Atomistry » Zinc » PDB 7pjg-7pvk » 7puj
Atomistry »
  Zinc »
    PDB 7pjg-7pvk »
      7puj »

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: Wed Oct 30 09:20:51 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy