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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: Wed Dec 16 05:51:37 2020

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