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Sodium in PDB 1tc8: Crystal Structure of Krait-Venom Phospholipase A2 in A Complex with A Natural Fatty Acid Tridecanoic Acid

Enzymatic activity of Crystal Structure of Krait-Venom Phospholipase A2 in A Complex with A Natural Fatty Acid Tridecanoic Acid

All present enzymatic activity of Crystal Structure of Krait-Venom Phospholipase A2 in A Complex with A Natural Fatty Acid Tridecanoic Acid:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Krait-Venom Phospholipase A2 in A Complex with A Natural Fatty Acid Tridecanoic Acid, PDB code: 1tc8 was solved by G.Singh, J.Jasti, K.Saravanan, S.Sharma, P.Kaur, A.Srinivasan, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.790, 53.790, 82.500, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Krait-Venom Phospholipase A2 in A Complex with A Natural Fatty Acid Tridecanoic Acid (pdb code 1tc8). 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 Crystal Structure of Krait-Venom Phospholipase A2 in A Complex with A Natural Fatty Acid Tridecanoic Acid, PDB code: 1tc8:

Sodium binding site 1 out of 1 in 1tc8

Go back to Sodium Binding Sites List in 1tc8
Sodium binding site 1 out of 1 in the Crystal Structure of Krait-Venom Phospholipase A2 in A Complex with A Natural Fatty Acid Tridecanoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Krait-Venom Phospholipase A2 in A Complex with A Natural Fatty Acid Tridecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na121

b:33.0
occ:1.00
 OD2 A:ASP49 2.5 25.4 1.0
O A:GLY32 2.6 36.0 1.0
O A:TYR28 2.7 31.3 1.0
O A:GLY30 2.7 37.5 1.0
OD1 A:ASP49 2.8 24.0 1.0
C A:GLY32 2.9 36.6 1.0
CG A:ASP49 3.0 23.5 1.0
N A:GLY32 3.2 37.1 1.0
CA A:GLY32 3.4 36.9 1.0
O A:HOH159 3.4 42.5 1.0
N A:GLY33 3.6 36.9 1.0
C A:LYS31 3.7 37.4 1.0
C A:TYR28 3.7 30.2 1.0
C A:GLY30 3.8 37.0 1.0
CA A:GLY33 4.1 37.0 1.0
CA A:TYR28 4.2 29.5 1.0
O A:LYS31 4.3 35.9 1.0
NH2 A:ARG114 4.3 66.4 1.0
CA A:LYS31 4.4 38.0 1.0
N A:GLY30 4.4 33.0 1.0
O A:HOH129 4.5 40.1 1.0
CB A:ASP49 4.5 21.9 1.0
CD2 A:TYR28 4.5 28.7 1.0
CB A:TYR28 4.5 29.6 1.0
N A:LYS31 4.5 38.1 1.0
CA A:GLY30 4.8 35.1 1.0
N A:CYS29 4.9 29.6 1.0
O A:HOH168 4.9 70.5 1.0
O A:CYS45 4.9 23.7 1.0
C A:CYS29 5.0 32.3 1.0
CG A:TYR28 5.0 28.5 1.0

Reference:

G.Singh, J.Jasti, K.Saravanan, S.Sharma, P.Kaur, A.Srinivasan, T.P.Singh. Crystal Structure of the Complex Formed Between A Group I Phospholipase A2 and A Naturally Occurring Fatty Acid at 2.7 A Resolution Protein Sci. V. 14 395 2005.
ISSN: ISSN 0961-8368
PubMed: 15659372
DOI: 10.1110/PS.041115505
Page generated: Sun Aug 17 07:51:56 2025

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