Nickel in PDB 7quo: Fimh Lectin Domain in Complex with Oligomannose-6

The structure of Fimh Lectin Domain in Complex with Oligomannose-6, PDB code: 7quo 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 / 3.00
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 (%)	23.6 / 27.6

The binding sites of Nickel atom in the Fimh Lectin Domain in Complex with Oligomannose-6 (pdb code 7quo). 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: 7quo:
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:37.7 occ:1.00 O A:HOH301 2.0 23.9 1.0 OD1 A:ASP47 2.0 38.0 1.0 O A:HOH340 2.1 39.9 1.0 O A:HOH345 2.1 21.2 1.0 NE2 A:HIS45 2.2 58.4 1.0 CG A:ASP47 2.9 44.4 1.0 CD2 A:HIS45 3.0 43.3 1.0 HD2 A:HIS45 3.1 51.9 1.0 CE1 A:HIS45 3.2 58.4 1.0 OD2 A:ASP47 3.3 44.7 1.0 HE1 A:HIS45 3.5 70.1 1.0 HB3 A:ALA2 4.1 46.8 1.0 CG A:HIS45 4.2 41.5 1.0 HA A:ASP47 4.2 53.9 1.0 CB A:ASP47 4.3 38.0 1.0 ND1 A:HIS45 4.3 54.4 1.0 HB3 A:ASP47 4.5 45.6 1.0 O A:HOH339 4.6 26.5 1.0 HG2 A:ARG98 4.6 77.8 1.0 CA A:ASP47 4.8 44.9 1.0 HB2 A:ALA2 4.8 46.8 1.0 CB A:ALA2 4.9 39.0 1.0 HG3 A:ARG98 4.9 77.8 1.0 HD11 A:ILE13 5.0 67.4 1.0 HB2 A:ASP47 5.0 45.6 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:60.3 occ:1.00 NE2 B:HIS45 2.1 58.6 1.0 O B:HOH317 2.1 18.1 1.0 OD1 B:ASP47 2.1 64.6 1.0 O B:HOH326 2.1 41.2 1.0 O B:HOH320 2.2 26.8 1.0 CG B:ASP47 2.8 59.4 1.0 CD2 B:HIS45 2.9 48.9 1.0 HD2 B:HIS45 2.9 58.7 1.0 OD2 B:ASP47 3.0 60.1 1.0 CE1 B:HIS45 3.2 44.2 1.0 HE1 B:HIS45 3.5 53.1 1.0 CG B:HIS45 4.1 40.5 1.0 ND1 B:HIS45 4.2 46.2 1.0 HB3 B:ALA2 4.2 73.0 1.0 CB B:ASP47 4.2 51.3 1.0 HA B:ASP47 4.3 52.7 1.0 H62 F:NAG2 4.4 81.6 1.0 HB3 B:ASP47 4.5 61.6 1.0 O B:HOH332 4.5 24.2 1.0 HO6 F:NAG2 4.5 88.5 1.0 HD11 B:ILE13 4.5 57.4 1.0 CA B:ASP47 4.8 43.9 1.0 H2 B:PHE1 4.9 46.2 1.0 HB2 B:ASP47 4.9 61.6 1.0 HB2 B:ALA2 4.9 73.0 1.0 H B:ALA2 5.0 64.4 1.0 H61 F:NAG2 5.0 81.6 1.0 HD1 B:HIS45 5.0 55.4 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:39.7 occ:1.00 NE2 C:HIS45 1.9 50.2 1.0 OD1 C:ASP47 2.0 27.5 1.0 O C:HOH301 2.0 24.8 1.0 O C:HOH312 2.2 26.2 1.0 O C:HOH321 2.3 22.6 1.0 CD2 C:HIS45 2.7 39.4 1.0 CG C:ASP47 2.8 34.6 1.0 HD2 C:HIS45 2.9 47.2 1.0 CE1 C:HIS45 2.9 50.1 1.0 OD2 C:ASP47 3.0 30.6 1.0 HE1 C:HIS45 3.2 60.1 1.0 O A:HOH324 3.7 26.1 1.0 CG C:HIS45 3.9 32.3 1.0 ND1 C:HIS45 4.0 47.3 1.0 HB3 C:ALA2 4.1 50.5 1.0 CB C:ASP47 4.2 29.1 1.0 HA C:ASP47 4.4 44.8 1.0 HB3 C:ASP47 4.5 34.9 1.0 OH A:TYR48 4.7 62.9 1.0 HH A:TYR48 4.7 75.4 1.0 HD1 C:HIS45 4.8 56.7 1.0 HB2 C:ALA2 4.8 50.5 1.0 CA C:ASP47 4.8 37.3 1.0 HB2 C:ASP47 4.8 34.9 1.0 HD11 C:ILE13 4.9 36.1 1.0 CB C:ALA2 4.9 42.1 1.0 O C:HOH341 4.9 11.7 1.0 H C:ALA2 5.0 38.4 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:48.6 occ:1.00 OD2 D:ASP47 1.9 77.0 1.0 NE2 D:HIS45 2.0 50.7 1.0 OD1 D:ASP47 2.0 62.7 1.0 CG D:ASP47 2.2 56.6 1.0 O D:HOH305 2.2 23.6 1.0 O D:HOH306 2.3 26.9 1.0 O B:HOH316 2.7 49.7 1.0 CD2 D:HIS45 2.8 48.8 1.0 HD2 D:HIS45 2.8 58.6 1.0 CE1 D:HIS45 3.1 48.2 1.0 HE1 D:HIS45 3.5 57.9 1.0 CB D:ASP47 3.7 43.7 1.0 HA D:ASP47 4.0 75.2 1.0 CG D:HIS45 4.0 46.0 1.0 HB3 D:ALA2 4.0 42.0 1.0 HB3 D:ASP47 4.0 52.4 1.0 ND1 D:HIS45 4.1 44.5 1.0 HB2 D:ASP47 4.2 52.4 1.0 CA D:ASP47 4.4 62.7 1.0 HD11 D:ILE13 4.6 55.8 1.0 O B:HOH313 4.6 26.2 1.0 OH B:TYR48 4.7 72.1 1.0 HB2 D:ALA2 4.7 42.0 1.0 CB D:ALA2 4.8 35.0 1.0 HH B:TYR48 4.8 86.5 1.0 H D:ALA2 4.8 30.9 1.0 N D:ASP47 4.9 65.2 1.0 H2 D:PHE1 4.9 49.5 1.0 HD1 D:HIS45 4.9 53.4 1.0 O D:HOH322 5.0 15.2 1.0 H D:ASP47 5.0 78.2 1.0

A.Wellens, C.Garofalo, H.Nguyen, N.Van Gerven, R.Slattegard, J.P.Hernalsteens, L.Wyns, S.Oscarson, H.De Greve, S.Hultgren, J.Bouckaert. Intervening with Urinary Tract Infections Using Anti-Adhesives Based on the Crystal Structure of the Fimh-Oligomannose-3 Complex. Plos One V. 3 E2040 2008.
ISSN: ESSN 1932-6203
PubMed: 18446213
DOI: 10.1371/JOURNAL.PONE.0002040