Calcium in PDB 3wh2: Human Mincle in Complex with Citrate

The structure of Human Mincle in Complex with Citrate, PDB code: 3wh2 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)	19.39 / 1.30
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	49.213, 49.213, 43.550, 90.00, 90.00, 120.00
R / Rfree (%)	12.8 / 15.6

The binding sites of Calcium atom in the Human Mincle in Complex with Citrate (pdb code 3wh2). 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 in Complex with Citrate, PDB code: 3wh2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Mincle in Complex with Citrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Mincle in Complex with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:6.1 occ:1.00 OD1 A:ASN171 2.4 7.0 1.0 OA1 A:FLC303 2.4 9.5 1.0 O A:ASP194 2.4 5.0 1.0 OD1 A:ASP194 2.4 5.0 1.0 OD1 A:ASN193 2.5 5.4 1.0 OB1 A:FLC303 2.5 15.0 1.0 OHB A:FLC303 2.6 14.9 1.0 OE1 A:GLU169 2.6 6.6 1.0 CBC A:FLC303 3.2 16.9 1.0 CB A:FLC303 3.4 16.1 1.0 CG A:ASN171 3.4 7.4 1.0 CAC A:FLC303 3.4 12.6 1.0 CD A:GLU169 3.5 6.3 1.0 CG A:ASN193 3.5 5.0 1.0 C A:ASP194 3.5 4.5 1.0 CG A:ASP194 3.5 5.0 1.0 N A:ASP194 3.6 4.2 1.0 OE2 A:GLU169 3.7 7.0 1.0 ND2 A:ASN171 3.9 9.4 1.0 ND2 A:ASN193 3.9 6.5 1.0 CA A:FLC303 3.9 14.6 1.0 CA A:ASP194 4.0 4.3 1.0 N A:ASN171 4.2 5.2 1.0 OB2 A:FLC303 4.3 19.0 1.0 CB A:ASP194 4.4 4.5 1.0 OD2 A:ASP194 4.4 5.5 1.0 OA2 A:FLC303 4.4 14.5 1.0 CB A:ASN172 4.5 7.8 1.0 CB A:ASN171 4.6 6.7 1.0 OG1 A:FLC303 4.6 18.9 1.0 N A:ASN172 4.6 6.5 1.0 O A:HOH490 4.6 26.7 1.0 N A:VAL195 4.7 4.4 1.0 CA A:ASN171 4.7 5.8 1.0 C A:ASN171 4.7 6.3 1.0 CG A:FLC303 4.7 17.2 1.0 C A:ASN193 4.7 4.7 1.0 CG A:GLU169 4.8 6.0 1.0 CB A:ASN193 4.8 5.2 1.0 CA A:ASN193 4.9 4.6 1.0

Calcium binding site 2 out of 2 in the Human Mincle in Complex with Citrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Mincle in Complex with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:6.8 occ:1.00 O A:VAL117 2.3 5.8 1.0 OD1 A:ASN119 2.3 9.8 1.0 O A:HOH426 2.4 11.1 1.0 OE2 A:GLU206 2.4 7.1 1.0 OE2 A:GLU123 2.5 7.5 1.0 O A:HOH437 2.5 11.0 1.0 OE1 A:GLU206 2.8 6.5 1.0 OE1 A:GLU123 2.8 6.9 1.0 CD A:GLU206 2.9 6.8 1.0 CD A:GLU123 3.0 6.4 1.0 C A:VAL117 3.5 4.5 1.0 CG A:ASN119 3.5 8.8 1.0 CB A:ASN119 4.2 8.5 1.0 CA A:VAL117 4.3 4.4 1.0 N A:ASN119 4.3 6.5 1.0 OH A:TYR92 4.3 7.9 1.0 CB A:VAL117 4.3 4.7 1.0 N A:VAL117 4.3 4.2 1.0 CG A:GLU206 4.5 5.7 1.0 O A:HOH531 4.5 22.1 1.0 N A:ILE118 4.5 4.6 1.0 CG A:GLU123 4.5 6.0 1.0 O A:HOH460 4.5 20.0 1.0 ND2 A:ASN119 4.6 10.1 1.0 CA A:ILE118 4.6 5.5 1.0 O A:HOH447 4.7 16.8 1.0 CG1 A:VAL117 4.8 5.5 1.0 O A:HOH419 4.8 11.7 1.0 C A:ILE118 4.9 6.3 1.0 CA A:ASN119 4.9 7.8 1.0 CG2 A:VAL116 4.9 5.3 1.0 O A:HOH570 5.0 27.4 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