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Calcium in PDB 2np0: Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain

Enzymatic activity of Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain

All present enzymatic activity of Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain:
3.4.24.69;

Protein crystallography data

The structure of Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain, PDB code: 2np0 was solved by Q.Chai, J.W.Arndt, R.C.Stevens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.62
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 170.415, 351.971, 101.968, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.7

Other elements in 2np0:

The structure of Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain (pdb code 2np0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain, PDB code: 2np0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2np0

Go back to Calcium Binding Sites List in 2np0
Calcium binding site 1 out of 3 in the Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1292

b:48.7
occ:1.00
 O A:ILE279 2.3 38.1 1.0
ND2 A:ASN483 2.4 41.2 1.0
O A:PRO276 2.6 39.5 1.0
OD2 A:ASP284 2.6 41.1 1.0
OD1 A:ASP284 2.9 37.7 1.0
CG A:ASP284 3.1 39.9 1.0
CG A:ASN483 3.4 44.3 1.0
C A:ILE279 3.4 38.7 1.0
C A:PRO276 3.5 40.0 1.0
OD1 A:ASN483 3.6 44.1 1.0
CB A:ILE279 3.9 39.4 1.0
CA A:ILE279 4.1 38.9 1.0
CA A:SER277 4.2 39.1 1.0
N A:SER277 4.3 39.4 1.0
O A:THR280 4.4 39.7 1.0
N A:ILE279 4.4 38.8 1.0
C A:THR280 4.4 38.7 1.0
CG2 A:ILE279 4.4 38.5 1.0
N A:THR280 4.5 38.7 1.0
CA A:PRO276 4.5 40.8 1.0
CB A:ASP284 4.6 39.7 1.0
CB A:PRO276 4.6 40.2 1.0
O A:HOH1407 4.6 23.5 1.0
C A:SER277 4.6 39.2 1.0
N A:PRO281 4.7 38.2 1.0
CB A:ASN483 4.7 46.2 1.0
CE1 A:TYR269 4.8 43.1 1.0
CA A:THR280 4.8 38.3 1.0
O A:SER277 4.9 38.9 1.0
OH A:TYR269 4.9 44.1 1.0
O A:HOH1437 4.9 47.2 1.0

Calcium binding site 2 out of 3 in 2np0

Go back to Calcium Binding Sites List in 2np0
Calcium binding site 2 out of 3 in the Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1293

b:68.0
occ:1.00
 O A:LYS567 2.4 39.2 1.0
O A:ALA561 2.4 40.4 1.0
O A:PHE564 2.5 40.6 1.0
O A:HOH1648 2.5 44.6 1.0
C A:ALA561 3.4 40.6 1.0
C A:LYS567 3.6 39.0 1.0
C A:PHE564 3.6 40.6 1.0
CA A:ALA561 3.9 40.6 1.0
CA A:SER565 4.0 39.9 1.0
O A:THR544 4.0 42.1 1.0
O A:SER565 4.0 39.1 1.0
C A:SER565 4.1 39.2 1.0
N A:LYS567 4.2 39.3 1.0
N A:SER565 4.3 40.0 1.0
CA A:LYS567 4.4 39.2 1.0
CB A:ALA561 4.4 40.0 1.0
N A:VAL568 4.5 38.5 1.0
N A:LEU562 4.6 40.7 1.0
CA A:VAL568 4.6 38.0 1.0
CB A:LYS567 4.6 39.7 1.0
O A:SER542 4.6 41.0 1.0
CA A:PHE564 4.8 41.2 1.0
N A:ASN566 4.8 39.1 1.0
N A:PHE564 4.9 41.4 1.0
CG2 A:VAL568 4.9 37.2 1.0
CA A:LEU562 4.9 41.2 1.0
O A:ASP560 5.0 41.0 1.0

Calcium binding site 3 out of 3 in 2np0

Go back to Calcium Binding Sites List in 2np0
Calcium binding site 3 out of 3 in the Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Botulinum Neurotoxin Type B Complexed with Synaptotagamin-II Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1295

b:44.1
occ:1.00
 O A:LEU453 2.5 43.1 1.0
O A:GLU451 2.7 49.0 1.0
O A:HOH1517 2.8 42.1 1.0
OE1 A:GLN258 2.9 47.9 1.0
O A:HOH1677 3.1 34.5 1.0
CD A:GLN258 3.6 42.9 1.0
C A:LEU453 3.7 43.2 1.0
OD1 A:ASP375 3.8 53.6 1.0
C A:GLU451 3.8 48.0 1.0
O A:HOH1326 4.0 42.7 1.0
OG1 A:THR713 4.1 42.8 1.0
N A:PHE455 4.1 41.4 1.0
NE2 A:GLN258 4.2 44.3 1.0
O A:HOH1586 4.2 36.8 1.0
C A:ASP452 4.2 45.4 1.0
N A:LEU453 4.2 44.5 1.0
O A:ASP452 4.5 44.7 1.0
CG A:GLN258 4.5 42.2 1.0
CA A:ASP452 4.6 46.5 1.0
CA A:LEU453 4.6 43.8 1.0
N A:PHE454 4.6 42.8 1.0
CA A:PHE454 4.6 42.3 1.0
C A:PHE454 4.6 42.0 1.0
CB A:GLN258 4.6 41.8 1.0
N A:ASP452 4.6 47.4 1.0
CA A:GLU451 4.7 48.4 1.0
CB A:PHE455 4.7 41.0 1.0
CA A:PHE455 5.0 41.1 1.0
CG A:ASP375 5.0 51.7 1.0

Reference:

Q.Chai, J.W.Arndt, M.Dong, W.H.Tepp, E.A.Johnson, E.R.Chapman, R.C.Stevens. Structural Basis of Cell Surface Receptor Recognition By Botulinum Neurotoxin B. Nature V. 444 1096 2006.
ISSN: ISSN 0028-0836
PubMed: 17167418
DOI: 10.1038/NATURE05411
Page generated: Fri Jul 12 14:27:48 2024

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