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Nickel in PDB 8bxy: Fimh in Complex with ALPHA1,6 Core-Fucosylated Oligomannose-3, Crystallized in the Trigonal Space Group

Protein crystallography data

The structure of Fimh in Complex with ALPHA1,6 Core-Fucosylated Oligomannose-3, Crystallized in the Trigonal Space Group, PDB code: 8bxy was solved by C.Bridot, J.Bouckaert, E.-M.Krammer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.08 / 1.45
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.056, 91.056, 79.578, 90, 90, 120
R / Rfree (%) 15.3 / 20.5

Nickel Binding Sites:

The binding sites of Nickel atom in the Fimh in Complex with ALPHA1,6 Core-Fucosylated Oligomannose-3, Crystallized in the Trigonal Space Group (pdb code 8bxy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Fimh in Complex with ALPHA1,6 Core-Fucosylated Oligomannose-3, Crystallized in the Trigonal Space Group, PDB code: 8bxy:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 8bxy

Go back to Nickel Binding Sites List in 8bxy
Nickel binding site 1 out of 2 in the Fimh in Complex with ALPHA1,6 Core-Fucosylated Oligomannose-3, Crystallized in the Trigonal Space Group


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Fimh in Complex with ALPHA1,6 Core-Fucosylated Oligomannose-3, Crystallized in the Trigonal Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:28.6
occ:1.00
OD1 A:ASP47 2.0 27.1 1.0
NE2 A:HIS45 2.0 29.2 1.0
O A:HOH325 2.0 33.6 1.0
O A:HOH395 2.1 32.2 1.0
O A:HOH323 2.1 26.4 1.0
O A:HOH358 2.1 30.5 0.9
O A:HOH451 2.5 64.0 1.0
CG A:ASP47 3.0 25.0 1.0
CD2 A:HIS45 3.0 25.8 1.0
CE1 A:HIS45 3.1 27.2 1.0
OD2 A:ASP47 3.4 27.4 1.0
O A:HOH478 4.0 50.3 1.0
O A:HOH486 4.1 66.0 1.0
O A:HOH397 4.1 47.1 1.0
ND1 A:HIS45 4.2 24.1 1.0
CG A:HIS45 4.2 24.9 1.0
O A:HOH341 4.3 38.8 1.0
O A:HOH446 4.3 44.6 1.0
CB A:ASP47 4.3 29.0 1.0
CA A:ASP47 4.8 25.8 1.0

Nickel binding site 2 out of 2 in 8bxy

Go back to Nickel Binding Sites List in 8bxy
Nickel binding site 2 out of 2 in the Fimh in Complex with ALPHA1,6 Core-Fucosylated Oligomannose-3, Crystallized in the Trigonal Space Group


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Fimh in Complex with ALPHA1,6 Core-Fucosylated Oligomannose-3, Crystallized in the Trigonal Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni201

b:42.8
occ:1.00
O B:HOH307 1.9 35.7 1.0
OD1 B:ASP47 1.9 37.5 1.0
NE2 B:HIS45 2.0 43.8 1.0
O B:HOH345 2.1 42.5 1.0
O B:HOH401 2.4 51.7 1.0
O B:HOH400 2.4 86.9 1.0
CD2 B:HIS45 2.9 34.9 1.0
CG B:ASP47 3.0 32.0 1.0
CE1 B:HIS45 3.1 38.4 1.0
OD2 B:ASP47 3.4 29.1 1.0
O B:HOH302 4.0 58.5 1.0
CG B:HIS45 4.1 32.2 1.0
ND1 B:HIS45 4.1 30.9 1.0
CB B:ASP47 4.3 33.2 1.0
CA B:ASP47 4.8 33.6 1.0

Reference:

E.M.Krammer, C.Bridot, S.Serna, B.Echeverria, S.Semwal, B.Roubinet, K.Van Noort, R.Wilbers, G.Bourenkov, J.De Ruyck, L.Landemarre, N.Reichardt, J.Bouckaert. Structural Insights Into A Cooperative Switch Between One and Two Fimh Bacterial Adhesins Binding Pauci- and High-Mannose Type N-Glycan Receptors J.Biol.Chem. 04627 2023.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2023.104627
Page generated: Thu Oct 10 09:37:18 2024

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