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Chlorine in PDB 6g4p: Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2

Enzymatic activity of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2

All present enzymatic activity of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2:
3.1.1.7;

Protein crystallography data

The structure of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2, PDB code: 6g4p was solved by G.Santoni, E.De La Mora, J.De Souza, I.Silman, J.Sussman, R.Baati, M.Weik, F.Nachon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.92 / 2.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.510, 106.560, 150.200, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 27.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 (pdb code 6g4p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2, PDB code: 6g4p:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 6g4p

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Chlorine binding site 1 out of 10 in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:0.9
occ:1.00
 CL1 A:JDS604 0.0 0.9 1.0
C12 A:JDS604 1.7 0.7 1.0
C11 A:JDS604 2.6 0.6 1.0
C13 A:JDS604 2.6 96.2 1.0
O A:HOH724 2.8 56.2 1.0
CE2 A:TYR70 3.4 57.0 1.0
CD2 A:TYR334 3.9 28.3 1.0
C10 A:JDS604 3.9 0.1 1.0
C08 A:JDS604 3.9 87.1 1.0
OH A:TYR70 4.0 70.0 1.0
C3 A:PG4608 4.0 96.1 1.0
CE2 A:TYR334 4.1 28.2 1.0
CZ A:TYR70 4.1 67.1 1.0
CD2 A:TYR70 4.3 41.7 1.0
CB A:ASP72 4.4 26.5 1.0
C07 A:JDS604 4.5 95.6 1.0
CG A:ASP72 4.5 45.9 1.0
OD2 A:ASP72 4.5 51.6 1.0
N03 A:JDS604 4.6 76.2 1.0
OH A:TYR121 4.7 28.1 1.0
CA A:ASP72 4.8 32.8 1.0
C4 A:PG4608 5.0 91.8 1.0

Chlorine binding site 2 out of 10 in 6g4p

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Chlorine binding site 2 out of 10 in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:71.1
occ:1.00
 N A:THR497 3.7 42.5 1.0
CB A:THR497 4.1 64.5 1.0
OG1 A:THR497 4.2 68.5 1.0
CA A:THR496 4.3 44.3 1.0
CB A:THR496 4.3 33.0 1.0
O A:HOH729 4.4 44.2 1.0
O A:THR412 4.4 32.4 1.0
CG2 A:THR412 4.5 29.3 1.0
C A:THR496 4.5 43.2 1.0
CA A:THR497 4.6 56.1 1.0

Chlorine binding site 3 out of 10 in 6g4p

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Chlorine binding site 3 out of 10 in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl606

b:57.3
occ:1.00
 ND1 A:HIS406 3.6 48.5 1.0
OD1 A:ASN525 3.8 36.0 1.0
ND2 A:ASN409 4.0 53.1 1.0
CA A:HIS406 4.2 38.0 1.0
CB A:ASN525 4.3 30.4 1.0
CG A:ASN525 4.5 40.6 1.0
CE1 A:HIS406 4.5 58.1 1.0
CG A:HIS406 4.5 36.3 1.0
CG A:ASN409 4.6 46.6 1.0
CB A:ASN409 4.6 36.1 1.0
CB A:HIS406 4.6 27.5 1.0
N A:HIS406 4.7 39.0 1.0
O A:MET405 4.8 40.6 1.0
C A:MET405 5.0 43.1 1.0

Chlorine binding site 4 out of 10 in 6g4p

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Chlorine binding site 4 out of 10 in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl607

b:68.9
occ:1.00
 CZ A:PHE422 4.1 31.6 1.0
CG A:LYS325 4.3 32.4 1.0
CE A:LYS325 4.3 55.9 1.0
NZ A:LYS325 4.5 65.9 1.0
NE A:ARG517 4.6 42.2 1.0
CE2 A:PHE422 4.6 38.1 1.0
CD A:LYS325 4.8 41.0 1.0
O A:LYS325 4.9 38.9 1.0
CE1 A:PHE422 5.0 38.0 1.0

Chlorine binding site 5 out of 10 in 6g4p

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Chlorine binding site 5 out of 10 in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl604

b:78.5
occ:1.00
 CL1 B:JDS604 0.0 78.5 1.0
C12 B:JDS604 1.7 67.2 1.0
C11 B:JDS604 2.6 56.1 1.0
C13 B:JDS604 2.7 64.9 1.0
O B:TRP279 3.9 73.7 1.0
C10 B:JDS604 3.9 51.7 1.0
CB B:TRP279 3.9 68.1 1.0
C08 B:JDS604 4.0 54.9 1.0
C20 B:JDS604 4.1 79.5 1.0
C B:TRP279 4.4 79.4 1.0
C07 B:JDS604 4.5 50.6 1.0
C21 B:JDS604 4.6 82.5 1.0
O02 B:JDS604 4.7 89.7 1.0
C19 B:JDS604 4.7 74.3 1.0
CA B:TRP279 4.9 72.3 1.0
CG B:TRP279 4.9 64.3 1.0
CA B:ASN280 5.0 0.6 1.0
N B:ASN280 5.0 90.8 1.0

Chlorine binding site 6 out of 10 in 6g4p

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Chlorine binding site 6 out of 10 in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl605

b:60.9
occ:1.00
 CD B:LYS491 3.9 68.4 1.0
ND2 B:ASN483 3.9 34.1 1.0
OD1 B:ASN481 3.9 57.1 1.0
ND2 B:ASN481 4.0 62.4 1.0
CB B:ASN483 4.1 47.4 1.0
CG B:ASN483 4.1 42.2 1.0
CE B:LYS491 4.3 79.4 1.0
CG B:ASN481 4.4 53.8 1.0
CB B:LYS491 4.5 57.8 1.0
CG B:LYS491 4.6 61.3 1.0
OD1 B:ASN483 4.7 39.0 1.0

Chlorine binding site 7 out of 10 in 6g4p

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Chlorine binding site 7 out of 10 in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl606

b:0.3
occ:1.00
 NZ B:LYS478 2.4 71.6 1.0
CE1 B:HIS471 3.1 75.0 1.0
ND1 B:HIS471 3.3 69.3 1.0
OE1 B:GLU139 3.5 70.3 1.0
OG1 B:THR475 3.7 41.3 1.0
CE B:LYS478 3.8 71.1 1.0
NE2 B:HIS471 4.1 77.7 1.0
CD B:LYS478 4.1 73.5 1.0
CG B:HIS471 4.5 64.2 1.0
O B:GLU139 4.5 31.5 1.0
N B:THR475 4.6 31.8 1.0
CB B:ALA474 4.7 50.1 1.0
CD B:GLU139 4.7 72.0 1.0
CA B:THR475 4.8 30.0 1.0
CD2 B:HIS471 4.8 71.6 1.0
CB B:THR475 4.8 30.9 1.0

Chlorine binding site 8 out of 10 in 6g4p

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Chlorine binding site 8 out of 10 in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl607

b:69.9
occ:1.00
 OE1 B:GLU461 3.7 71.3 1.0
OG1 B:THR459 3.9 41.4 1.0
CD B:GLU461 4.1 72.1 1.0
CG2 B:THR507 4.1 80.4 1.0
OG1 B:THR507 4.2 72.1 1.0
CB B:GLU461 4.3 50.9 1.0
CE1 B:HIS425 4.3 38.1 1.0
CG B:GLU461 4.5 62.9 1.0
CB B:THR507 4.5 74.6 1.0
CB B:THR459 4.7 44.7 1.0
CG2 B:THR459 4.7 30.5 1.0
OE2 B:GLU461 4.7 75.8 1.0
CG B:GLU462 4.8 49.2 1.0
NE2 B:HIS425 4.9 29.2 1.0

Chlorine binding site 9 out of 10 in 6g4p

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Chlorine binding site 9 out of 10 in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl608

b:98.0
occ:1.00
 NE B:ARG289 3.6 81.7 1.0
CD B:ARG289 4.1 63.6 1.0
CG B:ARG289 4.2 54.2 1.0
CG B:PRO283 4.5 90.8 1.0
NH2 B:ARG244 4.6 68.3 1.0
CZ B:ARG289 4.6 77.3 1.0
CB B:ARG289 4.6 49.1 1.0
CB B:PRO361 4.7 0.3 1.0
NH2 B:ARG289 4.7 65.2 1.0
CG B:PRO361 4.8 96.3 1.0
CD B:PRO283 4.9 85.5 1.0

Chlorine binding site 10 out of 10 in 6g4p

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Chlorine binding site 10 out of 10 in the Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Non-Aged Form of Torpedo Californica Acetylcholinesterase Inhibited By Tabun Analog Nedpa Bound to Uncharged Reactivator 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl609

b:90.6
occ:1.00
 N B:LEU23 3.7 58.2 1.0
OH B:TYR134 3.7 51.7 1.0
CE2 B:TYR134 3.9 43.4 1.0
CA B:VAL22 4.2 36.3 1.0
CZ B:TYR134 4.3 44.1 1.0
CE B:LYS133 4.3 48.1 1.0
NZ B:LYS133 4.4 36.9 1.0
CD2 B:LEU23 4.5 43.9 1.0
C B:VAL22 4.5 54.1 1.0
O B:PRO21 4.5 60.2 1.0
CA B:LEU23 4.6 54.5 1.0
N B:VAL22 4.8 41.1 1.0
CG1 B:VAL453 4.9 58.6 1.0
CG2 B:VAL453 4.9 36.4 1.0
C B:PRO21 4.9 58.9 1.0
OE2 B:GLU455 5.0 96.1 1.0

Reference:

G.Santoni, J.De Sousa, E.De La Mora, J.Dias, L.Jean, J.L.Sussman, I.Silman, P.Y.Renard, R.C.D.Brown, M.Weik, R.Baati, F.Nachon. Structure-Based Optimization of Nonquaternary Reactivators of Acetylcholinesterase Inhibited By Organophosphorus Nerve Agents. J. Med. Chem. V. 61 7630 2018.
ISSN: ISSN 1520-4804
PubMed: 30125110
DOI: 10.1021/ACS.JMEDCHEM.8B00592
Page generated: Sat Jul 27 23:42:46 2024

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