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Zinc in PDB 6rv5: X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis in Complex with Levanbiose

Enzymatic activity of X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis in Complex with Levanbiose

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

Protein crystallography data

The structure of X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis in Complex with Levanbiose, PDB code: 6rv5 was solved by I.Polsinelli, 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) 45.26 / 1.58
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.886, 127.886, 58.268, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 18.4

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis in Complex with Levanbiose (pdb code 6rv5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis in Complex with Levanbiose, PDB code: 6rv5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6rv5

Go back to Zinc Binding Sites List in 6rv5
Zinc binding site 1 out of 2 in the X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis in Complex with Levanbiose


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 in Complex with Levanbiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn512

b:37.1
occ:1.00
OD2 A:ASP52 2.0 29.4 1.0
O A:HOH866 2.1 27.6 1.0
OD2 A:ASP54 2.2 51.0 1.0
OD2 A:ASP56 2.2 33.8 1.0
CG A:ASP52 2.7 26.8 1.0
CG A:ASP54 2.8 41.8 1.0
OD1 A:ASP54 2.8 84.4 1.0
OD1 A:ASP52 3.0 22.6 1.0
CG A:ASP56 3.0 46.1 1.0
CB A:ASP56 3.4 30.0 1.0
O A:HOH828 3.7 58.2 1.0
NZ A:LYS410 3.9 22.5 0.3
OD1 A:ASP56 4.0 51.6 1.0
CE A:LYS410 4.0 25.6 0.4
O A:HOH898 4.1 31.7 1.0
CB A:ASP52 4.1 24.0 1.0
NZ A:LYS410 4.2 17.2 0.4
CB A:ASP54 4.2 29.6 1.0
CD A:LYS410 4.6 22.0 0.3
CE A:LYS410 4.6 25.1 0.3
N A:ASP56 4.6 26.1 1.0
CA A:ASP56 4.6 25.2 1.0
NZ A:LYS410 4.8 20.0 0.3
N A:ASP54 4.8 31.4 1.0
CA A:ASP54 5.0 28.3 1.0
O A:HOH849 5.0 48.0 1.0

Zinc binding site 2 out of 2 in 6rv5

Go back to Zinc Binding Sites List in 6rv5
Zinc binding site 2 out of 2 in the X-Ray Structure of the Levansucrase From Erwinia Tasmaniensis in Complex with Levanbiose


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 in Complex with Levanbiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn513

b:19.6
occ:0.85
OE1 A:GLU141 2.0 23.1 1.0
OD1 A:ASP140 2.1 19.9 1.0
O A:HOH923 2.1 20.2 1.0
O A:HOH865 2.3 30.3 1.0
CD A:GLU141 2.6 24.6 1.0
OE2 A:GLU141 2.6 20.9 1.0
CG A:ASP140 3.2 18.1 1.0
OD2 A:ASP140 3.6 24.1 1.0
CG A:GLU141 4.1 21.5 1.0
O A:HOH645 4.1 35.1 1.0
N A:ASP140 4.3 16.3 1.0
N A:GLU141 4.4 16.6 1.0
CB A:ASP140 4.4 20.8 1.0
O A:HOH963 4.5 45.9 1.0
C A:ASP140 4.5 16.9 1.0
CG A:LYS415 4.6 36.9 1.0
CA A:ASP140 4.6 17.6 1.0
CB A:ASN139 4.7 19.5 1.0
O A:HOH780 4.7 31.2 1.0

Reference:

I.Polsinelli, R.Caliandro, N.Demitri, S.Benini. The Structure of Sucrose-Soaked Levansucrase Crystals From Erwinia Tasmaniensis Reveals A Binding Pocket For Levanbiose Int J Mol Sci 2020.
ISSN: ESSN 1422-0067
Page generated: Wed Dec 16 12:42:39 2020

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