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Zinc in PDB 6h19: Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)

Enzymatic activity of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)

All present enzymatic activity of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form):
3.1.1.13; 3.1.1.3;

Protein crystallography data

The structure of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form), PDB code: 6h19 was solved by C.Touvrey, X.Brazzolotto, F.Nachon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.70 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.120, 97.810, 110.150, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23

Other elements in 6h19:

The structure of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) (pdb code 6h19). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form), PDB code: 6h19:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 6h19

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Zinc binding site 1 out of 10 in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:24.4
occ:1.00
 O A:HOH865 2.0 30.4 1.0
O A:ACT613 2.1 23.1 1.0
NE2 A:HIS48 2.1 25.0 1.0
O A:HOH722 2.2 22.1 1.0
O A:HOH749 2.2 30.0 1.0
OXT A:ACT613 2.2 33.5 1.0
C A:ACT613 2.4 27.0 1.0
CD2 A:HIS48 3.1 22.4 1.0
CE1 A:HIS48 3.2 26.0 1.0
OH A:TYR82 3.9 26.9 1.0
CH3 A:ACT613 4.0 28.4 1.0
CG A:HIS48 4.2 22.2 1.0
ND1 A:HIS48 4.3 26.6 1.0
OD2 A:ASP79 4.3 24.6 1.0
OD1 A:ASP79 4.3 23.0 1.0
CD A:PRO38 4.4 22.2 1.0
CB A:PRO34 4.4 21.5 1.0
O A:HOH792 4.5 22.4 1.0
CG A:ASP79 4.7 21.1 1.0
CG A:PRO38 4.7 23.0 1.0
CG A:PRO34 4.7 19.2 1.0
CZ A:TYR82 4.7 25.7 1.0
CE2 A:TYR82 4.9 22.5 1.0

Zinc binding site 2 out of 10 in 6h19

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Zinc binding site 2 out of 10 in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:24.3
occ:1.00
 OXT A:ACT612 2.0 23.6 1.0
NE2 A:HIS168 2.1 21.6 1.0
C A:ACT612 2.5 26.5 1.0
O A:ACT612 2.6 23.5 1.0
CD2 A:HIS168 3.0 19.9 1.0
CE1 A:HIS168 3.1 21.6 1.0
CH3 A:ACT612 4.1 25.7 1.0
CD2 A:TYR208 4.1 24.1 1.0
CG A:HIS168 4.2 21.7 1.0
ND1 A:HIS168 4.2 22.4 1.0
O A:HOH771 4.2 29.2 1.0
O A:TYR208 4.5 22.6 1.0
CE2 A:TYR208 4.7 20.8 1.0
CG A:TYR208 4.9 24.9 1.0
CB A:TYR208 4.9 24.8 1.0

Zinc binding site 3 out of 10 in 6h19

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Zinc binding site 3 out of 10 in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:22.1
occ:1.00
 OE2 A:GLU78 2.0 22.1 1.0
OD1 A:ASP77 2.0 21.6 1.0
CD A:GLU78 2.7 25.6 1.0
CG A:ASP77 2.8 18.9 1.0
OE1 A:GLU78 2.8 25.7 1.0
OD2 A:ASP77 2.9 19.4 1.0
CG A:GLU78 4.1 23.8 1.0
CB A:ASP77 4.2 21.8 1.0
N A:GLU78 4.5 21.9 1.0
CA A:ASP77 4.8 23.4 1.0

Zinc binding site 4 out of 10 in 6h19

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Zinc binding site 4 out of 10 in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:48.5
occ:1.00
 NE2 A:HIS115 2.2 33.7 1.0
O A:HOH878 2.3 32.3 1.0
O A:ACT614 2.5 49.7 1.0
OXT A:ACT615 2.9 51.3 1.0
C A:ACT615 3.0 38.4 1.0
C A:ACT614 3.0 27.8 1.0
OXT A:ACT614 3.0 36.8 1.0
CE1 A:HIS115 3.1 38.1 1.0
CD2 A:HIS115 3.2 35.1 1.0
O A:ACT615 3.3 41.4 1.0
CH3 A:ACT615 3.7 51.8 1.0
NH1 A:ARG63 4.1 42.5 1.0
ND1 A:HIS115 4.2 37.5 1.0
CG A:HIS115 4.3 34.5 1.0
CH3 A:ACT614 4.5 40.3 1.0
O A:HOH755 4.6 33.2 1.0

Zinc binding site 5 out of 10 in 6h19

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Zinc binding site 5 out of 10 in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:46.3
occ:1.00
 OD1 A:ASP457 2.0 37.5 1.0
NE2 A:HIS435 2.2 37.5 1.0
NE2 A:HIS420 2.5 49.4 1.0
CG A:ASP457 2.9 36.0 1.0
CD2 A:HIS435 3.0 41.6 1.0
OD2 A:ASP457 3.1 36.8 1.0
CD2 A:HIS420 3.2 43.9 1.0
CE1 A:HIS435 3.3 34.0 1.0
CE1 A:HIS420 3.6 48.5 1.0
OH A:TYR441 3.6 41.0 1.0
CG A:HIS435 4.2 43.1 1.0
CB A:ASP457 4.2 38.3 1.0
ND1 A:HIS435 4.3 37.5 1.0
CG A:HIS420 4.4 46.5 1.0
ND1 A:HIS420 4.6 52.5 1.0
CZ A:TYR441 4.7 34.3 1.0
CA A:ASP457 4.7 30.2 1.0
N A:ASP457 4.8 34.8 1.0
CE2 A:TYR441 4.8 36.5 1.0

Zinc binding site 6 out of 10 in 6h19

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Zinc binding site 6 out of 10 in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:23.1
occ:1.00
 O A:ACT611 2.0 26.0 1.0
OE1 A:GLU489 2.0 22.7 1.0
NE2 A:HIS487 2.1 21.5 1.0
C A:ACT611 2.5 23.7 1.0
OXT A:ACT611 2.5 24.2 1.0
CD A:GLU489 2.9 23.9 1.0
CD2 A:HIS487 3.0 22.1 1.0
CE1 A:HIS487 3.2 18.4 1.0
OE2 A:GLU489 3.2 24.6 1.0
CH3 A:ACT611 4.0 26.4 1.0
CG A:HIS487 4.2 19.1 1.0
ND1 A:HIS487 4.2 19.6 1.0
CG A:GLU489 4.3 20.6 1.0
CD A:PRO490 4.4 22.6 1.0
CA A:GLU489 4.5 17.6 1.0
CB A:GLU489 4.6 19.9 1.0
O A:HOH708 4.8 23.8 1.0

Zinc binding site 7 out of 10 in 6h19

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Zinc binding site 7 out of 10 in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn607

b:62.8
occ:1.00
 OD2 A:ASP97 2.3 41.7 1.0
OD1 A:ASP97 2.6 33.5 1.0
CG A:ASP97 2.7 31.3 1.0
CB A:ASP97 4.2 25.6 1.0
CD A:ARG96 4.8 55.7 1.0

Zinc binding site 8 out of 10 in 6h19

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Zinc binding site 8 out of 10 in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn608

b:90.9
occ:1.00
 O A:HOH705 2.4 64.7 1.0
CD2 A:HIS283 2.5 67.8 1.0
O A:ACT617 2.7 61.9 1.0
OXT A:ACT617 2.9 78.7 1.0
C A:ACT617 3.1 72.4 1.0
CG A:HIS283 3.2 61.8 1.0
CB A:HIS283 3.4 54.5 1.0
NE2 A:HIS283 3.7 69.9 1.0
CA A:HIS283 3.9 51.4 1.0
ND1 A:HIS283 4.4 59.8 1.0
O A:HOH891 4.4 54.6 1.0
CE1 A:HIS283 4.6 64.7 1.0
CH3 A:ACT617 4.6 54.2 1.0
O A:HIS283 4.7 52.2 1.0
C A:HIS283 4.8 51.5 1.0
N A:HIS283 4.9 48.7 1.0

Zinc binding site 9 out of 10 in 6h19

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Zinc binding site 9 out of 10 in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn609

b:75.0
occ:1.00
 OE1 A:GLU350 2.1 53.7 1.0
CD A:GLU350 3.1 50.7 1.0
CE1 A:TYR279 3.2 70.5 1.0
OE2 A:GLU350 3.4 60.1 1.0
CD1 A:TYR279 3.5 70.1 1.0
O A:HOH897 3.5 52.4 1.0
CZ A:TYR279 4.4 74.4 1.0
CG A:GLU350 4.5 41.2 1.0
CG2 A:ILE353 4.5 45.5 1.0
CA A:GLU350 4.8 32.2 1.0
CB A:GLU350 4.8 35.9 1.0
OH A:TYR279 4.8 76.7 1.0
CG A:TYR279 4.9 68.2 1.0

Zinc binding site 10 out of 10 in 6h19

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Zinc binding site 10 out of 10 in the Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Ethyl-Paraoxon Inhibited Recombinant Human Bile Salt Activated Lipase (Aged Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn610

b:59.0
occ:1.00
 OE2 A:GLU193 1.9 46.1 1.0
OD1 A:ASP437 2.3 43.8 1.0
O A:ACT616 2.8 51.8 1.0
CD A:GLU193 2.8 34.1 1.0
CG A:GLU193 3.2 33.8 1.0
CG A:ASP437 3.2 38.6 1.0
OXT A:ACT616 3.3 42.0 1.0
C A:ACT616 3.3 49.2 1.0
OD2 A:ASP437 3.5 38.3 1.0
OE1 A:GLU193 3.9 41.7 1.0
CD1 A:ILE439 4.1 29.6 1.0
CG1 A:ILE439 4.2 31.4 1.0
OD2 A:ASP438 4.3 37.9 1.0
CB A:ASP437 4.6 38.6 1.0
OD2 A:ASP320 4.6 33.5 1.0
CB A:GLU193 4.6 20.5 1.0
OG A:SER220 4.7 24.5 1.0
CB A:SER220 4.8 22.5 1.0
O A:HOH886 4.8 33.3 1.0
CH3 A:ACT616 4.9 40.8 1.0

Reference:

C.Touvrey, C.Courageux, V.Guillon, R.Terreux, F.Nachon, X.Brazzolotto. X-Ray Structures of Human Bile-Salt Activated Lipase Conjugated to Nerve Agents Surrogates. Toxicology V. 411 15 2019.
ISSN: ISSN 1879-3185
PubMed: 30359675
DOI: 10.1016/J.TOX.2018.10.015
Page generated: Mon Oct 28 22:18:24 2024

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