Zinc in PDB 7puj: Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis

Enzymatic activity of Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis

All present enzymatic activity of Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis:
3.2.1.52;

Protein crystallography data

The structure of Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis, PDB code: 7puj was solved by M.Garcia-Alija, J.J.Du, B.Trastoy, E.J.Sundberg, M.E.Guerin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.82 / 1.75
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 112.15, 112.15, 64.62, 90, 90, 120
R / Rfree (%) 18.6 / 22

Other elements in 7puj:

The structure of Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis (pdb code 7puj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis, PDB code: 7puj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7puj

Go back to Zinc Binding Sites List in 7puj
Zinc binding site 1 out of 4 in the Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:25.2
occ:1.00
 OD1 A:ASP215 2.0 27.2 1.0
CL A:CL506 2.2 37.8 1.0
CL A:CL505 2.2 27.1 1.0
CG A:ASP215 2.9 24.1 1.0
OD2 A:ASP215 3.2 23.3 1.0
O A:HOH733 3.6 30.3 1.0
O A:HOH751 4.1 34.7 1.0
CG A:ARG216 4.2 27.0 1.0
CB A:ASP215 4.3 24.9 1.0
N A:ASP215 4.3 23.1 1.0
CA A:ASP215 4.6 24.3 1.0
C A:ASP215 4.7 24.2 1.0
N A:ARG216 4.8 23.0 1.0
CD A:ARG216 4.9 28.5 1.0
CB A:THR214 5.0 22.7 1.0

Zinc binding site 2 out of 4 in 7puj

Go back to Zinc Binding Sites List in 7puj
Zinc binding site 2 out of 4 in the Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:26.3
occ:0.32
 NZ A:LYS339 2.7 17.7 1.0
O A:HOH673 2.7 25.4 1.0
O A:HOH684 2.8 23.4 1.0
CE A:LYS339 3.4 21.8 1.0
CA A:THR406 3.5 20.5 1.0
O A:ASN405 3.5 27.2 1.0
O A:HOH698 3.6 27.3 1.0
O A:THR406 3.8 23.2 1.0
CD1 A:LEU335 3.8 17.6 1.0
C A:THR406 3.9 17.9 1.0
O A:HOH814 4.0 35.4 1.0
O A:ASN334 4.1 19.7 1.0
CB A:THR406 4.2 22.1 1.0
CG2 A:THR406 4.3 26.3 1.0
CG A:LEU335 4.3 18.7 1.0
C A:ASN405 4.4 26.6 1.0
N A:THR406 4.4 21.4 1.0
CB A:LEU335 4.4 17.1 1.0
O A:HOH623 4.6 21.7 1.0
C A:ASN334 4.6 18.7 1.0
O A:HOH638 4.8 20.9 1.0
CD A:LYS339 4.9 18.9 1.0
O A:ASP93 4.9 20.2 1.0
O A:HOH815 4.9 27.0 1.0
O A:TYR407 5.0 19.1 1.0

Zinc binding site 3 out of 4 in 7puj

Go back to Zinc Binding Sites List in 7puj
Zinc binding site 3 out of 4 in the Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:26.2
occ:0.27
 O A:ASP316 2.4 18.6 1.0
O A:LYS331 2.8 25.9 1.0
O A:HOH750 2.9 20.9 1.0
NH1 A:ARG320 3.2 23.9 1.0
C A:ASP316 3.5 17.3 1.0
CG A:ARG320 3.5 24.6 1.0
CD A:ARG320 3.6 21.9 1.0
CA A:ARG317 3.7 20.6 1.0
NE1 A:TRP88 3.8 19.7 1.0
CB A:SER333 3.8 18.4 1.0
C A:LYS331 3.9 23.3 1.0
N A:ARG317 4.0 17.2 1.0
C A:ARG317 4.1 17.4 1.0
C A:PRO332 4.2 22.2 1.0
CZ A:ARG320 4.2 27.9 1.0
O A:HOH633 4.2 21.1 1.0
N A:SER333 4.3 19.4 1.0
CE2 A:TRP88 4.3 23.4 1.0
O A:PRO332 4.3 23.5 1.0
O A:ASP318 4.4 19.1 1.0
NE A:ARG320 4.4 22.1 1.0
CZ2 A:TRP88 4.4 19.7 1.0
N A:ASP318 4.4 19.7 1.0
CA A:SER333 4.5 20.2 1.0
CD A:ARG317 4.5 21.0 1.0
N A:LYS331 4.6 25.8 1.0
CD1 A:TRP88 4.6 19.6 1.0
O A:ARG317 4.6 19.9 1.0
CA A:LYS331 4.7 25.0 1.0
CA A:PRO332 4.7 20.8 1.0
N A:PRO332 4.8 23.9 1.0
CA A:ASP316 4.8 18.3 1.0
OG A:SER333 4.8 19.2 1.0
NH1 A:ARG317 4.9 21.0 1.0
CB A:ARG317 4.9 20.9 1.0
CB A:LYS331 4.9 27.6 1.0

Zinc binding site 4 out of 4 in 7puj

Go back to Zinc Binding Sites List in 7puj
Zinc binding site 4 out of 4 in the Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Endoglycosidase E GH18 Domain From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:28.4
occ:0.45
 OD2 A:ASP221 2.0 31.3 0.5
OD2 A:ASP221 2.0 25.8 0.5
OD1 A:ASP184 2.0 31.5 0.5
O A:HOH700 2.1 37.4 1.0
OD2 A:ASP184 2.1 28.5 0.5
CG A:ASP184 2.3 26.3 0.5
CG A:ASP221 2.8 26.5 0.5
CG A:ASP221 3.0 26.9 0.5
CB A:ASP221 3.2 23.8 0.5
CB A:ASP221 3.3 23.8 0.5
CB A:ASP182 3.8 27.5 1.0
O A:HOH794 3.8 42.0 1.0
CB A:ASP184 3.8 25.6 0.5
CG A:ASP184 3.8 30.3 0.6
OD1 A:ASP221 3.8 24.0 0.5
CB A:ASP184 3.9 25.5 0.6
OD2 A:ASP184 3.9 38.0 0.6
OH A:TYR67 3.9 23.8 1.0
OD2 A:ASP182 4.0 38.0 1.0
CE1 A:TYR67 4.0 21.6 1.0
OD1 A:ASP221 4.1 29.9 0.5
ND2 A:ASN102 4.1 26.6 1.0
CA A:GLY140 4.3 24.9 1.0
CG A:ASP182 4.3 32.1 1.0
CA A:ASP184 4.4 22.6 0.6
CA A:ASP184 4.4 22.6 0.5
OD1 A:ASP184 4.4 31.7 0.6
CZ A:TYR67 4.4 23.1 1.0
N A:ASP184 4.6 23.3 1.0
CA A:ASP221 4.8 20.8 0.5
CA A:ASP221 4.8 20.8 0.5
N A:GLY140 4.9 24.8 1.0
C A:ILE183 5.0 25.4 1.0

Reference:

M.Garcia-Alija, J.J.Du, I.Ordonez, A.Diz-Vallenilla, A.Moraleda-Montoya, N.Sultana, C.G.Huynh, C.Li, T.C.Donahue, L.X.Wang, B.Trastoy, E.J.Sundberg, M.E.Guerin. Mechanism of Cooperative N-Glycan Processing By the Multi-Modular Endoglycosidase Endoe. Nat Commun V. 13 1137 2022.
ISSN: ESSN 2041-1723
PubMed: 35241669
DOI: 10.1038/S41467-022-28722-W
Page generated: Sat Apr 8 01:40:23 2023

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