Nickel in PDB 5abz: Complex of the Fimh Lectin with A C-Linked Naphtyl Alpha-D-Mannoside in Soaked Trigonal Crystals at 2.40 A Resolution

The structure of Complex of the Fimh Lectin with A C-Linked Naphtyl Alpha-D-Mannoside in Soaked Trigonal Crystals at 2.40 A Resolution, PDB code: 5abz was solved by J.De Ruyck, J.Bouckaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.48 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.830, 90.830, 79.870, 90.00, 90.00, 120.00
R / Rfree (%)	13.5 / 20.6

The binding sites of Nickel atom in the Complex of the Fimh Lectin with A C-Linked Naphtyl Alpha-D-Mannoside in Soaked Trigonal Crystals at 2.40 A Resolution (pdb code 5abz). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Complex of the Fimh Lectin with A C-Linked Naphtyl Alpha-D-Mannoside in Soaked Trigonal Crystals at 2.40 A Resolution, PDB code: 5abz:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Complex of the Fimh Lectin with A C-Linked Naphtyl Alpha-D-Mannoside in Soaked Trigonal Crystals at 2.40 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Complex of the Fimh Lectin with A C-Linked Naphtyl Alpha-D-Mannoside in Soaked Trigonal Crystals at 2.40 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1159 b:28.6 occ:1.00 OD1 A:ASP47 2.0 20.4 1.0 NE2 A:HIS45 2.0 33.7 1.0 O A:HOH2042 2.1 25.1 1.0 O A:HOH2044 2.2 27.6 1.0 O A:HOH2043 2.2 29.8 1.0 O A:HOH2047 2.4 27.1 1.0 CE1 A:HIS45 2.8 21.4 1.0 HE1 A:HIS45 2.8 25.7 1.0 CG A:ASP47 3.0 20.0 1.0 CD2 A:HIS45 3.2 25.9 1.0 OD2 A:ASP47 3.4 20.5 1.0 HD2 A:HIS45 3.5 31.1 1.0 ND1 A:HIS45 4.0 20.4 1.0 O A:HOH2046 4.0 36.0 1.0 HA A:ASP47 4.2 37.0 1.0 CG A:HIS45 4.2 18.5 1.0 HB1 A:ALA2 4.3 18.8 1.0 CB A:ASP47 4.3 24.6 1.0 O A:HOH2097 4.4 33.8 1.0 HB3 A:ASP47 4.6 29.5 1.0 HD1 A:HIS45 4.7 24.5 1.0 CA A:ASP47 4.8 30.9 1.0

Nickel binding site 2 out of 2 in the Complex of the Fimh Lectin with A C-Linked Naphtyl Alpha-D-Mannoside in Soaked Trigonal Crystals at 2.40 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Complex of the Fimh Lectin with A C-Linked Naphtyl Alpha-D-Mannoside in Soaked Trigonal Crystals at 2.40 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1159 b:37.4 occ:1.00 OD1 B:ASP47 2.0 24.1 1.0 O B:HOH2038 2.0 23.4 1.0 NE2 B:HIS45 2.4 32.6 1.0 CG B:ASP47 2.8 23.6 1.0 O B:HOH2086 3.0 43.6 1.0 OD2 B:ASP47 3.1 28.9 1.0 CE1 B:HIS45 3.2 33.4 1.0 HE1 B:HIS45 3.2 40.1 1.0 CD2 B:HIS45 3.5 29.4 1.0 HD2 B:HIS45 3.7 35.3 1.0 HB1 B:ALA2 4.0 19.9 1.0 O B:HOH2039 4.1 41.5 1.0 CB B:ASP47 4.2 22.8 1.0 HD12 B:ILE13 4.3 16.9 1.0 HB3 B:ASP47 4.3 27.4 1.0 ND1 B:HIS45 4.4 27.6 1.0 HA B:ASP47 4.5 43.7 1.0 CG B:HIS45 4.5 24.9 1.0 HB3 B:ALA2 4.7 19.9 1.0 CB B:ALA2 4.8 16.6 1.0 HB2 B:ASP47 4.8 27.4 1.0 HG13 B:ILE13 4.9 24.3 1.0 CA B:ASP47 4.9 36.4 1.0 O B:HOH2016 4.9 37.5 1.0 H3 B:PHE1 4.9 25.9 1.0

J.De Ruyck, M.F.Lensink, J.Bouckaert. Structures of C-Mannosylated Anti-Adhesives Bound to the Type 1 Fimbrial Fimh Adhesin Iucrj V. 3 163 2016.
ISSN: ESSN 2052-2525
PubMed: 27158502
DOI: 10.1107/S2052252516002487