Zinc in PDB 6frw: X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis

All present enzymatic activity of X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis:
2.4.1.10;

The structure of X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis, PDB code: 6frw was solved by I.Polsinelli, M.Salomone-Stagni, R.Caliandro, N.Demitri, S.Benini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.15 / 1.52
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.493, 128.493, 58.945, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.9

The binding sites of Zinc atom in the X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis (pdb code 6frw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis, PDB code: 6frw:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:20.2 occ:0.76 OE2 A:GLU141 2.0 26.7 1.0 OD1 A:ASP140 2.0 23.5 1.0 O A:HOH927 2.2 16.2 1.0 CD A:GLU141 2.7 22.7 1.0 OE1 A:GLU141 2.9 23.6 1.0 CG A:ASP140 3.1 23.9 1.0 HG3 A:LYS415 3.3 34.5 1.0 OD2 A:ASP140 3.5 24.1 1.0 H A:ASP140 3.5 26.8 1.0 HB2 A:ASN139 3.8 27.8 1.0 O A:HOH651 4.0 34.5 1.0 CG A:GLU141 4.2 22.1 1.0 H A:GLU141 4.2 26.9 1.0 CG A:LYS415 4.2 28.8 1.0 N A:ASP140 4.2 22.4 1.0 HE2 A:LYS415 4.3 36.4 1.0 HG3 A:GLU141 4.3 26.5 1.0 CB A:ASP140 4.4 23.9 1.0 HG2 A:LYS415 4.4 34.5 1.0 N A:GLU141 4.4 22.5 1.0 C A:ASP140 4.5 24.8 1.0 CA A:ASP140 4.6 20.1 1.0 HB2 A:LYS415 4.6 32.2 1.0 HG2 A:GLU141 4.7 26.5 1.0 HZ3 A:LYS415 4.8 35.0 1.0 CB A:ASN139 4.8 23.1 1.0 HB2 A:ASP140 4.9 28.7 1.0 O A:ASP140 4.9 23.8 1.0 HB3 A:ASP140 4.9 28.7 1.0

Zinc binding site 2 out of 3 in the X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:31.7 occ:0.75 OD2 A:ASP54 2.1 34.9 1.0 OD2 A:ASP52 2.2 30.9 1.0 O A:HOH857 2.3 26.4 1.0 OD1 A:ASP56 2.4 42.0 1.0 HB2 A:ASP56 2.6 35.8 1.0 CG A:ASP52 2.9 30.7 1.0 CG A:ASP54 2.9 36.3 1.0 OD1 A:ASP52 3.1 26.1 1.0 CG A:ASP56 3.1 37.1 1.0 HZ2 A:LYS410 3.1 27.4 0.4 OD1 A:ASP54 3.2 36.9 1.0 CB A:ASP56 3.3 29.8 1.0 HZ3 A:LYS410 3.6 31.6 0.1 HB3 A:ASP56 3.7 35.8 1.0 HD3 A:LYS410 3.8 31.9 0.5 HD2 A:LYS410 3.8 31.9 0.5 HZ2 A:LYS410 3.8 34.0 0.5 H A:ASP56 3.8 32.8 1.0 O A:HOH618 3.9 46.2 1.0 HD2 A:LYS410 4.0 32.7 0.4 NZ A:LYS410 4.0 22.8 0.4 OD2 A:ASP56 4.1 34.3 1.0 HD2 A:LYS410 4.2 32.6 0.1 CD A:LYS410 4.2 26.5 0.5 H A:ASP54 4.3 35.9 1.0 CB A:ASP52 4.3 27.7 1.0 HZ1 A:LYS410 4.3 27.4 0.4 CB A:ASP54 4.3 34.5 1.0 HZ3 A:LYS410 4.4 34.0 0.5 HZ3 A:LYS410 4.4 27.4 0.4 NZ A:LYS410 4.4 26.4 0.1 NZ A:LYS410 4.5 28.3 0.5 HB3 A:ASP54 4.5 41.4 1.0 N A:ASP56 4.5 27.3 1.0 CA A:ASP56 4.5 28.0 1.0 HE3 A:LYS410 4.6 33.0 0.4 CE A:LYS410 4.7 27.5 0.4 CD A:LYS410 4.8 27.3 0.4 HZ1 A:LYS410 4.8 31.6 0.1 HZ2 A:LYS410 4.8 31.6 0.1 HB2 A:ASP54 4.9 41.4 1.0 HE2 A:LYS410 5.0 32.4 0.1 CE A:LYS410 5.0 27.1 0.5

Zinc binding site 3 out of 3 in the X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn510 b:26.5 occ:0.45 OD1 A:ASP317 2.1 25.0 1.0 ND1 A:HIS305 2.2 27.5 1.0 O A:HOH925 2.3 24.6 1.0 OD2 A:ASP317 2.7 26.8 1.0 CG A:ASP317 2.7 22.1 1.0 HB3 A:HIS305 2.9 26.1 1.0 CG A:HIS305 3.1 25.9 1.0 CE1 A:HIS305 3.2 23.6 1.0 HA A:HIS305 3.3 26.9 1.0 CB A:HIS305 3.4 21.7 1.0 HE1 A:PHE349 3.4 46.8 1.0 HE1 A:HIS305 3.4 28.3 1.0 HD1 A:PHE349 3.6 39.3 1.0 H A:LYS306 3.8 24.6 1.0 CA A:HIS305 3.8 22.4 1.0 CE1 A:PHE349 4.0 39.0 1.0 CD1 A:PHE349 4.1 32.7 1.0 CB A:ASP317 4.2 19.2 1.0 HB2 A:HIS305 4.2 26.1 1.0 O A:HOH659 4.3 23.0 1.0 CD2 A:HIS305 4.3 29.3 1.0 H A:TYR307 4.3 28.4 1.0 NE2 A:HIS305 4.3 26.9 1.0 N A:LYS306 4.3 20.5 1.0 HB3 A:ASP317 4.4 23.0 1.0 HE1 A:TYR352 4.4 26.2 1.0 C A:HIS305 4.6 22.8 1.0 CE1 A:TYR352 4.6 21.9 1.0 HD2 A:TYR307 4.6 43.5 1.0 HB2 A:ASP317 4.7 23.0 1.0 HA A:ASP317 4.8 23.7 1.0 HB3 A:LYS306 4.8 25.4 1.0 HD1 A:TYR352 4.8 22.2 1.0 CD1 A:TYR352 4.8 18.5 1.0 HB2 A:TYR307 4.9 38.0 1.0 N A:HIS305 5.0 22.6 1.0

I.Polsinelli, R.Caliandro, M.Salomone-Stagni, N.Demitri, M.Rejzek, R.A.Field, S.Benini. Comparison of the Levansucrase From the Epiphyte Erwinia Tasmaniensis Vs Its Homologue From the Phytopathogen Erwinia Amylovora. Int. J. Biol. Macromol. V. 127 496 2019.
ISSN: ISSN 1879-0003
PubMed: 30660564
DOI: 10.1016/J.IJBIOMAC.2019.01.074