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Zinc in PDB 1p9e: Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3

Enzymatic activity of Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3

All present enzymatic activity of Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3:
3.1.8.1;

Protein crystallography data

The structure of Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3, PDB code: 1p9e was solved by Y.Dong, L.Sun, M.Bartlam, Z.Rao, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.020, 85.020, 199.773, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.9

Other elements in 1p9e:

The structure of Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3 also contains other interesting chemical elements:

Potassium (K) 4 atoms
Cadmium (Cd) 1 atom
Sodium (Na) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3 (pdb code 1p9e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3, PDB code: 1p9e:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1p9e

Go back to Zinc Binding Sites List in 1p9e
Zinc binding site 1 out of 3 in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:18.4
occ:1.00
NE2 A:HIS152 2.1 20.6 1.0
OD2 A:ASP151 2.2 24.4 1.0
NE2 A:HIS302 2.2 17.2 1.0
O A:HOH608 2.2 10.7 1.0
OD2 A:ASP255 2.2 20.5 1.0
OD1 A:ASP255 2.7 22.0 1.0
CG A:ASP255 2.8 22.2 1.0
CD2 A:HIS152 3.0 21.3 1.0
CE1 A:HIS302 3.1 17.5 1.0
CG A:ASP151 3.1 25.9 1.0
CE1 A:HIS152 3.2 22.1 1.0
CD2 A:HIS302 3.2 19.1 1.0
OD1 A:ASP151 3.5 26.0 1.0
ZN A:ZN402 3.7 10.7 1.0
NE2 A:HIS147 4.0 24.9 1.0
CG A:HIS152 4.2 21.9 1.0
CE1 A:HIS147 4.2 25.2 1.0
ND1 A:HIS302 4.2 19.3 1.0
ND1 A:HIS152 4.3 22.9 1.0
CG A:HIS302 4.3 18.9 1.0
CB A:ASP255 4.4 20.9 1.0
O A:HOH772 4.4 12.8 1.0
CB A:ASP151 4.5 24.7 1.0
CB A:SER301 4.7 22.4 1.0

Zinc binding site 2 out of 3 in 1p9e

Go back to Zinc Binding Sites List in 1p9e
Zinc binding site 2 out of 3 in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:10.7
occ:1.00
NE2 A:HIS234 2.1 21.9 1.0
ND1 A:HIS149 2.1 27.5 1.0
O A:HOH608 2.2 10.7 1.0
OD2 A:ASP255 2.2 20.5 1.0
NE2 A:HIS147 2.4 24.9 1.0
O A:HOH772 2.5 12.8 1.0
CE1 A:HIS149 2.8 27.9 1.0
CD2 A:HIS234 3.0 24.4 1.0
CD2 A:HIS147 3.1 24.8 1.0
CE1 A:HIS234 3.1 24.4 1.0
CG A:HIS149 3.2 27.6 1.0
CG A:ASP255 3.3 22.2 1.0
CE1 A:HIS147 3.5 25.2 1.0
ZN A:ZN401 3.7 18.4 1.0
CB A:HIS149 3.7 28.3 1.0
CB A:ASP255 3.8 20.9 1.0
NE2 A:HIS149 4.0 26.9 1.0
ND1 A:HIS234 4.2 22.2 1.0
CD2 A:HIS149 4.2 26.0 1.0
CG A:HIS234 4.2 23.2 1.0
CG A:HIS147 4.3 26.4 1.0
OD1 A:ASP255 4.4 22.0 1.0
NE2 A:HIS152 4.4 20.6 1.0
ND1 A:HIS147 4.5 25.7 1.0
CD2 A:HIS152 4.6 21.3 1.0
OD1 A:ASP151 4.7 26.0 1.0

Zinc binding site 3 out of 3 in 1p9e

Go back to Zinc Binding Sites List in 1p9e
Zinc binding site 3 out of 3 in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1401

b:16.1
occ:1.00
NE2 B:HIS152 2.1 22.9 1.0
NE2 B:HIS302 2.2 21.4 1.0
OD2 B:ASP151 2.3 30.3 1.0
O B:HOH666 2.3 13.6 1.0
OD2 B:ASP255 2.4 21.2 1.0
OD1 B:ASP255 2.7 18.5 1.0
CG B:ASP255 2.9 21.6 1.0
CE1 B:HIS302 3.0 19.8 1.0
CG B:ASP151 3.1 28.5 1.0
CD2 B:HIS152 3.1 22.4 1.0
OD1 B:ASP151 3.1 28.4 1.0
CE1 B:HIS152 3.2 24.6 1.0
CD2 B:HIS302 3.3 20.6 1.0
CD B:CD1402 3.8 29.8 1.0
NE2 B:HIS147 4.1 25.2 1.0
ND1 B:HIS302 4.2 20.2 1.0
ND1 B:HIS152 4.3 23.6 1.0
CG B:HIS152 4.3 24.2 1.0
O B:HOH609 4.3 12.9 1.0
CE1 B:HIS147 4.3 25.2 1.0
CG B:HIS302 4.3 20.0 1.0
CB B:ASP255 4.4 21.4 1.0
CB B:ASP151 4.5 27.3 1.0
CB B:SER301 4.8 25.4 1.0

Reference:

Y.Dong, L.Sun, M.Bartlam, Z.Rao, X.Zhang. Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3 To Be Published.
Page generated: Wed Dec 16 03:00:35 2020

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