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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 6frw

Go back to Zinc Binding Sites List in 6frw
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 6frw

Go back to Zinc Binding Sites List in 6frw
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 6frw

Go back to Zinc Binding Sites List in 6frw
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

Reference:

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
Page generated: Wed Dec 16 11:49:11 2020

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