Zinc in PDB 8epv: 2.2 A Crystal Structure of the Lipocalin Cat Allergen Fel D 7

Protein crystallography data

The structure of 2.2 A Crystal Structure of the Lipocalin Cat Allergen Fel D 7, PDB code: 8epv was solved by J.Min, L.C.Pedersen, M.A.Geoffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.40 / 2.19
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.871, 85.871, 40.056, 90, 90, 90
R / Rfree (%) 24.1 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.2 A Crystal Structure of the Lipocalin Cat Allergen Fel D 7 (pdb code 8epv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the 2.2 A Crystal Structure of the Lipocalin Cat Allergen Fel D 7, PDB code: 8epv:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8epv

Go back to Zinc Binding Sites List in 8epv
Zinc binding site 1 out of 3 in the 2.2 A Crystal Structure of the Lipocalin Cat Allergen Fel D 7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.2 A Crystal Structure of the Lipocalin Cat Allergen Fel D 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:28.9
occ:0.46
OE1 A:GLU143 2.0 54.3 1.0
OE1 A:GLU146 2.0 41.4 1.0
O A:HOH310 2.4 34.1 1.0
O A:HOH313 2.5 25.7 1.0
O A:HOH328 2.5 38.1 0.3
O A:HOH315 2.8 41.2 0.5
CD A:GLU143 3.1 51.3 1.0
CD A:GLU146 3.2 45.5 1.0
OE2 A:GLU143 3.6 49.4 1.0
HB2 A:GLU146 3.7 41.0 1.0
HA A:GLU143 3.8 41.9 1.0
OE2 A:GLU146 3.9 48.0 1.0
HB3 A:GLU146 3.9 41.0 1.0
ZN A:ZN205 3.9 44.6 0.5
HB3 A:GLU143 4.0 50.7 1.0
CB A:GLU146 4.1 36.1 1.0
CG A:GLU146 4.2 52.6 1.0
CG A:GLU143 4.3 56.5 1.0
OE1 A:GLU110 4.3 42.7 1.0
CB A:GLU143 4.5 41.9 1.0
CA A:GLU143 4.6 36.9 1.0
HG3 A:GLU143 4.7 68.3 1.0
HG2 A:GLU146 4.7 63.6 1.0
HG3 A:GLU146 4.9 63.6 1.0
O A:GLU143 4.9 35.5 1.0
HD22 A:ASN147 5.0 42.3 1.0

Zinc binding site 2 out of 3 in 8epv

Go back to Zinc Binding Sites List in 8epv
Zinc binding site 2 out of 3 in the 2.2 A Crystal Structure of the Lipocalin Cat Allergen Fel D 7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.2 A Crystal Structure of the Lipocalin Cat Allergen Fel D 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:37.6
occ:0.33
OD2 A:ASP113 2.3 38.5 1.0
OD2 A:ASP137 2.4 43.4 1.0
O A:HOH307 2.7 43.2 0.9
CG A:ASP113 3.4 38.0 1.0
CG A:ASP137 3.5 49.4 1.0
HB3 A:ASP137 3.8 41.3 1.0
HE1 A:HIS114 4.0 41.4 1.0
OD1 A:ASP113 4.1 40.2 1.0
CB A:ASP137 4.2 34.0 1.0
HB2 A:ARG136 4.2 38.1 1.0
HB2 A:ASP113 4.4 41.3 1.0
OD1 A:ASP137 4.4 42.1 1.0
O A:HOH311 4.4 37.5 1.0
CB A:ASP113 4.4 36.4 1.0
HB3 A:ASP113 4.6 41.3 1.0
H A:ASP137 4.7 45.0 1.0
HB2 A:ASP137 4.8 41.3 1.0
CE1 A:HIS114 4.9 34.1 1.0
N A:ASP137 4.9 37.1 1.0

Zinc binding site 3 out of 3 in 8epv

Go back to Zinc Binding Sites List in 8epv
Zinc binding site 3 out of 3 in the 2.2 A Crystal Structure of the Lipocalin Cat Allergen Fel D 7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.2 A Crystal Structure of the Lipocalin Cat Allergen Fel D 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:44.6
occ:0.52
OE2 A:GLU142 2.0 55.0 1.0
OE2 A:GLU143 2.0 49.4 1.0
OE2 A:GLU146 2.1 48.0 1.0
CD A:GLU146 2.9 45.5 1.0
O A:HOH326 2.9 56.9 1.0
OE1 A:GLU146 3.0 41.4 1.0
CD A:GLU142 3.0 58.8 1.0
OXT A:ACT201 3.0 74.7 1.0
HG2 A:GLU142 3.0 62.8 1.0
CD A:GLU143 3.1 51.3 1.0
CG A:GLU142 3.4 51.9 1.0
HG3 A:GLU142 3.4 62.8 1.0
OE1 A:GLU143 3.5 54.3 1.0
C A:ACT201 3.7 81.3 1.0
ZN A:ZN203 3.9 28.9 0.5
O A:ACT201 3.9 64.2 1.0
OE1 A:GLU142 4.2 60.1 1.0
O A:HOH312 4.2 79.2 1.0
CG A:GLU146 4.3 52.6 1.0
HG2 A:GLU143 4.3 68.3 1.0
CG A:GLU143 4.4 56.5 1.0
HA A:GLU143 4.5 41.9 1.0
HG3 A:GLU146 4.5 63.6 1.0
H1 A:ACT201 4.6 73.5 1.0
O A:HOH310 4.6 34.1 1.0
HG2 A:GLU146 4.6 63.6 1.0
CH3 A:ACT201 4.7 60.8 1.0
H2 A:ACT201 4.8 73.5 1.0
CB A:GLU142 4.9 46.7 1.0
HG3 A:GLU143 4.9 68.3 1.0

Reference:

J.Min, A.C.Y.Foo, S.A.Gabel, L.Perera, E.F.Derose, A.Pomes, L.C.Pedersen, G.A.Mueller. Structural and Ligand Binding Analysis of the Pet Allergens Can F 1 and Fel D 7. Front Allergy V. 4 33412 2023.
ISSN: ESSN 2673-6101
PubMed: 36960093
DOI: 10.3389/FALGY.2023.1133412
Page generated: Tue Apr 11 18:27:35 2023

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