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Zinc in PDB 3ddb: Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Serotype A with A Substrate Analog Peptide

Enzymatic activity of Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Serotype A with A Substrate Analog Peptide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Serotype A with A Substrate Analog Peptide:
3.4.24.69;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Serotype A with A Substrate Analog Peptide, PDB code: 3ddb 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) 32.42 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.871, 66.581, 65.062, 90.00, 98.34, 90.00
R / Rfree (%) 20 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Serotype A with A Substrate Analog Peptide (pdb code 3ddb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Serotype A with A Substrate Analog Peptide, PDB code: 3ddb:

Zinc binding site 1 out of 1 in 3ddb

Go back to Zinc Binding Sites List in 3ddb
Zinc binding site 1 out of 1 in the Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Serotype A with A Substrate Analog Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Serotype A with A Substrate Analog Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:17.4
occ:1.00
 OE1 A:GLU262 2.0 16.9 1.0
NE2 A:HIS227 2.2 15.3 1.0
NE2 A:HIS223 2.2 15.4 1.0
N B:ARG197 2.2 20.8 1.0
O B:ARG197 2.4 18.7 1.0
OE2 A:GLU262 2.5 21.4 1.0
CD A:GLU262 2.6 18.8 1.0
C B:ARG197 2.9 20.6 1.0
CD2 A:HIS227 3.0 16.9 1.0
CA B:ARG197 3.0 21.3 1.0
CD2 A:HIS223 3.1 12.0 1.0
CE1 A:HIS223 3.2 13.3 1.0
CE1 A:HIS227 3.2 15.6 1.0
CB B:ARG197 3.6 24.7 1.0
OH A:TYR366 4.1 16.1 1.0
CG A:GLU262 4.1 16.6 1.0
N B:ARG198 4.1 20.8 1.0
OE2 A:GLU224 4.2 17.6 1.0
CG A:HIS227 4.2 14.4 1.0
CG A:HIS223 4.3 12.7 1.0
ND1 A:HIS227 4.3 15.5 1.0
ND1 A:HIS223 4.3 12.7 1.0
O B:HOH151 4.5 24.7 1.0
CE1 A:TYR366 4.5 13.4 1.0
CZ A:TYR366 4.6 14.4 1.0
OE1 A:GLU224 4.7 14.5 1.0
CB A:GLU262 4.8 14.6 1.0
CD A:GLU224 4.8 15.8 1.0
CA B:ARG198 4.9 19.3 1.0
CG2 A:THR265 4.9 12.7 1.0
CA A:GLU262 5.0 14.4 1.0

Reference:

D.Kumaran, R.Rawat, S.A.Ahmed, S.Swaminathan. Substrate Binding Mode and Its Implication on Drug Design For Botulinum Neurotoxin A Plos Pathog. V. 4 E1000 2008.
ISSN: ISSN 1553-7366
PubMed: 18818739
DOI: 10.1371/JOURNAL.PPAT.1000165
Page generated: Wed Dec 16 04:12:50 2020

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