Calcium in PDB 3wh3: Human Mincle, Ligand Free Form

The structure of Human Mincle, Ligand Free Form, PDB code: 3wh3 was solved by A.Furukawa, J.Kamishikiryo, D.Mori, K.Toyonaga, Y.Okabe, A.Toji, R.Kanda, Y.Miyake, T.Ose, S.Yamasaki, K.Maenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.54 / 1.32
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	49.074, 49.074, 43.042, 90.00, 90.00, 120.00
R / Rfree (%)	13.7 / 17.1

The binding sites of Calcium atom in the Human Mincle, Ligand Free Form (pdb code 3wh3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Mincle, Ligand Free Form, PDB code: 3wh3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Mincle, Ligand Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Mincle, Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:9.7 occ:1.00 OD1 A:ASN171 2.4 12.5 1.0 O A:HOH715 2.4 18.2 1.0 OD1 A:ASP194 2.4 8.9 1.0 OD1 A:ASN193 2.4 9.6 1.0 O A:ASP194 2.5 8.0 1.0 O A:HOH625 2.5 16.2 1.0 OE1 A:GLU169 2.6 10.5 1.0 CG A:ASN171 3.4 12.4 1.0 CG A:ASN193 3.4 8.9 1.0 CD A:GLU169 3.5 11.0 1.0 C A:ASP194 3.5 7.7 1.0 CG A:ASP194 3.5 9.5 1.0 N A:ASP194 3.6 8.0 1.0 OE2 A:GLU169 3.7 11.7 1.0 O A:HOH753 3.8 14.8 1.0 ND2 A:ASN193 3.8 10.6 1.0 ND2 A:ASN171 3.9 14.3 1.0 CA A:ASP194 4.0 8.1 1.0 N A:ASN171 4.2 9.4 1.0 CB A:ASP194 4.4 8.3 1.0 OD2 A:ASP194 4.4 10.1 1.0 O A:HOH738 4.5 31.4 1.0 CB A:ASN172 4.5 13.1 1.0 CB A:ASN171 4.6 11.6 1.0 N A:ASN172 4.7 11.3 1.0 N A:VAL195 4.7 7.8 1.0 C A:ASN193 4.7 8.9 1.0 CA A:ASN171 4.7 10.4 1.0 CB A:ASN193 4.7 8.5 1.0 C A:ASN171 4.7 11.3 1.0 CG A:GLU169 4.8 10.1 1.0 CA A:ASN193 4.9 8.3 1.0

Calcium binding site 2 out of 2 in the Human Mincle, Ligand Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Mincle, Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:17.3 occ:1.00 OD1 A:ASN119 2.4 21.9 1.0 O A:VAL117 2.4 9.1 1.0 O A:HOH636 2.4 27.9 1.0 OE2 A:GLU206 2.4 12.8 1.0 O A:HOH626 2.4 26.4 1.0 OE2 A:GLU123 2.6 18.2 1.0 OE1 A:GLU206 2.9 12.0 1.0 OE1 A:GLU123 2.9 12.4 1.0 CD A:GLU206 3.0 12.3 1.0 CD A:GLU123 3.1 13.0 1.0 CG A:ASN119 3.5 20.0 1.0 C A:VAL117 3.5 8.3 1.0 OH A:TYR92 4.1 13.4 1.0 CB A:ASN119 4.2 16.7 1.0 N A:ASN119 4.3 11.6 1.0 CA A:VAL117 4.3 8.3 1.0 CB A:VAL117 4.3 8.5 1.0 N A:VAL117 4.4 7.7 1.0 CG A:GLU206 4.5 10.6 1.0 N A:ILE118 4.5 8.4 1.0 ND2 A:ASN119 4.6 20.1 1.0 CG A:GLU123 4.6 11.8 1.0 CA A:ILE118 4.7 9.4 1.0 O A:HOH654 4.7 24.0 1.0 O A:HOH618 4.8 21.3 1.0 CG1 A:VAL117 4.8 9.2 1.0 OG A:SER90 4.9 21.4 1.0 CA A:ASN119 4.9 13.8 1.0 C A:ILE118 4.9 10.6 1.0 CG2 A:VAL116 4.9 8.9 1.0 CE2 A:TYR92 5.0 10.9 1.0

A.Furukawa, J.Kamishikiryo, D.Mori, K.Toyonaga, Y.Okabe, A.Toji, R.Kanda, Y.Miyake, T.Ose, S.Yamasaki, K.Maenaka. Structural Analysis For Glycolipid Recognition By the C-Type Lectins Mincle and Mcl Proc.Natl.Acad.Sci.Usa V. 110 17438 2013.
ISSN: ISSN 0027-8424
PubMed: 24101491
DOI: 10.1073/PNAS.1312649110