Calcium in PDB 6gtw: Crystal Structure of the Fimh Lectin Domain From E.Coli F18 in Complex with Trimannose

The structure of Crystal Structure of the Fimh Lectin Domain From E.Coli F18 in Complex with Trimannose, PDB code: 6gtw was solved by R.P.Jakob, M.M.Sauer, T.Luber, F.Canonica, G.Navarra, B.Ernst, C.Unverzagt, T.Maier, R.Glockshuber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.80 / 2.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	175.180, 175.180, 124.660, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 21.6

The binding sites of Calcium atom in the Crystal Structure of the Fimh Lectin Domain From E.Coli F18 in Complex with Trimannose (pdb code 6gtw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Fimh Lectin Domain From E.Coli F18 in Complex with Trimannose, PDB code: 6gtw:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Fimh Lectin Domain From E.Coli F18 in Complex with Trimannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Fimh Lectin Domain From E.Coli F18 in Complex with Trimannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:45.9 occ:1.00 OD1 A:ASP100 3.0 82.5 1.0 O A:ARG98 3.0 48.2 1.0 HZ2 A:LYS4 3.2 0.8 1.0 ND1 A:HIS45 3.5 51.9 1.0 HD1 A:HIS45 3.6 62.3 1.0 CG A:HIS45 3.6 51.2 1.0 HB3 A:HIS45 3.8 58.0 1.0 CE1 A:HIS45 3.8 52.7 1.0 CG A:ASP100 3.9 78.5 1.0 HZ1 A:LYS4 4.0 0.8 1.0 NZ A:LYS4 4.0 0.6 1.0 CD2 A:HIS45 4.0 52.6 1.0 CB A:HIS45 4.1 48.3 1.0 HB2 A:HIS45 4.1 58.0 1.0 NE2 A:HIS45 4.1 52.1 1.0 H A:ASP100 4.1 68.8 1.0 HE1 A:HIS45 4.2 63.3 1.0 OD2 A:ASP100 4.2 82.6 1.0 C A:ARG98 4.3 47.7 1.0 N A:ASP100 4.5 57.4 1.0 HA A:THR99 4.5 62.1 1.0 HE3 A:LYS4 4.5 0.8 1.0 HZ3 A:LYS4 4.5 0.8 1.0 HD2 A:HIS45 4.6 63.2 1.0 HB3 A:ARG98 4.6 65.1 1.0 HE2 A:HIS45 4.6 62.5 1.0 HA A:ASP100 4.8 72.4 1.0 CE A:LYS4 4.9 99.8 1.0 HA A:ARG98 5.0 58.9 1.0 C A:THR99 5.0 52.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Fimh Lectin Domain From E.Coli F18 in Complex with Trimannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Fimh Lectin Domain From E.Coli F18 in Complex with Trimannose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:50.7 occ:1.00 O B:ARG98 2.8 56.2 1.0 OD1 B:ASP100 3.1 76.6 1.0 O B:HOH481 3.5 61.3 1.0 ND1 B:HIS45 3.6 69.2 1.0 CG B:HIS45 3.7 65.8 1.0 HB3 B:HIS45 3.8 65.2 1.0 HD1 B:HIS45 3.8 83.0 1.0 CG B:ASP100 3.9 72.2 1.0 CE1 B:HIS45 4.0 70.6 1.0 H B:ASP100 4.0 59.1 1.0 CD2 B:HIS45 4.0 69.3 1.0 HB2 B:HIS45 4.0 65.2 1.0 C B:ARG98 4.0 49.8 1.0 CB B:HIS45 4.1 54.4 1.0 HZ1 B:LYS4 4.1 0.6 1.0 NE2 B:HIS45 4.2 69.4 1.0 HZ2 B:LYS4 4.2 0.6 1.0 HA B:THR99 4.3 55.2 1.0 OD2 B:ASP100 4.3 75.3 1.0 N B:ASP100 4.3 49.3 1.0 HB3 B:ARG98 4.4 62.9 1.0 HE1 B:HIS45 4.4 84.7 1.0 HD2 B:HIS45 4.4 83.2 1.0 NZ B:LYS4 4.6 0.5 1.0 HE2 B:HIS45 4.7 83.3 1.0 HA B:ASP100 4.8 63.2 1.0 C B:THR99 4.8 45.7 1.0 HA B:ARG98 4.8 59.2 1.0 CA B:THR99 4.8 46.0 1.0 N B:THR99 4.9 44.0 1.0 CA B:ARG98 4.9 49.3 1.0 CA B:ASP100 5.0 52.6 1.0 O B:HOH443 5.0 63.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Fimh Lectin Domain From E.Coli F18 in Complex with Trimannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Fimh Lectin Domain From E.Coli F18 in Complex with Trimannose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca304 b:42.6 occ:1.00 O D:ARG98 2.8 53.5 1.0 OD1 D:ASP100 3.0 70.6 1.0 ND1 D:HIS45 3.5 53.5 1.0 CG D:HIS45 3.6 52.0 1.0 HD1 D:HIS45 3.7 64.2 1.0 HB3 D:HIS45 3.7 56.1 1.0 CG D:ASP100 3.8 66.0 1.0 HZ2 D:LYS4 3.8 0.6 1.0 CE1 D:HIS45 3.9 55.6 1.0 CD2 D:HIS45 4.0 54.0 1.0 H D:ASP100 4.0 58.4 1.0 CB D:HIS45 4.0 46.7 1.0 HB2 D:HIS45 4.0 56.1 1.0 C D:ARG98 4.1 51.8 1.0 NE2 D:HIS45 4.1 54.4 1.0 OD2 D:ASP100 4.1 75.2 1.0 O D:HOH456 4.2 48.2 1.0 HE1 D:HIS45 4.3 66.7 1.0 HZ3 D:LYS4 4.3 0.6 1.0 N D:ASP100 4.3 48.6 1.0 HA D:THR99 4.4 63.4 1.0 HB3 D:ARG98 4.4 67.3 1.0 HD2 D:HIS45 4.4 64.8 1.0 NZ D:LYS4 4.5 86.3 1.0 HE2 D:HIS45 4.6 65.2 1.0 HA D:ASP100 4.7 57.2 1.0 HA D:ARG98 4.8 62.8 1.0 C D:THR99 4.8 50.9 1.0 O D:HOH428 4.9 47.2 1.0 HZ1 D:LYS4 4.9 0.6 1.0 CA D:THR99 4.9 52.9 1.0 CA D:ASP100 4.9 47.7 1.0 CB D:ASP100 4.9 53.4 1.0 CA D:ARG98 4.9 52.4 1.0 N D:THR99 5.0 51.9 1.0

M.M.Sauer, R.P.Jakob, T.Luber, F.Canonica, G.Navarra, B.Ernst, C.Unverzagt, T.Maier, R.Glockshuber. Binding of the Bacterial Adhesin Fimh to Its Natural, Multivalent High-Mannose Type Glycan Targets. J.Am.Chem.Soc. V. 141 936 2019.
ISSN: ESSN 1520-5126
PubMed: 30543411
DOI: 10.1021/JACS.8B10736