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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: Sun Oct 6 18:18:42 2024

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