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Sodium 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
Zinc (Zn) 3 atoms
Cadmium (Cd) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3, PDB code: 1p9e:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 1p9e

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Sodium binding site 1 out of 5 in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na505

b:27.2
occ:1.00
 K A:K501 2.8 4.3 1.0
CD A:LYS214 3.2 34.2 1.0
NZ A:LYS214 3.6 36.9 1.0
CG2 A:VAL168 3.6 26.8 1.0
NE A:ARG170 3.9 35.3 1.0
CE A:LYS214 4.0 37.0 1.0
OE1 A:GLU142 4.1 28.9 1.0
CD A:ARG170 4.2 32.6 1.0
OE2 A:GLU142 4.4 31.6 1.0
CB A:VAL168 4.4 27.4 1.0
CG A:LYS214 4.4 31.5 1.0
CB A:LYS214 4.5 29.0 1.0
O A:HOH693 4.5 18.9 1.0
CD A:GLU142 4.5 30.0 1.0
CZ A:ARG170 4.6 35.3 1.0
CG1 A:VAL168 4.6 26.7 1.0
NH2 A:ARG170 4.9 35.3 1.0

Sodium binding site 2 out of 5 in 1p9e

Go back to Sodium Binding Sites List in 1p9e
Sodium binding site 2 out of 5 in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na506

b:17.0
occ:1.00
 OE2 A:GLU244 2.7 40.6 1.0
CD A:GLU244 3.3 38.7 1.0
CG A:GLU244 3.7 34.3 1.0
N A:GLY247 4.1 27.5 1.0
OE1 A:GLU244 4.2 40.0 1.0
N A:GLN246 4.2 28.1 1.0
CA A:GLN246 4.8 27.3 1.0
O A:GLU244 4.8 25.4 1.0
C A:SER245 4.8 27.2 1.0
CA A:GLY247 4.8 26.8 1.0
CA A:SER245 4.9 26.5 1.0
C A:GLN246 4.9 27.3 1.0

Sodium binding site 3 out of 5 in 1p9e

Go back to Sodium Binding Sites List in 1p9e
Sodium binding site 3 out of 5 in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na507

b:16.4
occ:1.00
 OE2 B:GLU138 2.6 41.7 1.0
NE2 B:GLN136 2.7 40.8 1.0
OE1 B:GLU138 2.7 40.2 1.0
CD B:GLU138 3.0 38.9 1.0
CD B:GLN136 3.7 40.9 1.0
CG B:GLN136 4.0 37.1 1.0
CD B:PRO137 4.1 28.2 1.0
CG B:GLU138 4.5 34.7 1.0
CB B:GLN136 4.7 33.3 1.0
OE1 B:GLN136 4.8 40.5 1.0
CG B:PRO137 4.8 29.0 1.0
CE B:LYS131 4.8 36.2 1.0
N B:PRO137 5.0 28.3 1.0

Sodium binding site 4 out of 5 in 1p9e

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Sodium binding site 4 out of 5 in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 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:Na508

b:15.9
occ:1.00
 ND1 B:HIS232 2.6 30.5 1.0
NZ B:LYS174 2.7 47.3 1.0
CG B:HIS232 3.5 31.0 1.0
O B:HOH720 3.6 36.6 1.0
CE1 B:HIS232 3.6 30.4 1.0
CB B:HIS232 3.7 28.8 1.0
CE B:LYS174 3.9 46.1 1.0
CD B:LYS174 3.9 44.1 1.0
O B:PRO236 4.1 29.8 1.0
CD2 B:HIS232 4.7 30.4 1.0
NE2 B:HIS232 4.7 30.9 1.0
O B:HOH727 5.0 35.7 1.0

Sodium binding site 5 out of 5 in 1p9e

Go back to Sodium Binding Sites List in 1p9e
Sodium binding site 5 out of 5 in the Crystal Structure Analysis of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 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:Na509

b:18.6
occ:1.00
 OD2 B:ASP221 2.5 38.5 1.0
OD1 B:ASP221 2.6 35.7 1.0
NZ B:LYS227 2.7 35.8 1.0
CG B:ASP221 2.8 34.9 1.0
CE B:LYS227 3.5 34.2 1.0
CB B:ASP221 4.3 31.5 1.0
CD B:LYS227 4.4 31.8 1.0
CG B:LYS227 4.9 30.9 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: Sun Oct 6 21:14:55 2024

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