Atomistry » Sodium » PDB 1oar-1ph6 » 1p9e
Atomistry »
  Sodium »
    PDB 1oar-1ph6 »
      1p9e »

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

Go back to Sodium Binding Sites List in 1p9e
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

Go back to Sodium Binding Sites List in 1p9e
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy