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Zinc in PDB 4gy1: Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate

Enzymatic activity of Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate

All present enzymatic activity of Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate:
3.1.8.1;

Protein crystallography data

The structure of Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate, PDB code: 4gy1 was solved by C.J.Jackson, N.Tokuriki, D.S.Tawfik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.60 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.223, 87.019, 88.939, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.5

Other elements in 4gy1:

The structure of Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate (pdb code 4gy1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate, PDB code: 4gy1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4gy1

Go back to Zinc Binding Sites List in 4gy1
Zinc binding site 1 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.5
occ:0.80
 O2 A:CAC404 2.0 14.7 0.5
NE2 A:HIS57 2.0 11.5 1.0
O A:HOH643 2.1 22.4 0.8
OD1 A:ASP301 2.2 9.6 0.4
OD1 A:ASP301 2.2 12.3 0.6
NE2 A:HIS55 2.2 18.3 1.0
ZN A:ZN403 2.4 16.3 0.2
OQ2 A:KCX169 2.5 11.1 0.5
CE1 A:HIS57 2.9 10.9 1.0
CG A:ASP301 2.9 12.1 0.4
OD2 A:ASP301 3.0 12.8 0.4
CD2 A:HIS55 3.1 14.6 1.0
CG A:ASP301 3.1 12.2 0.6
AS A:CAC404 3.1 33.9 0.5
CD2 A:HIS57 3.1 8.4 1.0
CX A:KCX169 3.2 15.0 0.5
C1 A:CAC404 3.3 16.8 0.5
CE1 A:HIS55 3.3 17.5 1.0
OD2 A:ASP301 3.4 13.5 0.6
OQ1 A:KCX169 3.5 15.8 0.5
ZN A:ZN402 3.6 16.1 0.4
CG2 A:VAL101 4.0 11.9 0.2
ND1 A:HIS57 4.1 10.6 1.0
CG2 A:VAL101 4.1 7.9 0.8
NZ A:KCX169 4.2 15.0 0.5
O1 A:CAC404 4.2 14.6 0.5
CG A:HIS57 4.2 9.4 1.0
CE1 A:HIS230 4.3 19.7 0.8
CG A:HIS55 4.3 15.5 1.0
ND1 A:HIS55 4.4 20.1 1.0
O A:HOH670 4.4 32.3 1.0
CB A:ASP301 4.4 11.7 0.4
CB A:ASP301 4.4 11.7 0.6
NE2 A:HIS230 4.4 19.4 0.8
NE2 A:HIS230 4.5 19.3 0.2
C2 A:CAC404 4.6 30.0 0.5
CA A:ASP301 4.9 9.3 0.6
CA A:ASP301 4.9 9.3 0.4
NZ A:KCX169 4.9 24.5 0.5

Zinc binding site 2 out of 6 in 4gy1

Go back to Zinc Binding Sites List in 4gy1
Zinc binding site 2 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:16.1
occ:0.38
 OQ1 A:KCX169 2.0 15.8 0.5
ND1 A:HIS201 2.1 16.4 0.5
O1 A:CAC404 2.2 14.6 0.5
NE2 A:HIS230 2.2 19.4 0.8
O2 A:CAC404 2.3 14.7 0.5
CE1 A:HIS230 2.5 20.0 0.2
O A:HOH643 2.6 22.4 0.8
CE1 A:HIS201 2.6 19.2 0.5
NE2 A:HIS230 2.6 19.3 0.2
ZN A:ZN403 2.6 16.3 0.2
AS A:CAC404 2.8 33.9 0.5
NE2 A:HIS201 3.0 18.4 0.5
CE1 A:HIS201 3.0 18.9 0.5
CX A:KCX169 3.1 15.0 0.5
ND1 A:HIS201 3.1 18.1 0.5
CE1 A:HIS230 3.2 19.7 0.8
CG A:HIS201 3.2 19.1 0.5
CD2 A:HIS230 3.2 19.2 0.8
OQ2 A:KCX169 3.4 11.1 0.5
CB A:HIS201 3.6 15.9 0.5
ZN A:ZN401 3.6 16.5 0.8
ND1 A:HIS230 3.7 14.6 0.2
CD2 A:HIS201 3.7 21.5 0.5
CG A:HIS201 3.8 17.9 0.5
CD2 A:HIS230 3.9 14.8 0.2
NZ A:KCX169 3.9 24.5 0.5
OD2 A:ASP301 4.0 12.8 0.4
C2 A:CAC404 4.1 30.0 0.5
NE2 A:HIS201 4.2 19.0 0.5
NZ A:KCX169 4.2 15.0 0.5
NE2 A:HIS55 4.3 18.3 1.0
CE1 A:HIS55 4.3 17.5 1.0
CD2 A:HIS201 4.3 20.1 0.5
NE1 A:TRP131 4.3 18.8 0.4
ND1 A:HIS230 4.3 18.6 0.8
C1 A:CAC404 4.3 16.8 0.5
NE1 A:TRP131 4.3 12.1 0.6
CG A:HIS230 4.3 15.2 0.8
OD2 A:ASP301 4.4 13.5 0.6
CG A:HIS230 4.4 18.4 0.2
CA A:HIS201 4.6 18.7 0.5
CE A:KCX169 4.7 18.7 0.5
CE A:KCX169 4.7 16.2 0.5
CD1 A:TRP131 4.8 16.7 0.4
CD1 A:TRP131 4.9 15.4 0.6
OD1 A:ASP301 4.9 12.3 0.6
CG A:ASP301 4.9 12.1 0.4
CB A:HIS201 4.9 16.6 0.5

Zinc binding site 3 out of 6 in 4gy1

Go back to Zinc Binding Sites List in 4gy1
Zinc binding site 3 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:16.3
occ:0.22
 CE1 A:HIS230 1.9 19.7 0.8
NE2 A:HIS55 2.1 18.3 1.0
O2 A:CAC404 2.2 14.7 0.5
OD2 A:ASP301 2.2 12.8 0.4
NE2 A:HIS230 2.2 19.3 0.2
NE2 A:HIS230 2.3 19.4 0.8
CE1 A:HIS55 2.4 17.5 1.0
ZN A:ZN401 2.4 16.5 0.8
ZN A:ZN402 2.6 16.1 0.4
CG A:ASP301 2.8 12.1 0.4
O A:HOH643 2.8 22.4 0.8
OD2 A:ASP301 3.0 13.5 0.6
OD1 A:ASP301 3.0 9.6 0.4
OD1 A:ASP301 3.1 12.3 0.6
CG A:ASP301 3.1 12.2 0.6
CD2 A:HIS230 3.1 14.8 0.2
ND1 A:HIS230 3.1 18.6 0.8
CD2 A:HIS55 3.1 14.6 1.0
OQ1 A:KCX169 3.2 15.8 0.5
CE1 A:HIS230 3.3 20.0 0.2
ND1 A:HIS55 3.4 20.1 1.0
CD2 A:HIS230 3.6 19.2 0.8
CX A:KCX169 3.7 15.0 0.5
OQ2 A:KCX169 3.7 11.1 0.5
CG A:HIS55 3.8 15.5 1.0
AS A:CAC404 3.8 33.9 0.5
CG A:HIS230 4.0 15.2 0.8
CB A:ASP301 4.1 11.7 0.4
CB A:ASP301 4.1 11.7 0.6
NZ A:KCX169 4.2 24.5 0.5
CG A:HIS230 4.3 18.4 0.2
ND1 A:HIS230 4.3 14.6 0.2
O1 A:CAC404 4.4 14.6 0.5
NE2 A:HIS57 4.4 11.5 1.0
ND1 A:HIS201 4.5 18.1 0.5
NZ A:KCX169 4.6 15.0 0.5
ND1 A:HIS201 4.6 16.4 0.5
CE1 A:HIS201 4.6 19.2 0.5
CD A:ARG254 4.7 18.6 0.5
NE A:ARG254 4.7 22.5 0.5
CD A:ARG254 4.7 18.6 0.5
CG A:ARG254 4.8 17.9 0.5
OD1 A:ASP253 4.8 22.1 0.5
CG A:ARG254 4.8 14.4 0.5
O A:HOH767 4.8 37.2 1.0
C1 A:CAC404 5.0 16.8 0.5

Zinc binding site 4 out of 6 in 4gy1

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Zinc binding site 4 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:17.4
occ:0.72
 ZN B:ZN403 1.9 42.7 0.4
NE2 B:HIS57 2.0 15.0 1.0
O2 B:CAC404 2.1 38.5 0.6
OD1 B:ASP301 2.2 14.9 0.7
NE2 B:HIS55 2.2 15.7 0.8
OQ1 B:KCX169 2.2 17.6 0.5
OD1 B:ASP301 2.5 17.9 0.3
CE1 B:HIS57 2.9 12.1 1.0
CG B:ASP301 3.0 13.7 0.7
CX B:KCX169 3.1 18.9 0.5
CD2 B:HIS57 3.1 16.0 1.0
CD2 B:HIS55 3.1 11.1 0.8
CE1 B:HIS55 3.2 15.9 0.8
OD2 B:ASP301 3.2 14.6 0.7
NE2 B:HIS55 3.2 17.3 0.2
CG B:ASP301 3.3 15.6 0.3
O B:HOH785 3.3 13.3 0.5
AS B:CAC404 3.3 59.3 0.6
OQ2 B:KCX169 3.5 22.1 0.5
ZN B:ZN402 3.5 15.4 0.4
OD2 B:ASP301 3.6 15.9 0.3
CD2 B:HIS55 3.7 13.2 0.2
O1 B:CAC404 3.8 23.4 0.6
CE1 B:HIS55 4.0 17.2 0.2
C1 B:CAC404 4.1 32.8 0.6
ND1 B:HIS57 4.1 13.9 1.0
NZ B:KCX169 4.1 16.9 0.5
CG B:HIS57 4.2 12.9 1.0
NE2 B:HIS230 4.2 20.4 0.2
CE1 B:HIS230 4.3 20.7 0.8
CG2 B:VAL101 4.3 12.7 1.0
ND1 B:HIS55 4.3 15.3 0.8
CG B:HIS55 4.3 13.9 0.8
NE2 B:HIS230 4.3 19.8 0.8
CB B:ASP301 4.4 12.4 0.7
CB B:ASP301 4.4 12.6 0.3
O B:HOH695 4.5 34.0 1.0
CG B:HIS55 4.7 16.8 0.2
CE1 B:HIS230 4.7 23.5 0.2
ND1 B:HIS55 4.8 20.9 0.2
CA B:ASP301 4.9 14.1 0.7
CA B:ASP301 4.9 14.2 0.3

Zinc binding site 5 out of 6 in 4gy1

Go back to Zinc Binding Sites List in 4gy1
Zinc binding site 5 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:15.4
occ:0.36
 OQ2 B:KCX169 2.0 22.1 0.5
CE1 B:HIS230 2.1 23.5 0.2
ZN B:ZN403 2.2 42.7 0.4
NE2 B:HIS230 2.2 19.8 0.8
O1 B:CAC404 2.2 23.4 0.6
ND1 B:HIS201 2.5 22.7 0.4
NE2 B:HIS230 2.6 20.4 0.2
CE1 B:HIS201 2.7 23.7 0.6
NE2 B:HIS201 2.8 19.9 0.6
CX B:KCX169 3.0 18.9 0.5
CD2 B:HIS230 3.0 25.1 0.8
ND1 B:HIS201 3.1 18.4 0.6
OQ1 B:KCX169 3.2 17.6 0.5
CE1 B:HIS230 3.2 20.7 0.8
O2 B:CAC404 3.2 38.5 0.6
AS B:CAC404 3.2 59.3 0.6
CD2 B:HIS201 3.3 22.7 0.6
CE1 B:HIS201 3.3 22.9 0.4
ND1 B:HIS230 3.3 18.9 0.2
O B:HOH785 3.4 13.3 0.5
CG B:HIS201 3.5 20.9 0.6
ZN B:ZN401 3.5 17.4 0.7
CG B:HIS201 3.6 23.4 0.4
CD2 B:HIS230 3.9 17.5 0.2
CB B:HIS201 4.0 18.5 0.4
OD2 B:ASP301 4.0 14.6 0.7
NE2 B:HIS55 4.1 17.3 0.2
NZ B:KCX169 4.1 24.3 0.5
CE1 B:HIS55 4.1 15.9 0.8
NE1 B:TRP131 4.1 19.9 0.4
NZ B:KCX169 4.2 16.9 0.5
NE2 B:HIS55 4.2 15.7 0.8
CG B:HIS230 4.2 16.6 0.8
CG B:HIS230 4.2 17.2 0.2
ND1 B:HIS230 4.3 17.3 0.8
C2 B:CAC404 4.3 35.3 0.6
OD2 B:ASP301 4.5 15.9 0.3
NE2 B:HIS201 4.5 16.8 0.4
CB B:HIS201 4.6 16.7 0.6
NE1 B:TRP131 4.6 14.7 0.6
CD2 B:HIS201 4.7 28.9 0.4
CE1 B:HIS55 4.8 17.2 0.2
CG B:ASP301 4.8 13.7 0.7
CE B:KCX169 4.8 21.8 0.5
OD1 B:ASP301 4.9 14.9 0.7
CD1 B:TRP131 4.9 17.9 0.4
C1 B:CAC404 4.9 32.8 0.6

Zinc binding site 6 out of 6 in 4gy1

Go back to Zinc Binding Sites List in 4gy1
Zinc binding site 6 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:42.7
occ:0.36
 ZN B:ZN401 1.9 17.4 0.7
ZN B:ZN402 2.2 15.4 0.4
NE2 B:HIS230 2.3 20.4 0.2
OD2 B:ASP301 2.4 14.6 0.7
NE2 B:HIS230 2.4 19.8 0.8
O2 B:CAC404 2.4 38.5 0.6
CE1 B:HIS230 2.5 20.7 0.8
NE2 B:HIS55 2.5 15.7 0.8
NE2 B:HIS55 2.6 17.3 0.2
OD1 B:ASP301 2.8 14.9 0.7
CE1 B:HIS55 2.8 15.9 0.8
CE1 B:HIS230 2.8 23.5 0.2
CG B:ASP301 2.8 13.7 0.7
OQ2 B:KCX169 2.8 22.1 0.5
OQ1 B:KCX169 2.9 17.6 0.5
OD2 B:ASP301 3.0 15.9 0.3
OD1 B:ASP301 3.1 17.9 0.3
CG B:ASP301 3.1 15.6 0.3
CX B:KCX169 3.2 18.9 0.5
CD2 B:HIS55 3.3 13.2 0.2
O1 B:CAC404 3.5 23.4 0.6
AS B:CAC404 3.5 59.3 0.6
CD2 B:HIS55 3.6 11.1 0.8
CD2 B:HIS230 3.6 17.5 0.2
O B:HOH785 3.8 13.3 0.5
CE1 B:HIS55 3.8 17.2 0.2
CD2 B:HIS230 3.8 25.1 0.8
ND1 B:HIS230 3.8 17.3 0.8
ND1 B:HIS55 3.9 15.3 0.8
NE2 B:HIS57 4.0 15.0 1.0
ND1 B:HIS230 4.1 18.9 0.2
CB B:ASP301 4.2 12.4 0.7
CB B:ASP301 4.2 12.6 0.3
CG B:HIS55 4.3 13.9 0.8
NZ B:KCX169 4.4 16.9 0.5
CG B:HIS230 4.4 16.6 0.8
CG B:HIS230 4.5 17.2 0.2
NZ B:KCX169 4.5 24.3 0.5
CG B:HIS55 4.6 16.8 0.2
ND1 B:HIS201 4.6 22.7 0.4
CE1 B:HIS201 4.7 23.7 0.6
NE B:ARG254 4.7 22.9 1.0
ND1 B:HIS201 4.7 18.4 0.6
ND1 B:HIS55 4.7 20.9 0.2
CE1 B:HIS57 4.8 12.1 1.0
C2 B:CAC404 4.8 35.3 0.6
O B:HOH695 4.9 34.0 1.0
NE2 B:HIS201 4.9 19.9 0.6
CD B:ARG254 4.9 17.9 1.0
CD2 B:HIS57 5.0 16.0 1.0

Reference:

N.Tokuriki, C.J.Jackson, L.Afriat-Jurnou, K.T.Wyganowski, R.Tang, D.S.Tawfik. Diminishing Returns and Tradeoffs Constrain the Laboratory Optimization of An Enzyme Nat Commun V. 3 1257 2012.
ISSN: ESSN 2041-1723
PubMed: 23212386
DOI: 10.1038/NCOMMS2246
Page generated: Sat Oct 26 23:45:14 2024

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