Calcium in PDB 5kth: Structure of Cow Mincle Complexed with Brartemicin

The structure of Structure of Cow Mincle Complexed with Brartemicin, PDB code: 5kth was solved by H.Feinberg, N.D.S.Rambaruth, S.A.F.Jegouzo, K.M.Jacobsen, R.Djurhuus, T.B.Poulsen, M.E.Taylor, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.45 / 2.21
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.332, 98.332, 45.636, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 21

The binding sites of Calcium atom in the Structure of Cow Mincle Complexed with Brartemicin (pdb code 5kth). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Cow Mincle Complexed with Brartemicin, PDB code: 5kth:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Cow Mincle Complexed with Brartemicin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Cow Mincle Complexed with Brartemicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:28.9 occ:1.00 OD1 A:ASP193 2.3 28.5 1.0 OD1 A:ASN170 2.3 34.0 1.0 OD1 A:ASN192 2.4 28.7 1.0 OE1 A:GLU168 2.4 34.8 1.0 O4P A:TRE301 2.4 32.3 1.0 OE1 A:GLU176 2.5 29.3 1.0 O3P A:TRE301 2.5 29.7 1.0 O A:ASP193 2.5 25.4 1.0 C3P A:TRE301 3.2 34.4 1.0 C4P A:TRE301 3.3 36.4 1.0 CG A:ASP193 3.3 26.6 1.0 CD A:GLU168 3.4 33.2 1.0 CG A:ASN170 3.4 33.4 1.0 CD A:GLU176 3.4 32.0 1.0 CG A:ASN192 3.5 28.4 1.0 C A:ASP193 3.5 23.6 1.0 N A:ASP193 3.6 28.3 1.0 OE2 A:GLU168 3.7 37.0 1.0 OE2 A:GLU176 3.7 35.0 1.0 ND2 A:ASN170 3.9 31.5 1.0 ND2 A:ASN192 4.0 27.9 1.0 CA A:ASP193 4.0 26.4 1.0 OD2 A:ASP193 4.1 26.2 1.0 N A:ASN170 4.2 33.7 1.0 CB A:ASP193 4.2 27.0 1.0 C A:ASN192 4.6 33.3 1.0 CB A:ASN170 4.7 32.1 1.0 C5P A:TRE301 4.7 37.5 1.0 CG A:GLU168 4.7 32.1 1.0 CG A:GLU176 4.7 30.7 1.0 C2P A:TRE301 4.7 30.8 1.0 N A:VAL194 4.7 23.7 1.0 CB A:ASN192 4.7 28.0 1.0 N A:ASN171 4.7 30.1 1.0 CB A:GLU176 4.8 28.6 1.0 CA A:ASN170 4.8 35.3 1.0 CG A:LEU172 4.8 34.3 1.0 CA A:ASN192 4.9 26.6 1.0

Calcium binding site 2 out of 3 in the Structure of Cow Mincle Complexed with Brartemicin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Cow Mincle Complexed with Brartemicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:30.2 occ:1.00 O A:VAL116 2.3 29.3 1.0 OD1 A:ASN118 2.3 31.8 1.0 OE2 A:GLU205 2.3 35.2 1.0 O A:HOH424 2.3 31.0 1.0 OE2 A:GLU122 2.4 35.7 1.0 O A:HOH444 2.4 38.8 1.0 OE1 A:GLU205 2.5 35.5 1.0 CD A:GLU205 2.8 36.1 1.0 OE1 A:GLU122 2.8 35.5 1.0 CD A:GLU122 3.0 33.3 1.0 C A:VAL116 3.5 30.7 1.0 CG A:ASN118 3.5 33.3 1.0 N A:ASN118 4.2 32.4 1.0 CA A:VAL116 4.2 28.0 1.0 N A:VAL116 4.3 28.4 1.0 OH A:TYR91 4.3 32.7 1.0 CB A:VAL116 4.3 28.4 1.0 CG A:GLU205 4.3 29.7 1.0 CB A:ASN118 4.4 37.3 1.0 N A:ILE117 4.4 28.5 1.0 O A:HOH409 4.4 49.0 1.0 ND2 A:ASN118 4.5 31.8 1.0 CG A:GLU122 4.5 35.6 1.0 O A:HOH415 4.5 34.2 1.0 O A:HOH410 4.5 48.0 1.0 CA A:ILE117 4.6 31.6 1.0 CG1 A:VAL116 4.8 28.1 1.0 CG2 A:VAL115 4.8 28.0 1.0 C A:ILE117 4.9 33.3 1.0 CA A:ASN118 5.0 34.4 1.0 CE1 A:HIS113 5.0 29.4 1.0 OG A:SER89 5.0 49.5 1.0

Calcium binding site 3 out of 3 in the Structure of Cow Mincle Complexed with Brartemicin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Cow Mincle Complexed with Brartemicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:31.8 occ:1.00 O A:HOH417 2.3 31.4 1.0 OD1 A:ASP177 2.4 31.0 1.0 OD1 A:ASN171 2.4 31.5 1.0 O A:GLU176 2.5 29.6 1.0 OE1 A:GLU146 2.5 38.2 1.0 OD2 A:ASP142 2.5 30.5 1.0 OE2 A:GLU146 2.6 37.4 1.0 OD1 A:ASP142 2.6 32.9 1.0 CD A:GLU146 2.9 38.3 1.0 CG A:ASP142 3.0 34.5 1.0 CG A:ASN171 3.3 36.5 1.0 C A:GLU176 3.4 28.8 1.0 CG A:ASP177 3.5 36.0 1.0 CA A:ASP177 3.7 26.0 1.0 N A:ASP177 4.0 24.4 1.0 CB A:ASP177 4.1 27.6 1.0 ND2 A:ASN171 4.1 32.6 1.0 CB A:ASN171 4.2 28.4 1.0 CZ2 A:TRP149 4.3 26.9 1.0 CG A:GLU146 4.4 35.8 1.0 OD2 A:ASP177 4.4 38.0 1.0 O A:HOH440 4.4 41.8 1.0 CB A:ASP142 4.5 31.4 1.0 N A:GLU176 4.5 25.1 1.0 CA A:GLU176 4.5 27.8 1.0 CH2 A:TRP149 4.6 28.6 1.0 CA A:ASN171 4.7 31.9 1.0 OD2 A:ASP193 4.7 26.2 1.0 O A:ASP142 4.8 32.7 1.0 N A:GLY147 4.9 38.4 1.0 C A:ASP177 5.0 28.8 1.0

H.Feinberg, N.D.Rambaruth, S.A.Jegouzo, K.M.Jacobsen, R.Djurhuus, T.B.Poulsen, W.I.Weis, M.E.Taylor, K.Drickamer. Binding Sites For Acylated Trehalose Analogs of Glycolipid Ligands on An Extended Carbohydrate Recognition Domain of the Macrophage Receptor Mincle. J.Biol.Chem. V. 291 21222 2016.
ISSN: ESSN 1083-351X
PubMed: 27542410
DOI: 10.1074/JBC.M116.749515