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Sodium in PDB 3qw8: Crystal Structure of the Protease Domain of Botulinum Neurotoxin Serotype A with A Peptide Inhibitor Crgc

Enzymatic activity of Crystal Structure of the Protease Domain of Botulinum Neurotoxin Serotype A with A Peptide Inhibitor Crgc

All present enzymatic activity of Crystal Structure of the Protease Domain of Botulinum Neurotoxin Serotype A with A Peptide Inhibitor Crgc:
3.4.24.69;

Protein crystallography data

The structure of Crystal Structure of the Protease Domain of Botulinum Neurotoxin Serotype A with A Peptide Inhibitor Crgc, PDB code: 3qw8 was solved by D.Kumaran, S.Swaminathan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.44 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.668, 66.278, 64.768, 90.00, 98.42, 90.00
R / Rfree (%) 19.9 / 21.7

Other elements in 3qw8:

The structure of Crystal Structure of the Protease Domain of Botulinum Neurotoxin Serotype A with A Peptide Inhibitor Crgc also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Protease Domain of Botulinum Neurotoxin Serotype A with A Peptide Inhibitor Crgc (pdb code 3qw8). 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 the Protease Domain of Botulinum Neurotoxin Serotype A with A Peptide Inhibitor Crgc, PDB code: 3qw8:

Sodium binding site 1 out of 1 in 3qw8

Go back to Sodium Binding Sites List in 3qw8
Sodium binding site 1 out of 1 in the Crystal Structure of the Protease Domain of Botulinum Neurotoxin Serotype A with A Peptide Inhibitor Crgc


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 the Protease Domain of Botulinum Neurotoxin Serotype A with A Peptide Inhibitor Crgc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:76.0
occ:1.00
 O2 A:EDO506 2.1 30.3 1.0
SG B:CYS196 2.1 28.8 1.0
NE2 A:GLN162 2.2 35.6 1.0
C2 A:EDO506 3.0 29.1 1.0
CB B:CYS196 3.1 19.9 1.0
CD A:GLN162 3.3 32.8 1.0
O A:PHE163 3.3 15.9 1.0
CB A:GLU164 3.5 21.4 1.0
CD A:GLU164 3.6 28.0 1.0
O A:HOH686 3.6 23.0 1.0
CG A:GLN162 3.8 28.1 1.0
OE2 A:GLU164 3.8 31.3 1.0
CA B:CYS196 3.8 17.7 1.0
OE1 A:GLU164 3.9 26.7 1.0
CG A:GLU164 3.9 24.8 1.0
O A:HOH792 4.1 36.7 1.0
OE1 A:GLN162 4.3 35.8 1.0
C1 A:EDO506 4.3 30.1 1.0
C A:PHE163 4.3 15.7 1.0
CA A:GLU164 4.5 18.1 1.0
O1 A:EDO506 4.6 33.6 1.0
O A:HOH629 4.8 21.0 1.0
N B:CYS196 4.8 16.7 1.0
C A:GLN162 4.9 15.9 1.0
C B:CYS196 4.9 17.8 1.0
N A:GLU164 4.9 16.2 1.0
N B:ARG197 5.0 19.0 1.0

Reference:

G.Kumar, D.Kumaran, S.A.Ahmed, S.Swaminathan. Peptide Inhibitors of Botulinum Neurotoxin Serotype A: Design, Inhibition, Cocrystal Structures, Structure-Activity Relationship and Pharmacophore Modeling. Acta Crystallogr.,Sect.D V. 68 511 2012.
ISSN: ISSN 0907-4449
PubMed: 22525749
DOI: 10.1107/S0907444912003551
Page generated: Mon Oct 7 12:43:30 2024

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