Calcium in PDB 9kpl: Crystal Structure of T. Rubripes Mincle with Glucose

The structure of Crystal Structure of T. Rubripes Mincle with Glucose, PDB code: 9kpl was solved by T.Ito, M.Nagae, S.Yamasaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.45 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.353, 69.86, 51.584, 90, 115.77, 90
R / Rfree (%)	18 / 21.6

The binding sites of Calcium atom in the Crystal Structure of T. Rubripes Mincle with Glucose (pdb code 9kpl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of T. Rubripes Mincle with Glucose, PDB code: 9kpl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of T. Rubripes Mincle with Glucose


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 T. Rubripes Mincle with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:14.6 occ:1.00 O A:ILE91 2.3 13.8 1.0 OD1 A:ASN93 2.4 18.1 1.0 OE2 A:GLU175 2.4 14.0 1.0 OE2 A:GLU97 2.5 14.1 1.0 O A:HOH351 2.5 14.7 1.0 O A:HOH377 2.5 16.9 1.0 OE1 A:GLU175 2.6 15.2 1.0 OE1 A:GLU97 2.6 18.6 1.0 CD A:GLU97 2.9 15.8 1.0 CD A:GLU175 2.9 13.2 1.0 C A:ILE91 3.5 10.6 1.0 CG A:ASN93 3.6 18.0 1.0 OH A:TYR66 4.2 12.3 1.0 CB A:ILE91 4.3 11.6 1.0 N A:ASN93 4.3 14.3 1.0 CA A:ILE91 4.3 12.5 1.0 N A:ILE91 4.3 11.2 1.0 CB A:ASN93 4.3 19.2 1.0 CG A:GLU97 4.4 13.5 1.0 CG A:GLU175 4.4 12.8 1.0 N A:ILE92 4.5 10.8 1.0 O A:HOH339 4.6 18.5 1.0 O A:HOH358 4.6 22.3 1.0 ND2 A:ASN93 4.6 18.0 1.0 CA A:ILE92 4.6 14.6 1.0 O A:HOH386 4.6 19.4 1.0 CG2 A:ILE91 4.7 12.1 1.0 OG A:SER64 4.7 14.8 1.0 O A:HOH382 4.8 22.2 1.0 O A:HOH385 4.8 29.1 1.0 C A:ILE92 4.8 16.6 1.0 CA A:ASN93 5.0 18.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of T. Rubripes Mincle with Glucose


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 T. Rubripes Mincle with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:15.3 occ:1.00 OD1 A:ASN162 2.4 15.2 1.0 OD1 A:ASP163 2.4 14.4 1.0 OE1 A:GLU147 2.4 16.1 1.0 OD1 A:ASN140 2.4 15.3 1.0 O A:ASP163 2.5 13.0 1.0 O3 A:GLC201 2.5 19.6 0.8 O4 A:GLC201 2.6 19.4 0.8 O3 A:BGC202 2.6 19.5 0.3 OE1 A:GLU138 2.6 16.9 1.0 O4 A:BGC202 2.6 19.7 0.3 C4 A:BGC202 3.3 22.1 0.3 C3 A:GLC201 3.3 22.0 0.8 CD A:GLU147 3.3 17.5 1.0 CG A:ASP163 3.4 13.6 1.0 C3 A:BGC202 3.4 22.2 0.3 CG A:ASN162 3.4 15.6 1.0 C4 A:GLC201 3.4 22.2 0.8 CG A:ASN140 3.4 17.8 1.0 CD A:GLU138 3.4 17.3 1.0 C A:ASP163 3.6 14.3 1.0 OE2 A:GLU147 3.7 18.2 1.0 OE2 A:GLU138 3.8 18.1 1.0 N A:ASP163 3.8 11.2 1.0 ND2 A:ASN162 3.9 14.1 1.0 ND2 A:ASN140 4.0 18.4 1.0 CA A:ASP163 4.1 12.0 1.0 OD2 A:ASP163 4.1 11.5 1.0 N A:ASN140 4.2 15.4 1.0 CB A:ASP163 4.3 12.4 1.0 CB A:TYR142 4.4 21.1 1.0 N A:TYR142 4.5 17.7 1.0 N A:ASN141 4.6 16.2 1.0 C A:ASN162 4.6 13.5 1.0 CG A:GLU147 4.6 14.4 1.0 CB A:ASN140 4.6 16.7 1.0 CG A:GLU138 4.7 16.1 1.0 CB A:ASN162 4.7 15.1 1.0 CB A:GLU147 4.7 15.2 1.0 N A:LEU164 4.7 13.2 1.0 CA A:ASN140 4.8 16.3 1.0 C5 A:BGC202 4.8 25.0 0.3 C2 A:BGC202 4.8 24.4 0.3 C2 A:GLC201 4.8 24.9 0.8 C5 A:GLC201 4.8 24.4 0.8 CA A:ASN162 4.8 14.3 1.0 C A:ASN140 4.9 17.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of T. Rubripes Mincle with Glucose


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 T. Rubripes Mincle with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca203 b:18.0 occ:1.00 OD1 E:ASN93 2.3 19.5 1.0 O E:ILE91 2.3 15.3 1.0 O E:HOH346 2.4 20.7 1.0 O E:HOH352 2.5 21.0 1.0 OE2 E:GLU97 2.5 17.5 1.0 OE2 E:GLU175 2.5 21.3 1.0 OE1 E:GLU175 2.6 15.7 1.0 OE1 E:GLU97 2.7 20.7 1.0 CD E:GLU175 2.9 19.7 1.0 CD E:GLU97 2.9 17.4 1.0 C E:ILE91 3.5 14.6 1.0 CG E:ASN93 3.5 22.3 1.0 CB E:ILE91 4.2 13.5 1.0 CA E:ILE91 4.2 13.8 1.0 CB E:ASN93 4.3 23.7 1.0 N E:ASN93 4.3 19.8 1.0 OH E:TYR66 4.3 17.1 1.0 N E:ILE91 4.3 13.5 1.0 NH1 E:ARG177 4.4 55.1 1.0 O E:HOH311 4.4 33.0 1.0 CG E:GLU175 4.4 17.6 1.0 CG E:GLU97 4.5 15.9 1.0 N E:ILE92 4.5 12.0 1.0 ND2 E:ASN93 4.5 21.6 1.0 O E:HOH375 4.6 21.4 1.0 CG2 E:ILE91 4.6 15.1 1.0 CA E:ILE92 4.7 16.9 1.0 OG E:SER64 4.7 22.1 1.0 O E:HOH356 4.8 29.8 1.0 O E:HOH372 4.8 25.1 1.0 C E:ILE92 4.8 19.8 1.0 O E:HOH330 4.9 38.9 1.0 CA E:ASN93 4.9 20.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of T. Rubripes Mincle with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of T. Rubripes Mincle with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca204 b:17.0 occ:1.00 OD1 E:ASN162 2.4 14.6 1.0 OD1 E:ASP163 2.4 15.1 1.0 OD1 E:ASN140 2.4 17.9 1.0 OE1 E:GLU147 2.5 18.2 1.0 O E:ASP163 2.5 15.5 1.0 O3 E:GLC201 2.5 19.9 0.6 OE1 E:GLU138 2.5 18.7 1.0 O3 E:BGC202 2.5 18.1 0.4 O4 E:GLC201 2.5 18.1 0.6 O4 E:BGC202 2.6 19.9 0.4 C4 E:BGC202 3.3 21.1 0.4 C3 E:GLC201 3.3 21.1 0.6 C3 E:BGC202 3.4 21.6 0.4 CD E:GLU138 3.4 20.3 1.0 CG E:ASP163 3.4 13.3 1.0 C4 E:GLC201 3.4 21.6 0.6 CG E:ASN162 3.4 15.7 1.0 CG E:ASN140 3.4 19.2 1.0 CD E:GLU147 3.4 17.4 1.0 C E:ASP163 3.5 14.5 1.0 OE2 E:GLU138 3.7 18.6 1.0 OE2 E:GLU147 3.8 15.9 1.0 N E:ASP163 3.8 13.6 1.0 ND2 E:ASN162 3.9 15.2 1.0 ND2 E:ASN140 3.9 19.2 1.0 CA E:ASP163 4.1 13.0 1.0 OD2 E:ASP163 4.1 12.5 1.0 N E:ASN140 4.2 14.2 1.0 CB E:ASP163 4.3 12.5 1.0 CB E:TYR142 4.4 21.4 1.0 N E:TYR142 4.5 19.6 1.0 C E:ASN162 4.6 14.0 1.0 CB E:ASN140 4.6 16.6 1.0 N E:ASN141 4.6 15.4 1.0 CG E:GLU138 4.6 18.7 1.0 CG E:GLU147 4.7 17.1 1.0 CB E:ASN162 4.7 15.1 1.0 N E:LEU164 4.7 13.2 1.0 CB E:GLU147 4.7 15.4 1.0 C2 E:BGC202 4.8 21.6 0.4 C5 E:BGC202 4.8 23.9 0.4 CA E:ASN140 4.8 17.2 1.0 C2 E:GLC201 4.8 23.9 0.6 CA E:ASN162 4.8 14.5 1.0 C5 E:GLC201 4.8 21.7 0.6 C E:ASN140 5.0 14.8 1.0

T.Ito, C.Guenther, E.Ishikawa, T.Yabuki, M.Nagae, Y.Nakatani, S.Yamasaki. Phylogenetic and Structural Insights Into the Origin of C-Type Lectin Mincle in Vertebrates. Immunogenetics V. 77 18 2025.
ISSN: ISSN 0093-7711
PubMed: 40119899
DOI: 10.1007/S00251-025-01375-X