Atomistry » Zinc » PDB 4wnt-4x3o » 4wtb
Atomistry »
  Zinc »
    PDB 4wnt-4x3o »
      4wtb »

Zinc in PDB 4wtb: Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions

Protein crystallography data

The structure of Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions, PDB code: 4wtb was solved by R.J.Borges, M.R.M.Fontes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.83 / 2.16
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 56.580, 56.580, 129.530, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 23.4

Other elements in 4wtb:

The structure of Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions (pdb code 4wtb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions, PDB code: 4wtb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4wtb

Go back to Zinc Binding Sites List in 4wtb
Zinc binding site 1 out of 3 in the Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:39.7
occ:0.54
ND1 A:HIS47 2.1 26.0 1.0
O A:HOH347 2.1 33.5 0.7
O A:HOH349 2.1 33.0 1.0
O A:HOH350 2.1 32.3 0.7
CE1 A:HIS47 2.8 21.8 1.0
CG A:HIS47 3.3 24.4 1.0
CB A:HIS47 3.8 20.2 1.0
NE2 A:HIS47 4.0 24.1 1.0
NZ A:LYS48 4.2 36.7 1.0
CD2 A:HIS47 4.2 21.4 1.0
CE2 A:TYR51 4.4 18.8 1.0
CG A:LYS48 4.4 26.2 1.0
N A:LYS48 4.7 22.8 1.0
O A:CYS44 4.7 24.1 1.0
C A:HIS47 4.7 28.5 1.0
CD2 A:LEU5 4.8 18.5 1.0
CZ A:TYR51 4.8 21.5 1.0
CD2 A:TYR51 4.9 26.6 1.0
OH A:TYR51 4.9 23.1 1.0
CA A:HIS47 4.9 26.1 1.0

Zinc binding site 2 out of 3 in 4wtb

Go back to Zinc Binding Sites List in 4wtb
Zinc binding site 2 out of 3 in the Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:38.8
occ:0.69
ND1 A:HIS110 2.0 35.7 1.0
O A:HOH304 2.1 40.2 0.9
O A:HOH344 2.1 30.0 1.0
O A:HOH345 2.1 31.8 1.0
CE1 A:HIS110 2.9 32.6 1.0
CG A:HIS110 3.1 33.6 1.0
CB A:HIS110 3.6 35.3 1.0
CA A:HIS110 3.8 38.3 1.0
O2 A:SO4203 3.8 45.7 0.7
NE2 A:HIS110 4.0 36.2 1.0
CD2 A:HIS110 4.2 36.8 1.0
N A:LEU111 4.2 40.8 1.0
C A:HIS110 4.5 38.9 1.0
CE A:LYS37 4.9 33.0 1.0
CD2 A:TYR107 4.9 34.8 1.0
N A:HIS110 5.0 47.7 1.0
CD2 A:PHE114 5.0 47.6 1.0
O A:HOH308 5.0 48.4 1.0

Zinc binding site 3 out of 3 in 4wtb

Go back to Zinc Binding Sites List in 4wtb
Zinc binding site 3 out of 3 in the Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bthtx-I, A SVPLA2S-Like Toxin, Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:51.8
occ:0.58
ND1 B:HIS110 2.0 48.2 1.0
O B:HOH341 2.1 51.9 0.9
CE1 B:HIS110 2.9 40.5 1.0
CG B:HIS110 3.1 42.0 1.0
O A:HOH341 3.4 39.4 1.0
CB B:HIS110 3.5 38.5 1.0
NE2 B:HIS110 4.1 39.9 1.0
CD2 B:HIS110 4.2 42.5 1.0
CB A:ALA18 4.6 31.3 1.0
ND2 A:ASN16 4.9 38.9 1.0
CA B:HIS110 5.0 39.8 1.0

Reference:

R.J.Borges, F.F.Cardoso, C.A.Fernandes, T.R.Dreyer, D.S.De Moraes, R.S.Floriano, L.Rodrigues-Simioni, M.R.Fontes. Functional and Structural Studies of A Phospholipase A2-Like Protein Complexed to Zinc Ions: Insights on Its Myotoxicity and Inhibition Mechanism. Biochim. Biophys. Acta V.1861 3199 2017.
ISSN: ISSN 0006-3002
PubMed: 27531710
DOI: 10.1016/J.BBAGEN.2016.08.003
Page generated: Sun Oct 27 10:04:54 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy