Calcium in PDB 3whd: C-Type Lectin, Human Mcl

The structure of C-Type Lectin, Human Mcl, PDB code: 3whd 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)	40.48 / 2.29
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	85.190, 96.056, 104.826, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.8

The binding sites of Calcium atom in the C-Type Lectin, Human Mcl (pdb code 3whd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the C-Type Lectin, Human Mcl, PDB code: 3whd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the C-Type Lectin, Human Mcl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C-Type Lectin, Human Mcl within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:32.9 occ:1.00 OD1 A:ASN195 2.3 27.2 1.0 OD1 A:ASP196 2.4 30.0 1.0 OE1 A:GLU173 2.4 36.2 1.0 OD1 A:ASP175 2.4 33.8 1.0 O A:HOH680 2.5 38.5 1.0 O A:ASP196 2.5 31.3 1.0 O A:HOH687 2.5 33.5 1.0 CD A:GLU173 3.2 31.1 1.0 CG A:ASP175 3.4 38.1 1.0 CG A:ASP196 3.4 32.7 1.0 OE2 A:GLU173 3.4 34.9 1.0 CG A:ASN195 3.5 31.6 1.0 OD1 A:ASN176 3.5 46.1 1.0 C A:ASP196 3.5 30.0 1.0 N A:ASP196 3.6 25.1 1.0 OD2 A:ASP175 3.8 42.2 1.0 CA A:ASP196 4.0 25.2 1.0 ND2 A:ASN195 4.1 32.1 1.0 OD2 A:ASP196 4.1 35.2 1.0 O A:HOH719 4.3 42.9 1.0 N A:ASP175 4.3 30.9 1.0 CB A:ASP196 4.3 28.2 1.0 CG A:ASN176 4.3 44.9 1.0 C A:ASN195 4.5 29.6 1.0 CG A:GLU173 4.6 27.3 1.0 CB A:ASP175 4.6 35.7 1.0 ND2 A:ASN176 4.7 38.1 1.0 N A:VAL197 4.7 29.1 1.0 CB A:ASN195 4.7 28.4 1.0 CA A:ASN195 4.8 30.5 1.0 CA A:ASP175 4.8 35.6 1.0 N A:ASN176 4.9 33.5 1.0

Calcium binding site 2 out of 2 in the C-Type Lectin, Human Mcl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C-Type Lectin, Human Mcl within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:27.2 occ:1.00 O C:ASP196 2.3 23.9 1.0 OE1 C:GLU173 2.4 25.7 1.0 OD1 C:ASP196 2.4 26.2 1.0 OD1 C:ASP175 2.4 26.9 1.0 O C:HOH693 2.4 28.2 1.0 O C:HOH624 2.4 26.3 1.0 OD1 C:ASN195 2.4 25.6 1.0 CD C:GLU173 3.3 29.3 1.0 C C:ASP196 3.4 25.8 1.0 OE2 C:GLU173 3.5 29.3 1.0 CG C:ASP175 3.5 31.7 1.0 CG C:ASP196 3.6 26.5 1.0 N C:ASP196 3.6 25.9 1.0 CG C:ASN195 3.6 28.8 1.0 CA C:ASP196 3.9 26.8 1.0 OD2 C:ASP175 4.0 33.1 1.0 O C:HOH633 4.0 34.6 1.0 N C:ASN176 4.2 27.9 1.0 N C:ASP175 4.2 28.5 1.0 ND2 C:ASN195 4.3 27.8 1.0 CB C:ASP196 4.4 23.0 1.0 C C:ASN195 4.4 27.4 1.0 OD2 C:ASP196 4.4 27.1 1.0 C C:ASP175 4.5 30.2 1.0 N C:VAL197 4.6 25.1 1.0 O C:HOH668 4.6 34.8 1.0 CB C:ASN176 4.6 27.6 1.0 CA C:ASN176 4.6 29.7 1.0 CG C:GLU173 4.6 28.0 1.0 CB C:ASP175 4.7 28.6 1.0 CA C:ASP175 4.7 29.8 1.0 CA C:ASN195 4.7 25.5 1.0 CB C:ASN195 4.8 23.7 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