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Calcium in PDB 4kzw: Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle

Protein crystallography data

The structure of Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle, PDB code: 4kzw 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) 33.72 / 1.85
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 64.290, 64.290, 127.160, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 22.7

Other elements in 4kzw:

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

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle (pdb code 4kzw). 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, PDB code: 4kzw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4kzw

Go back to Calcium Binding Sites List in 4kzw
Calcium binding site 1 out of 4 in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:39.5
occ:1.00
OD1 A:ASN192 2.3 36.0 1.0
OD1 A:ASN170 2.4 61.2 1.0
OB1 A:FLC301 2.5 64.5 1.0
OE1 A:GLU168 2.5 44.1 1.0
OA2 A:FLC301 2.5 71.4 1.0
O A:ASP193 2.5 42.0 1.0
OHB A:FLC301 2.5 73.6 1.0
OE2 A:GLU168 2.6 42.1 1.0
CD A:GLU168 2.8 43.0 1.0
CBC A:FLC301 3.3 68.6 1.0
CG A:ASN192 3.3 37.5 1.0
CB A:FLC301 3.4 72.7 1.0
CG A:ASN170 3.4 60.8 1.0
C A:ASP193 3.5 41.4 1.0
CAC A:FLC301 3.6 74.5 1.0
N A:ASP193 3.7 40.1 1.0
ND2 A:ASN192 3.7 40.4 1.0
ND2 A:ASN170 3.8 55.2 1.0
CA A:ASP193 4.0 39.9 1.0
CA A:FLC301 4.0 76.2 1.0
CB A:ASP193 4.1 44.1 1.0
OG1 A:FLC301 4.2 71.8 1.0
O A:HOH481 4.2 45.3 1.0
CG A:GLU168 4.3 45.1 1.0
OB2 A:FLC301 4.5 66.0 1.0
O A:HOH457 4.6 61.8 1.0
CB A:ASN192 4.6 35.1 1.0
C A:ASN192 4.6 37.0 1.0
OA1 A:FLC301 4.7 76.5 1.0
N A:VAL194 4.7 37.9 1.0
CG A:FLC301 4.7 80.3 1.0
CB A:ASN170 4.7 59.7 1.0
CA A:ASN192 4.8 36.2 1.0
CG1 A:VAL194 4.8 37.8 1.0
NH1 A:ARG182 4.9 39.1 1.0
CGC A:FLC301 4.9 73.5 1.0

Calcium binding site 2 out of 4 in 4kzw

Go back to Calcium Binding Sites List in 4kzw
Calcium binding site 2 out of 4 in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:34.3
occ:1.00
O A:VAL116 2.4 33.4 1.0
OE2 A:GLU205 2.4 41.0 1.0
OD1 A:ASN118 2.4 47.7 1.0
OE2 A:GLU122 2.4 38.7 1.0
O A:HOH402 2.5 35.4 1.0
O A:HOH401 2.5 33.2 1.0
OE1 A:GLU205 2.5 34.9 1.0
OE1 A:GLU122 2.6 36.4 1.0
CD A:GLU205 2.8 34.0 1.0
CD A:GLU122 2.8 36.3 1.0
C A:VAL116 3.6 39.3 1.0
CG A:ASN118 3.6 48.1 1.0
N A:ASN118 4.2 32.9 1.0
O A:HOH445 4.2 52.4 1.0
OH A:TYR91 4.3 31.2 1.0
N A:VAL116 4.3 28.6 1.0
CG A:GLU205 4.3 33.3 1.0
CA A:VAL116 4.3 29.2 1.0
CB A:ASN118 4.4 44.6 1.0
CG A:GLU122 4.4 37.8 1.0
CB A:VAL116 4.4 36.6 1.0
N A:ILE117 4.5 36.1 1.0
OG A:SER89 4.6 46.4 1.0
ND2 A:ASN118 4.6 47.9 1.0
O A:HOH414 4.6 44.4 1.0
CA A:ILE117 4.6 33.7 1.0
CG2 A:VAL115 4.9 25.3 1.0
CG1 A:VAL116 4.9 39.1 1.0
C A:ILE117 4.9 38.4 1.0
O A:HOH443 4.9 40.8 1.0
CE2 A:TYR91 5.0 27.8 1.0
CA A:ASN118 5.0 33.5 1.0

Calcium binding site 3 out of 4 in 4kzw

Go back to Calcium Binding Sites List in 4kzw
Calcium binding site 3 out of 4 in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca400

b:57.3
occ:1.00
OD1 B:ASP193 2.4 64.4 1.0
OD1 B:ASN170 2.5 63.0 1.0
OD1 B:ASN192 2.5 40.4 1.0
O B:ASP193 2.5 46.9 1.0
OE1 B:GLU168 2.5 61.4 1.0
CD B:GLU168 3.3 52.6 1.0
CG B:ASN170 3.4 71.3 1.0
CG B:ASN192 3.5 40.8 1.0
CG B:ASP193 3.5 58.2 1.0
OE2 B:GLU168 3.5 67.3 1.0
C B:ASP193 3.6 44.4 1.0
N B:ASP193 3.7 39.3 1.0
ND2 B:ASN170 3.8 76.5 1.0
ND2 B:ASN192 3.8 34.4 1.0
CA B:ASP193 4.1 42.2 1.0
OD1 B:ASN171 4.1 80.6 1.0
OD2 B:ASP193 4.2 60.2 1.0
N B:ASN170 4.3 71.2 1.0
CB B:ASP193 4.4 47.5 1.0
CG B:GLU168 4.6 55.3 1.0
CB B:ASN170 4.7 74.7 1.0
N B:VAL194 4.7 37.6 1.0
C B:ASN192 4.8 39.6 1.0
CB B:ASN192 4.8 35.1 1.0
CA B:ASN170 4.9 76.2 1.0
CA B:ASN192 5.0 31.0 1.0

Calcium binding site 4 out of 4 in 4kzw

Go back to Calcium Binding Sites List in 4kzw
Calcium binding site 4 out of 4 in the Structure of the Carbohydrate-Recognition Domain of the C-Type Lectin Mincle


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:35.8
occ:1.00
OE2 B:GLU205 2.3 47.0 1.0
OE2 B:GLU122 2.4 48.4 1.0
OD1 B:ASN118 2.5 66.8 1.0
O B:VAL116 2.5 52.7 1.0
O B:HOH501 2.5 38.3 1.0
O B:HOH502 2.5 46.7 1.0
OE1 B:GLU205 2.6 42.2 1.0
OE1 B:GLU122 2.6 45.4 1.0
CD B:GLU205 2.8 46.9 1.0
CD B:GLU122 2.9 42.7 1.0
CG B:ASN118 3.6 61.1 1.0
C B:VAL116 3.7 44.2 1.0
CG B:GLU205 4.3 51.7 1.0
OH B:TYR91 4.3 44.6 1.0
OG B:SER89 4.3 66.8 1.0
N B:VAL116 4.3 37.9 1.0
CG B:GLU122 4.4 44.5 1.0
CB B:ASN118 4.4 57.3 1.0
CA B:VAL116 4.5 38.0 1.0
N B:ASN118 4.5 50.2 1.0
ND2 B:ASN118 4.5 64.5 1.0
CB B:VAL116 4.6 44.0 1.0
O B:HOH543 4.6 48.4 1.0
N B:ILE117 4.7 45.8 1.0
CG2 B:VAL115 4.7 32.1 1.0
O B:HOH527 4.7 48.8 1.0
CE2 B:TYR91 4.8 36.9 1.0
O B:HOH563 4.8 35.5 1.0
O B:HOH562 4.9 51.8 1.0
CA B:ILE117 4.9 44.0 1.0

Reference:

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
Page generated: Tue Jul 8 23:42:45 2025

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