Calcium in PDB 4kzv: Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose

The structure of Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose, PDB code: 4kzv was solved by H.Feinberg, S.A.F.Jegouzo, T.J.W.Rowntree, Y.Guan, M.A.Brash, M.E.Taylor, W.I.Weis, K.Drickamer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.74 / 1.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.480, 73.480, 99.340, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.7

The structure of Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose (pdb code 4kzv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose, PDB code: 4kzv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:13.1 occ:1.00 OD1 A:ASP193 2.3 12.7 1.0 OD1 A:ASN170 2.4 15.2 1.0 OE1 A:GLU176 2.4 14.8 1.0 OD1 A:ASN192 2.4 13.2 1.0 O A:ASP193 2.5 12.9 1.0 O3P A:TRE301 2.5 14.8 1.0 O4P A:TRE301 2.5 15.1 1.0 OE1 A:GLU168 2.5 14.2 1.0 CG A:ASP193 3.3 12.4 1.0 C3P A:TRE301 3.3 14.9 1.0 CD A:GLU176 3.4 15.0 1.0 C4P A:TRE301 3.4 13.8 1.0 CG A:ASN170 3.4 15.6 1.0 CD A:GLU168 3.4 14.2 1.0 CG A:ASN192 3.5 12.0 1.0 C A:ASP193 3.5 11.6 1.0 OE2 A:GLU176 3.7 15.7 1.0 N A:ASP193 3.7 12.1 1.0 OE2 A:GLU168 3.7 15.6 1.0 ND2 A:ASN192 3.9 13.5 1.0 ND2 A:ASN170 3.9 18.0 1.0 CA A:ASP193 4.0 11.8 1.0 OD2 A:ASP193 4.1 11.9 1.0 N A:ASN170 4.1 13.3 1.0 CB A:ASP193 4.3 11.9 1.0 N A:ASN171 4.6 13.9 1.0 CB A:ASN170 4.6 14.4 1.0 N A:LEU172 4.6 17.2 1.0 CG A:GLU176 4.6 13.8 1.0 C A:ASN192 4.7 12.5 1.0 N A:VAL194 4.7 11.5 1.0 CG A:GLU168 4.7 14.6 1.0 CA A:ASN170 4.7 14.5 1.0 CB A:LEU172 4.7 20.5 1.0 C2P A:TRE301 4.8 15.2 1.0 CB A:ASN192 4.8 13.6 1.0 C5P A:TRE301 4.8 14.8 1.0 CB A:GLU176 4.8 12.4 1.0 CA A:ASN192 4.9 12.1 1.0 C A:ASN170 4.9 14.1 1.0

Calcium binding site 2 out of 4 in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:13.2 occ:1.00 OD1 A:ASN118 2.4 14.7 1.0 O A:VAL116 2.4 11.9 1.0 O A:HOH405 2.4 16.7 1.0 O A:HOH415 2.4 16.4 1.0 OE2 A:GLU122 2.4 13.3 1.0 OE2 A:GLU205 2.4 14.1 1.0 OE1 A:GLU205 2.6 13.7 1.0 OE1 A:GLU122 2.8 14.1 1.0 CD A:GLU205 2.9 13.5 1.0 CD A:GLU122 2.9 13.0 1.0 C A:VAL116 3.5 11.1 1.0 CG A:ASN118 3.6 14.9 1.0 N A:ASN118 4.3 13.0 1.0 CA A:VAL116 4.3 10.5 1.0 N A:VAL116 4.3 10.8 1.0 CB A:VAL116 4.3 11.6 1.0 OH A:TYR91 4.3 14.0 1.0 O A:HOH537 4.3 32.0 1.0 CB A:ASN118 4.4 14.0 1.0 O A:HOH435 4.4 24.3 1.0 CG A:GLU205 4.4 13.0 1.0 CG A:GLU122 4.5 14.0 1.0 O A:HOH414 4.5 18.6 1.0 ND2 A:ASN118 4.5 16.6 1.0 N A:ILE117 4.6 10.7 1.0 CA A:ILE117 4.7 12.0 1.0 CG1 A:VAL116 4.7 13.2 1.0 O A:HOH427 4.7 22.9 1.0 OG A:SER89 4.8 18.1 1.0 O A:HOH417 4.8 22.2 1.0 CG2 A:VAL115 4.9 14.5 1.0 C A:ILE117 5.0 11.7 1.0 CA A:ASN118 5.0 14.8 1.0

Calcium binding site 3 out of 4 in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:39.9 occ:1.00 OD1 B:ASN192 2.3 41.0 1.0 OD1 B:ASP193 2.5 32.6 1.0 OD1 B:ASN170 2.5 50.8 1.0 OE1 B:GLU168 2.5 39.6 1.0 O B:ASP193 2.6 36.7 1.0 OD1 B:ASN171 2.8 83.8 1.0 CD B:GLU168 3.4 73.4 1.0 CG B:ASN192 3.4 58.0 1.0 CG B:ASN170 3.4 50.3 1.0 CG B:ASP193 3.6 70.0 1.0 N B:ASP193 3.6 37.4 1.0 C B:ASP193 3.6 38.9 1.0 OE2 B:GLU168 3.7 52.6 1.0 ND2 B:ASN170 3.8 77.4 1.0 ND2 B:ASN192 3.9 42.4 1.0 CG B:ASN171 4.0 30.8 1.0 CA B:ASP193 4.0 29.4 1.0 N B:ASN170 4.3 43.5 1.0 OD2 B:ASP193 4.3 32.6 1.0 CB B:ASP193 4.4 31.4 1.0 C B:ASN192 4.6 33.9 1.0 CB B:ASN192 4.7 36.9 1.0 N B:ASN171 4.7 54.7 1.0 CG B:GLU168 4.7 70.9 1.0 CB B:ASN170 4.7 37.5 1.0 CA B:ASN192 4.8 47.3 1.0 ND2 B:ASN171 4.8 81.6 1.0 N B:VAL194 4.8 32.5 1.0 NH1 B:ARG182 4.9 44.4 1.0 CA B:ASN170 4.9 76.8 1.0

Calcium binding site 4 out of 4 in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle Bound to Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:18.9 occ:1.00 O B:VAL116 2.3 18.5 1.0 OD1 B:ASN118 2.4 17.4 1.0 OE2 B:GLU205 2.4 23.4 1.0 O B:HOH513 2.4 20.9 1.0 OE2 B:GLU122 2.4 24.5 1.0 O B:HOH514 2.5 20.2 1.0 OE1 B:GLU205 2.6 23.5 1.0 OE1 B:GLU122 2.6 25.3 1.0 CD B:GLU205 2.9 25.4 1.0 CD B:GLU122 2.9 24.9 1.0 C B:VAL116 3.5 18.0 1.0 CG B:ASN118 3.6 17.2 1.0 N B:ASN118 4.2 19.0 1.0 CA B:VAL116 4.2 17.5 1.0 CB B:VAL116 4.2 16.6 1.0 N B:VAL116 4.2 16.7 1.0 O B:HOH567 4.2 36.0 1.0 CG B:GLU122 4.4 26.6 1.0 CG B:GLU205 4.4 23.1 1.0 CB B:ASN118 4.4 19.2 1.0 OH B:TYR91 4.4 24.3 1.0 N B:ILE117 4.5 16.9 1.0 ND2 B:ASN118 4.5 19.3 1.0 O B:HOH566 4.6 34.5 1.0 CA B:ILE117 4.6 19.0 1.0 O B:HOH508 4.7 19.5 1.0 CG1 B:VAL116 4.7 16.4 1.0 OG B:SER89 4.7 24.3 1.0 O B:HOH515 4.8 22.8 1.0 CG2 B:VAL115 4.8 20.1 1.0 O B:HOH564 4.9 32.6 1.0 C B:ILE117 4.9 17.7 1.0 CA B:ASN118 5.0 18.0 1.0 CE1 B:HIS113 5.0 16.4 1.0

H.Feinberg, S.A.Jegouzo, T.J.Rowntree, Y.Guan, M.A.Brash, M.E.Taylor, W.I.Weis, K.Drickamer. Mechanism For Recognition of An Unusual Mycobacterial Glycolipid By the Macrophage Receptor Mincle. J.Biol.Chem. V. 288 28457 2013.
ISSN: ISSN 0021-9258
PubMed: 23960080
DOI: 10.1074/JBC.M113.497149