jh9

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Arsenic binding site 3 out of 8 in the Crystal Structure of PRAPE1


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of PRAPE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As603

b:30.7
occ:1.00
 AS B:CAC603 0.0 30.7 1.0
O1 B:CAC603 1.7 28.1 1.0
O2 B:CAC603 1.7 29.1 1.0
C2 B:CAC603 2.0 29.3 1.0
C1 B:CAC603 2.0 29.6 1.0
ZN B:ZN602 2.8 32.9 1.0
ZN B:ZN601 3.1 61.4 1.0
OE2 B:GLU339 3.3 26.2 1.0
O B:HOH852 3.4 24.6 1.0
OE1 B:GLU339 3.6 26.6 1.0
OE1 B:GLU340 3.6 27.6 1.0
CD B:GLU339 3.9 26.4 1.0
NE2 A:HIS210 4.0 28.0 1.0
OD2 B:ASP385 4.1 29.0 1.0
O B:GLY454 4.1 33.2 1.0
OE2 B:GLU340 4.1 27.5 1.0
OD2 B:ASP303 4.2 27.2 1.0
CD B:GLU340 4.2 27.6 1.0
O B:HOH864 4.3 34.8 1.0
NE2 B:HIS479 4.5 27.3 1.0
OD1 B:ASP303 4.6 27.7 1.0
CD2 A:HIS210 4.8 28.0 1.0
CG B:ASP303 4.8 27.6 1.0
NE2 B:HIS132 4.9 31.1 1.0

Arsenic binding site 4 out of 8 in 5jh9

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Arsenic binding site 4 out of 8 in the Crystal Structure of PRAPE1


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of PRAPE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As604

b:89.1
occ:1.00
 AS B:CAC604 0.0 89.1 1.0
O1 B:CAC604 1.7 84.9 1.0
O2 B:CAC604 1.7 80.2 1.0
C2 B:CAC604 2.0 85.9 1.0
C1 B:CAC604 2.0 85.7 1.0
OE1 B:GLN224 3.9 29.8 1.0
NE2 B:GLN224 3.9 29.5 1.0
O B:PRO214 3.9 30.9 1.0
O B:GLU216 4.0 34.6 1.0
O B:HOH843 4.1 45.6 1.0
O A:HOH741 4.2 41.3 1.0
CD B:GLN224 4.3 29.4 1.0
O B:PRO218 4.4 33.6 1.0
CA B:PRO214 4.6 31.6 1.0
C B:PRO214 4.6 31.3 1.0
CD1 B:PHE219 4.6 29.7 1.0
O B:LYS213 4.8 32.9 1.0
CE1 B:PHE219 4.9 29.7 1.0

Arsenic binding site 5 out of 8 in 5jh9

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Arsenic binding site 5 out of 8 in the Crystal Structure of PRAPE1


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Crystal Structure of PRAPE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As603

b:27.2
occ:1.00
 AS C:CAC603 0.0 27.2 1.0
O2 C:CAC603 1.7 24.6 1.0
O1 C:CAC603 1.7 26.2 1.0
C2 C:CAC603 2.0 26.8 1.0
C1 C:CAC603 2.0 26.4 1.0
ZN C:ZN602 2.9 29.8 1.0
ZN C:ZN601 3.4 56.0 1.0
O C:HOH861 3.4 22.2 1.0
OE2 C:GLU339 3.6 24.6 1.0
OE1 C:GLU340 3.6 24.8 1.0
OE1 C:GLU339 3.7 24.3 1.0
NE2 D:HIS210 4.0 27.6 1.0
CD C:GLU339 4.0 24.3 1.0
O C:GLY454 4.1 31.6 1.0
OD2 C:ASP303 4.2 24.4 1.0
OD2 C:ASP385 4.2 24.1 1.0
OE2 C:GLU340 4.2 25.3 1.0
CD C:GLU340 4.2 25.0 1.0
NE2 C:HIS479 4.4 24.1 1.0
OD1 C:ASP303 4.7 24.6 1.0
CD2 D:HIS210 4.7 27.5 1.0
NE2 C:HIS132 4.9 24.6 1.0
CG C:ASP303 4.9 24.5 1.0
CE1 C:HIS479 4.9 24.4 1.0
CE1 D:HIS210 5.0 27.0 1.0

Arsenic binding site 6 out of 8 in 5jh9

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Arsenic binding site 6 out of 8 in the Crystal Structure of PRAPE1


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Crystal Structure of PRAPE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As604

b:86.3
occ:1.00
 AS C:CAC604 0.0 86.3 1.0
O2 C:CAC604 1.7 80.2 1.0
O1 C:CAC604 1.7 77.3 1.0
C2 C:CAC604 2.0 83.2 1.0
C1 C:CAC604 2.0 81.4 1.0
O C:GLU216 3.9 33.3 1.0
O C:PRO214 3.9 30.3 1.0
NE2 C:GLN224 4.1 27.1 1.0
O D:HOH766 4.2 37.3 1.0
OE1 C:GLN224 4.2 27.1 1.0
O C:PRO218 4.4 31.4 1.0
CA C:PRO214 4.6 30.7 1.0
C C:PRO214 4.6 30.3 1.0
CD C:GLN224 4.6 27.0 1.0
O C:LYS213 4.6 31.1 1.0
CD1 C:PHE219 4.8 28.9 1.0
CE1 C:PHE219 5.0 29.0 1.0

Arsenic binding site 7 out of 8 in 5jh9

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Arsenic binding site 7 out of 8 in the Crystal Structure of PRAPE1


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Crystal Structure of PRAPE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As603

b:31.2
occ:1.00
 AS D:CAC603 0.0 31.2 1.0
O1 D:CAC603 1.7 29.3 1.0
O2 D:CAC603 1.7 29.3 1.0
C1 D:CAC603 2.0 29.8 1.0
C2 D:CAC603 2.0 30.2 1.0
ZN D:ZN602 3.0 33.9 1.0
ZN D:ZN601 3.2 54.8 1.0
OE2 D:GLU339 3.3 26.7 1.0
OE1 D:GLU339 3.5 26.5 1.0
O D:HOH829 3.5 23.9 1.0
OE1 D:GLU340 3.6 27.4 1.0
CD D:GLU339 3.8 26.4 1.0
OD2 D:ASP385 4.0 30.6 1.0
NE2 C:HIS210 4.0 28.9 1.0
O D:GLY454 4.1 36.5 1.0
OD2 D:ASP303 4.2 26.7 1.0
CD D:GLU340 4.3 27.7 1.0
OE2 D:GLU340 4.4 28.1 1.0
NE2 D:HIS479 4.5 26.9 1.0
O D:HOH891 4.5 36.1 1.0
OD1 D:ASP303 4.6 26.8 1.0
CD2 C:HIS210 4.8 28.6 1.0
CG D:ASP303 4.9 26.9 1.0
NE2 D:HIS132 4.9 28.8 1.0

Arsenic binding site 8 out of 8 in 5jh9

Go back to Arsenic Binding Sites List in 5jh9
Arsenic binding site 8 out of 8 in the Crystal Structure of PRAPE1


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of Crystal Structure of PRAPE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As604

b:86.2
occ:1.00
 AS D:CAC604 0.0 86.2 1.0
O1 D:CAC604 1.7 79.4 1.0
O2 D:CAC604 1.7 76.0 1.0
C2 D:CAC604 2.0 82.8 1.0
C1 D:CAC604 2.0 82.0 1.0
NE2 D:GLN224 3.8 26.9 1.0
OE1 D:GLN224 3.9 27.5 1.0
O D:GLU216 3.9 32.1 1.0
O D:PRO214 4.0 29.2 1.0
O D:PRO218 4.2 31.0 1.0
CD D:GLN224 4.3 26.9 1.0
O C:HOH804 4.4 36.1 1.0
CD1 D:PHE219 4.6 28.8 1.0
C D:PRO214 4.7 29.2 1.0
CA D:PRO214 4.8 29.2 1.0
CE1 D:PHE219 4.8 28.8 1.0
O D:LYS213 4.9 30.3 1.0

Reference:

A.Yamasaki, Y.Watanabe, W.Adachi, K.Suzuki, K.Matoba, H.Kirisako, H.Kumeta, H.Nakatogawa, Y.Ohsumi, F.Inagaki, N.N.Noda. Structural Basis For Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates Cell Rep V. 16 19 2016.
ISSN: ESSN 2211-1247
PubMed: 27320913
DOI: 10.1016/J.CELREP.2016.05.066
Page generated: Wed Jul 10 12:52:06 2024

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