Atomistry » Sodium » PDB 1det-1ev6 » 1dpy
Atomistry »
  Sodium »
    PDB 1det-1ev6 »
      1dpy »

Sodium in PDB 1dpy: Three-Dimensional Structure of A Novel Phospholipase A2 From Indian Common Krait at 2.45 A Resolution

Enzymatic activity of Three-Dimensional Structure of A Novel Phospholipase A2 From Indian Common Krait at 2.45 A Resolution

All present enzymatic activity of Three-Dimensional Structure of A Novel Phospholipase A2 From Indian Common Krait at 2.45 A Resolution:
3.1.1.4;

Protein crystallography data

The structure of Three-Dimensional Structure of A Novel Phospholipase A2 From Indian Common Krait at 2.45 A Resolution, PDB code: 1dpy was solved by G.Singh, S.Gourinath, S.Sharma, M.Paramasivam, A.Srinivasan, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.99 / 2.45
Space group R 3 2
Cell size a, b, c (Å), α, β, γ (°) 57.980, 57.980, 57.980, 92.02, 92.02, 92.02
R / Rfree (%) 20.2 / 28.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Three-Dimensional Structure of A Novel Phospholipase A2 From Indian Common Krait at 2.45 A Resolution (pdb code 1dpy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Three-Dimensional Structure of A Novel Phospholipase A2 From Indian Common Krait at 2.45 A Resolution, PDB code: 1dpy:

Sodium binding site 1 out of 1 in 1dpy

Go back to Sodium Binding Sites List in 1dpy
Sodium binding site 1 out of 1 in the Three-Dimensional Structure of A Novel Phospholipase A2 From Indian Common Krait at 2.45 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Three-Dimensional Structure of A Novel Phospholipase A2 From Indian Common Krait at 2.45 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na150

b:4.9
occ:1.00
 O A:GLY30 2.6 33.4 1.0
O A:TYR28 2.6 22.7 1.0
OD2 A:ASP49 2.7 32.1 1.0
O A:GLY32 2.8 31.3 1.0
OD1 A:ASP49 2.9 31.0 1.0
CG A:ASP49 3.1 29.2 1.0
O A:HOH263 3.5 30.2 1.0
C A:GLY30 3.7 31.9 1.0
C A:TYR28 3.8 23.1 1.0
C A:GLY32 3.9 31.0 1.0
N A:GLY30 4.0 28.4 1.0
N A:GLY32 4.2 32.7 1.0
C A:LYS31 4.3 33.6 1.0
CB A:ASP49 4.4 26.2 1.0
CA A:GLY32 4.5 31.9 1.0
CA A:GLY30 4.5 31.0 1.0
CA A:TYR28 4.6 22.2 1.0
N A:LYS31 4.7 32.7 1.0
C A:CYS29 4.7 26.2 1.0
CA A:LYS31 4.7 33.6 1.0
O A:LYS31 4.7 35.6 1.0
CA A:CYS29 4.8 25.6 1.0
N A:CYS29 4.8 24.1 1.0
O A:CYS45 5.0 22.6 1.0
CB A:TYR28 5.0 22.4 1.0
N A:GLY33 5.0 29.4 1.0

Reference:

G.Singh, S.Gourinath, S.Sharma, M.Paramasivam, A.Srinivasan, T.P.Singh. Sequence and Crystal Structure Determination of A Basic Phospholipase A2 From Common Krait (Bungarus Caeruleus) at 2.4 A Resolution: Identification and Characterization of Its Pharmacological Sites. J.Mol.Biol. V. 307 1049 2001.
ISSN: ISSN 0022-2836
PubMed: 11286555
DOI: 10.1006/JMBI.2001.4550
Page generated: Tue Dec 15 05:23:14 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy