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Arsenic in PDB 4l3t: Crystal Structure of Substrate-Free Human Presequence Protease

Protein crystallography data

The structure of Crystal Structure of Substrate-Free Human Presequence Protease, PDB code: 4l3t was solved by J.V.King, W.G.Liang, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.55 / 2.03
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 245.782, 85.093, 158.459, 90.00, 127.54, 90.00
R / Rfree (%) 17.1 / 21

Other elements in 4l3t:

The structure of Crystal Structure of Substrate-Free Human Presequence Protease also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Arsenic Binding Sites:

Pages:

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

Binding sites:

The binding sites of Arsenic atom in the Crystal Structure of Substrate-Free Human Presequence Protease (pdb code 4l3t). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 12 binding sites of Arsenic where determined in the Crystal Structure of Substrate-Free Human Presequence Protease, PDB code: 4l3t:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 12 in 4l3t

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Arsenic binding site 1 out of 12 in the Crystal Structure of Substrate-Free Human Presequence Protease


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Substrate-Free Human Presequence Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As171

b:86.8
occ:1.00
 AS A:CAS171 0.0 86.8 1.0
CE1 A:CAS171 2.0 55.5 1.0
CE2 A:CAS171 2.0 1.0 1.0
SG A:CAS171 2.2 36.3 1.0
CB A:CAS171 3.1 46.8 1.0
CA A:CAS171 3.5 34.9 1.0
O A:HOH1503 4.2 57.1 1.0
NH1 A:ARG173 4.2 37.8 1.0
N A:CAS171 4.4 27.3 1.0
NE2 A:GLN115 4.4 55.1 1.0
C A:CAS171 4.5 32.0 1.0
O A:CAS171 4.5 19.7 1.0
O A:SER114 4.6 21.4 1.0
C A:SER114 4.6 26.6 1.0
CD A:GLN115 4.7 48.2 1.0
CB A:PRO118 4.9 36.8 1.0
N A:GLN115 4.9 23.4 1.0
OE1 A:GLN115 4.9 44.1 1.0
CG A:ARG173 5.0 33.7 1.0

Arsenic binding site 2 out of 12 in 4l3t

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Arsenic binding site 2 out of 12 in the Crystal Structure of Substrate-Free Human Presequence Protease


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Substrate-Free Human Presequence Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As241

b:0.1
occ:1.00
 AS A:CAS241 0.0 0.1 1.0
CE2 A:CAS241 2.0 71.3 1.0
CE1 A:CAS241 2.0 69.5 1.0
SG A:CAS241 2.2 55.0 1.0
CB A:CAS241 3.1 48.8 1.0
CA A:CAS241 3.4 39.7 1.0
O A:LEU240 3.9 46.2 1.0
CH1 A:MLY521 4.1 87.7 1.0
N A:CAS241 4.2 33.2 1.0
C A:LEU240 4.3 34.0 1.0
CG A:GLU244 4.5 40.2 1.0
C A:CAS241 4.5 34.0 1.0
O A:CAS241 4.7 22.4 1.0

Arsenic binding site 3 out of 12 in 4l3t

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Arsenic binding site 3 out of 12 in the Crystal Structure of Substrate-Free Human Presequence Protease


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of Substrate-Free Human Presequence Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As313

b:0.7
occ:1.00
 AS A:CAS313 0.0 0.7 1.0
CE1 A:CAS313 2.0 92.5 1.0
CE2 A:CAS313 2.0 93.3 1.0
SG A:CAS313 2.2 57.7 1.0
CB A:CAS313 3.1 55.1 1.0
O A:GLY314 3.5 45.8 1.0
CE A:MET504 3.9 23.8 1.0
CG A:ASN213 3.9 41.9 1.0
ND2 A:ASN213 4.0 45.3 1.0
CA A:PRO506 4.0 51.7 1.0
CB A:ASN213 4.1 36.9 1.0
CB A:PRO506 4.1 52.4 1.0
O A:CAS313 4.1 54.9 1.0
C A:CAS313 4.1 56.4 1.0
N A:PRO506 4.2 50.0 1.0
OD1 A:ASN213 4.2 39.7 1.0
CA A:CAS313 4.4 59.1 1.0
SD A:MET504 4.4 34.8 1.0
N A:GLY314 4.5 55.9 1.0
CG A:MET504 4.5 28.4 1.0
C A:GLY314 4.5 52.6 1.0
CD A:PRO506 4.6 52.0 1.0
C A:ARG505 4.7 41.8 1.0
N A:CAS313 4.8 55.7 1.0
CG A:PRO506 4.9 52.9 1.0
O A:GLN325 4.9 46.5 1.0
O A:ARG505 5.0 34.4 1.0

Arsenic binding site 4 out of 12 in 4l3t

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Arsenic binding site 4 out of 12 in the Crystal Structure of Substrate-Free Human Presequence Protease


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of Substrate-Free Human Presequence Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As477

b:0.1
occ:1.00
 AS A:CAS477 0.0 0.1 1.0
CE1 A:CAS477 2.0 64.7 1.0
CE2 A:CAS477 2.0 77.2 1.0
SG A:CAS477 2.2 57.4 1.0
CB A:CAS477 3.1 52.5 1.0
CA A:CAS477 3.7 44.9 1.0
CE1 A:PHE484 4.1 46.0 1.0
CZ A:PHE484 4.5 45.6 1.0
CD1 A:PHE484 4.5 43.3 1.0
N A:CAS477 4.7 43.9 1.0
O A:CAS477 4.8 40.3 1.0
C A:CAS477 4.8 42.9 1.0

Arsenic binding site 5 out of 12 in 4l3t

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Arsenic binding site 5 out of 12 in the Crystal Structure of Substrate-Free Human Presequence Protease


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Crystal Structure of Substrate-Free Human Presequence Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As556

b:90.8
occ:1.00
 AS A:CAS556 0.0 90.8 1.0
CE2 A:CAS556 2.0 70.3 1.0
CE1 A:CAS556 2.0 0.4 1.0
SG A:CAS556 2.2 32.5 1.0
CB A:CAS556 3.1 45.1 1.0
CG A:PRO118 4.0 35.7 1.0
CD A:PRO118 4.1 32.8 1.0
CB A:CYS119 4.2 40.3 1.0
N A:CYS119 4.2 33.9 1.0
CA A:CAS556 4.3 36.9 1.0
O A:ASP553 4.3 53.8 1.0
N A:CAS556 4.5 31.8 1.0
CA A:CYS119 4.6 35.9 1.0
N A:PRO118 4.8 31.4 1.0
C A:PRO118 5.0 35.4 1.0

Arsenic binding site 6 out of 12 in 4l3t

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Arsenic binding site 6 out of 12 in the Crystal Structure of Substrate-Free Human Presequence Protease


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Crystal Structure of Substrate-Free Human Presequence Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As692

b:0.8
occ:1.00
 AS A:CAS692 0.0 0.8 1.0
CE1 A:CAS692 2.0 0.4 1.0
CE2 A:CAS692 2.0 46.7 1.0
SG A:CAS692 2.2 69.6 1.0
CB A:CAS692 3.1 48.2 1.0
CA A:CAS692 3.3 43.0 1.0
N A:CAS692 4.2 39.6 1.0
O A:PRO691 4.2 28.5 1.0
C A:CAS692 4.3 42.0 1.0
O A:HOH1458 4.4 48.4 1.0
C A:PRO691 4.5 32.4 1.0
N A:PHE693 4.6 29.3 1.0
O A:GLY628 4.6 28.6 1.0
O A:ASN690 4.7 31.4 1.0
O A:HOH1366 4.7 49.1 1.0

Arsenic binding site 7 out of 12 in 4l3t

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Arsenic binding site 7 out of 12 in the Crystal Structure of Substrate-Free Human Presequence Protease


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Crystal Structure of Substrate-Free Human Presequence Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As112

b:0.1
occ:1.00
 AS B:CAS112 0.0 0.1 1.0
CE2 B:CAS112 2.0 61.6 1.0
CE1 B:CAS112 2.0 0.2 1.0
SG B:CAS112 2.2 33.2 1.0
CB B:CAS112 3.1 51.6 1.0
CA B:CAS112 3.4 34.0 1.0
CB B:ASP121 4.0 50.6 1.0
O B:CAS112 4.1 40.5 1.0
CG B:ASP121 4.1 66.9 1.0
CA B:ASP121 4.1 36.6 1.0
N B:ASP121 4.1 30.6 1.0
NE2 B:GLN179 4.1 33.5 1.0
C B:CAS112 4.2 32.2 1.0
OD1 B:ASP176 4.3 39.4 1.0
OD1 B:ASP121 4.3 74.9 1.0
N B:CAS112 4.5 25.2 1.0
OD2 B:ASP121 4.5 72.2 1.0
CG B:ASP176 4.5 34.0 1.0
O B:HOH1317 4.6 38.0 1.0
OE2 B:GLU901 4.7 40.4 1.0
O B:LEU111 4.7 26.0 1.0
OE2 B:GLU180 4.7 29.0 1.0
CG B:GLU180 4.7 31.2 1.0
NH1 B:ARG120 4.8 40.3 1.0
CB B:ASP176 4.8 25.8 1.0
C B:LEU111 4.9 28.9 1.0
CD B:GLN179 4.9 31.2 1.0
OD2 B:ASP176 5.0 34.0 1.0
CD B:GLU180 5.0 33.3 1.0

Arsenic binding site 8 out of 12 in 4l3t

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Arsenic binding site 8 out of 12 in the Crystal Structure of Substrate-Free Human Presequence Protease


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Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of Crystal Structure of Substrate-Free Human Presequence Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As171

b:90.8
occ:1.00
 AS B:CAS171 0.0 90.8 1.0
CE2 B:CAS171 2.0 70.3 1.0
CE1 B:CAS171 2.0 0.4 1.0
SG B:CAS171 2.2 32.5 1.0
CB B:CAS171 3.1 45.1 1.0
CA B:CAS171 3.4 36.9 1.0
N B:CAS171 4.3 31.8 1.0
C B:CAS171 4.4 31.8 1.0
O B:SER114 4.4 25.9 1.0
O B:CAS171 4.4 24.0 1.0
C B:SER114 4.4 25.1 1.0
N B:GLN115 4.6 28.7 1.0
NH1 B:ARG173 4.6 35.4 1.0
CA B:GLN115 4.7 31.2 1.0
CB B:PRO118 4.8 36.0 1.0
O B:PRO170 4.9 27.0 1.0
C B:PRO170 4.9 31.1 1.0
CA B:SER114 5.0 21.4 1.0

Arsenic binding site 9 out of 12 in 4l3t

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Arsenic binding site 9 out of 12 in the Crystal Structure of Substrate-Free Human Presequence Protease


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 9 of Crystal Structure of Substrate-Free Human Presequence Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As313

b:0.1
occ:1.00
 AS B:CAS313 0.0 0.1 1.0
CE2 B:CAS313 2.0 86.5 1.0
CE1 B:CAS313 2.0 0.9 1.0
SG B:CAS313 2.2 59.9 1.0
O B:GLY314 2.8 41.3 1.0
CB B:CAS313 3.1 48.9 1.0
ND2 B:ASN213 3.6 50.4 1.0
CG B:ASN213 3.8 42.1 1.0
CG B:PRO506 3.9 50.1 1.0
O B:HOH1689 4.0 40.8 1.0
C B:GLY314 4.0 46.0 1.0
CB B:PRO506 4.0 49.9 1.0
CA B:PRO506 4.1 49.1 1.0
CB B:ASN213 4.1 31.9 1.0
N B:PRO506 4.3 47.8 1.0
OD1 B:ASN213 4.3 41.9 1.0
CA B:CAS313 4.3 54.1 1.0
C B:CAS313 4.4 49.8 1.0
O B:CAS313 4.4 55.8 1.0
CD B:PRO506 4.5 48.2 1.0
CA B:PRO315 4.5 52.7 1.0
CE B:MET504 4.6 31.1 1.0
N B:PRO315 4.8 47.1 1.0
N B:GLY314 4.8 45.8 1.0
C B:ARG505 4.8 40.3 1.0
O B:GLN325 4.9 34.1 1.0
C B:PRO315 5.0 59.1 1.0

Arsenic binding site 10 out of 12 in 4l3t

Go back to Arsenic Binding Sites List in 4l3t
Arsenic binding site 10 out of 12 in the Crystal Structure of Substrate-Free Human Presequence Protease


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 10 of Crystal Structure of Substrate-Free Human Presequence Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As477

b:0.9
occ:1.00
 AS B:CAS477 0.0 0.9 1.0
CE2 B:CAS477 2.0 0.4 1.0
CE1 B:CAS477 2.0 0.1 1.0
SG B:CAS477 2.2 55.6 1.0
CB B:CAS477 3.1 56.4 1.0
CA B:CAS477 3.2 47.3 1.0
N B:CAS477 4.1 42.3 1.0
C B:CAS477 4.4 42.2 1.0
CE1 B:PHE484 4.4 51.9 1.0
O B:CAS477 4.5 35.4 1.0
CD1 B:PHE484 4.8 53.5 1.0
CZ B:PHE484 4.9 49.1 1.0
O B:MLY473 4.9 33.0 1.0

Reference:

J.V.King, W.G.Liang, K.P.Scherpelz, A.B.Schilling, S.C.Meredith, W.J.Tang. Molecular Basis of Substrate Recognition and Degradation By Human Presequence Protease. Structure V. 22 996 2014.
ISSN: ISSN 0969-2126
PubMed: 24931469
DOI: 10.1016/J.STR.2014.05.003
Page generated: Sat Dec 12 01:44:09 2020

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