Nickel in PDB 8by3: Fimh Lectin Domain in Complex with Oligomannose-6

The structure of Fimh Lectin Domain in Complex with Oligomannose-6, PDB code: 8by3 was solved by J.Bouckaert, G.P.Bourenkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	114.93 / 3.19
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	153.11, 153.11, 230.41, 90, 90, 120
R / Rfree (%)	20.5 / 23.8

The binding sites of Nickel atom in the Fimh Lectin Domain in Complex with Oligomannose-6 (pdb code 8by3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Fimh Lectin Domain in Complex with Oligomannose-6, PDB code: 8by3:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Fimh Lectin Domain in Complex with Oligomannose-6


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Fimh Lectin Domain in Complex with Oligomannose-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni200 b:64.1 occ:1.00 O A:HOH327 1.9 57.5 1.0 OD1 A:ASP47 1.9 65.2 1.0 O A:HOH344 1.9 51.2 1.0 O A:HOH303 2.0 53.6 1.0 NE2 A:HIS45 2.0 76.4 1.0 CG A:ASP47 2.9 66.0 1.0 CD2 A:HIS45 2.9 72.2 1.0 CE1 A:HIS45 3.1 80.9 1.0 OD2 A:ASP47 3.3 67.7 1.0 CG A:HIS45 4.1 71.5 1.0 ND1 A:HIS45 4.1 79.9 1.0 CB A:ASP47 4.3 65.2 1.0 O A:HOH338 4.5 54.5 1.0 CA A:ASP47 4.8 66.6 1.0 CB A:ALA2 5.0 63.0 1.0

Nickel binding site 2 out of 4 in the Fimh Lectin Domain in Complex with Oligomannose-6


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Fimh Lectin Domain in Complex with Oligomannose-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:82.6 occ:1.00 O B:HOH312 1.9 48.1 1.0 O B:HOH318 1.9 70.7 1.0 OD1 B:ASP47 1.9 82.4 1.0 O B:HOH319 2.0 56.8 1.0 NE2 B:HIS45 2.0 83.3 1.0 CG B:ASP47 2.8 79.0 1.0 CD2 B:HIS45 2.9 78.9 1.0 OD2 B:ASP47 3.0 81.9 1.0 CE1 B:HIS45 3.1 74.2 1.0 CG B:HIS45 4.1 70.5 1.0 CB B:ASP47 4.1 77.7 1.0 ND1 B:HIS45 4.2 76.2 1.0 O B:HOH332 4.5 54.2 1.0 CA B:ASP47 4.7 73.9 1.0 CB B:ALA2 5.0 85.8 1.0

Nickel binding site 3 out of 4 in the Fimh Lectin Domain in Complex with Oligomannose-6


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Fimh Lectin Domain in Complex with Oligomannose-6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni200 b:62.1 occ:1.00 OD1 C:ASP47 1.9 57.5 1.0 O C:HOH307 1.9 54.7 1.0 O C:HOH315 1.9 52.6 1.0 O C:HOH302 1.9 53.9 1.0 NE2 C:HIS45 2.0 78.2 1.0 CG C:ASP47 2.8 62.4 1.0 CD2 C:HIS45 2.9 69.3 1.0 CE1 C:HIS45 3.1 79.2 1.0 OD2 C:ASP47 3.1 56.7 1.0 O A:HOH332 3.2 48.8 1.0 CG C:HIS45 4.1 62.3 1.0 ND1 C:HIS45 4.1 74.3 1.0 CB C:ASP47 4.2 59.1 1.0 OH A:TYR48 4.7 92.9 1.0 CA C:ASP47 4.8 67.3 1.0 O C:HOH340 4.9 33.2 1.0 CB C:ALA2 5.0 66.9 1.0

Nickel binding site 4 out of 4 in the Fimh Lectin Domain in Complex with Oligomannose-6


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Fimh Lectin Domain in Complex with Oligomannose-6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni201 b:75.3 occ:1.00 OD2 D:ASP47 1.9 92.0 1.0 O D:HOH303 1.9 53.6 1.0 O D:HOH304 1.9 55.1 1.0 OD1 D:ASP47 2.0 86.8 1.0 O D:HOH312 2.0 71.8 1.0 NE2 D:HIS45 2.0 80.7 1.0 CG D:ASP47 2.2 86.7 1.0 CD2 D:HIS45 2.9 78.8 1.0 CE1 D:HIS45 3.2 78.2 1.0 CB D:ASP47 3.7 73.7 1.0 CG D:HIS45 4.1 76.0 1.0 ND1 D:HIS45 4.2 74.5 1.0 CA D:ASP47 4.4 92.7 1.0 O B:HOH320 4.6 51.1 1.0 OH B:TYR48 4.7 90.5 1.0 CB D:ALA2 4.9 65.0 1.0 O D:HOH322 5.0 44.8 1.0

E.M.Krammer, C.Bridot, S.Serna, B.Echeverria, S.Semwal, B.Roubinet, K.Van Noort, R.P.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
PubMed: 36944399
DOI: 10.1016/J.JBC.2023.104627