Calcium in PDB 8hb5: Crystal Structure of Mincle in Complex with Hd-275

The structure of Crystal Structure of Mincle in Complex with Hd-275, PDB code: 8hb5 was solved by S.Ishizuka, M.Nagae, S.Yamasaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.76 / 2.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.515, 97.515, 46.49, 90, 90, 120
R / Rfree (%)	29.6 / 33.6

The binding sites of Calcium atom in the Crystal Structure of Mincle in Complex with Hd-275 (pdb code 8hb5). 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 Mincle in Complex with Hd-275, PDB code: 8hb5:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Mincle in Complex with Hd-275


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 Mincle in Complex with Hd-275 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:38.7 occ:1.00 OD1 A:ASN170 2.3 66.9 1.0 OD1 A:ASP193 2.4 48.1 1.0 O4 A:L6N1004 2.4 41.1 1.0 OE1 A:GLU168 2.4 35.4 1.0 OE1 A:GLU176 2.5 26.6 1.0 OD1 A:ASN192 2.5 55.5 1.0 O A:ASP193 2.8 49.1 1.0 O3 A:L6N1004 3.1 53.0 1.0 CG A:ASN170 3.1 52.9 1.0 CD A:GLU168 3.2 47.0 1.0 ND2 A:ASN170 3.3 58.7 1.0 C4 A:L6N1004 3.4 60.8 1.0 CD A:GLU176 3.4 35.3 1.0 OE2 A:GLU168 3.5 54.7 1.0 C3 A:L6N1004 3.5 65.8 1.0 CG A:ASP193 3.5 47.6 1.0 CG A:ASN192 3.7 45.7 1.0 OE2 A:GLU176 3.7 31.4 1.0 C A:ASP193 3.9 29.0 1.0 N A:ASP193 3.9 32.9 1.0 ND2 A:ASN192 4.1 51.4 1.0 OD2 A:ASP193 4.2 43.4 1.0 CA A:ASP193 4.3 22.4 1.0 N A:ASN170 4.4 39.3 1.0 CG A:LEU172 4.5 37.2 1.0 CB A:ASP193 4.5 31.4 1.0 CG A:GLU168 4.5 46.5 1.0 CB A:ASN170 4.6 44.8 1.0 C5 A:L6N1004 4.7 57.6 1.0 CD1 A:LEU172 4.7 32.4 1.0 CG A:GLU176 4.8 29.1 1.0 CB A:ASN192 4.9 43.8 1.0 N A:ASN171 5.0 37.8 1.0 CA A:ASN170 5.0 39.7 1.0 C A:ASN192 5.0 41.9 1.0 C2 A:L6N1004 5.0 71.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Mincle in Complex with Hd-275


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 Mincle in Complex with Hd-275 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:62.5 occ:1.00 OD1 A:ASN171 2.3 57.9 1.0 OD1 A:ASP177 2.3 53.4 1.0 OE2 A:GLU146 2.4 53.8 1.0 O A:GLU176 2.4 35.0 1.0 OD1 A:ASP142 2.8 55.0 1.0 OD2 A:ASP142 2.8 53.4 1.0 OE1 A:GLU146 3.1 44.3 1.0 CD A:GLU146 3.1 38.8 1.0 CG A:ASP142 3.2 54.0 1.0 C A:GLU176 3.3 32.7 1.0 CA A:ASP177 3.3 48.4 1.0 CG A:ASP177 3.4 52.2 1.0 CG A:ASN171 3.5 52.0 1.0 N A:ASP177 3.7 61.0 1.0 CB A:ASP177 3.8 51.9 1.0 CZ2 A:TRP149 4.1 45.1 1.0 CH2 A:TRP149 4.2 50.5 1.0 ND2 A:ASN171 4.2 54.7 1.0 OD2 A:ASP177 4.5 52.9 1.0 C A:ASP177 4.5 47.3 1.0 CG A:GLU146 4.5 56.3 1.0 CA A:GLU176 4.5 24.3 1.0 CB A:ASN171 4.5 41.1 1.0 CB A:ASP142 4.7 53.6 1.0 N A:GLU176 4.7 45.5 1.0 OD2 A:ASP193 4.7 43.4 1.0 O A:ASP142 4.8 54.5 1.0 O A:ASP177 4.8 48.1 1.0 CE2 A:TRP149 4.9 40.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Mincle in Complex with Hd-275


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 Mincle in Complex with Hd-275 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:37.1 occ:1.00 OD1 A:ASN118 2.3 57.6 1.0 OE2 A:GLU205 2.4 48.2 1.0 O A:VAL116 2.4 51.4 1.0 O A:HOH1102 2.5 43.9 1.0 OE2 A:GLU122 2.5 30.1 1.0 OE1 A:GLU122 2.8 36.6 1.0 OE1 A:GLU205 2.8 63.6 1.0 CD A:GLU205 2.9 43.7 1.0 CD A:GLU122 3.0 32.1 1.0 CG A:ASN118 3.5 46.3 1.0 C A:VAL116 3.6 28.7 1.0 OH A:TYR91 4.1 47.5 1.0 N A:ASN118 4.2 39.1 1.0 CA A:VAL116 4.3 22.7 1.0 CB A:VAL116 4.4 31.3 1.0 N A:VAL116 4.4 48.9 1.0 CB A:ASN118 4.4 38.8 1.0 CG A:GLU205 4.4 49.1 1.0 ND2 A:ASN118 4.4 52.3 1.0 CG1 A:VAL116 4.4 36.1 1.0 CG A:GLU122 4.5 27.3 1.0 N A:ILE117 4.6 37.7 1.0 CA A:ILE117 4.8 37.8 1.0 C A:ILE117 5.0 53.6 1.0 CE2 A:TYR91 5.0 39.6 1.0 CA A:ASN118 5.0 34.8 1.0 CG2 A:VAL115 5.0 47.3 1.0

S.Ishizuka, J.H.M.Van Dijk, T.Kawakita, Y.Miyamoto, Y.Maeda, M.Goto, G.Le Calvez, L.M.Groot, M.D.Witte, A.J.Minnaard, G.A.Van Der Marel, M.Ato, M.Nagae, J.D.C.Codee, S.Yamasaki. Pgl-III, A Rare Intermediate of Mycobacterium Leprae Phenolic Glycolipid Biosynthesis, Is A Potent Mincle Ligand. Acs Cent.Sci. V. 9 1388 2023.
ISSN: ESSN 2374-7951
PubMed: 37521780
DOI: 10.1021/ACSCENTSCI.3C00040