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Calcium in PDB 5g6u: Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S

Protein crystallography data

The structure of Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S, PDB code: 5g6u was solved by V.Porkolab, E.Chabrol, N.Varga, S.Ordanini, I.Sutkeviciute, M.Thepaut, A.Bernardi, F.Fieschi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.40 / 1.84
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 79.483, 79.483, 90.710, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 18

Other elements in 5g6u:

The structure of Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms
Europium (Eu) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S (pdb code 5g6u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S, PDB code: 5g6u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5g6u

Go back to Calcium Binding Sites List in 5g6u
Calcium binding site 1 out of 4 in the Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1329

b:32.0
occ:0.70
EU A:EU1328 0.3 32.4 0.3
OD1 A:ASP308 2.4 30.8 1.0
OE1 A:GLU285 2.5 30.3 1.0
OD1 A:ASN307 2.5 33.1 1.0
OD1 A:ASN287 2.6 32.5 1.0
O A:ASP308 2.6 25.5 1.0
OE1 A:GLU293 2.7 30.1 1.0
O08 A:YJM1327 2.8 34.1 1.0
O09 A:YJM1327 2.9 39.8 1.0
CD A:GLU285 3.2 31.1 1.0
H A:ASP308 3.3 30.8 1.0
H A:ASN287 3.3 36.5 1.0
CG A:ASP308 3.3 30.0 1.0
HD22 A:ASN307 3.5 38.9 1.0
CG A:ASN307 3.5 30.8 1.0
OE2 A:GLU285 3.5 31.5 1.0
CG A:ASN287 3.5 35.6 1.0
CD A:GLU293 3.5 30.3 1.0
C03 A:YJM1327 3.6 42.8 1.0
C A:ASP308 3.6 24.5 1.0
C04 A:YJM1327 3.6 43.0 1.0
N A:ASP308 3.7 25.7 1.0
HD22 A:ASN287 3.8 47.2 1.0
OE2 A:GLU293 3.8 29.0 1.0
ND2 A:ASN307 3.8 32.4 1.0
OD2 A:ASP308 3.9 34.4 1.0
ND2 A:ASN287 4.0 39.4 1.0
H A:ASN288 4.0 41.7 1.0
CA A:ASP308 4.0 24.1 1.0
H A:ALA289 4.1 48.6 1.0
N A:ASN287 4.1 30.4 1.0
HA A:PRO286 4.2 32.9 1.0
CB A:ASP308 4.2 25.7 1.0
HB3 A:GLU285 4.4 34.4 1.0
CG A:GLU285 4.5 29.5 1.0
HB3 A:GLU293 4.5 32.2 1.0
HA A:ASN307 4.5 30.4 1.0
N A:ASN288 4.6 34.8 1.0
HB3 A:ALA289 4.6 54.5 1.0
HA A:ALA309 4.6 29.3 1.0
HG3 A:GLU285 4.6 35.4 1.0
HD21 A:ASN307 4.6 38.9 1.0
CB A:ASN287 4.7 37.1 1.0
C A:ASN307 4.7 23.2 1.0
CB A:ASN307 4.7 27.2 1.0
N A:ALA309 4.8 22.7 1.0
HB2 A:ASP308 4.8 30.8 1.0
CA A:ASN287 4.8 33.5 1.0
HD21 A:ASN287 4.8 47.2 1.0
CG A:GLU293 4.8 28.3 1.0
HB1 A:ALA289 4.8 54.5 1.0
HB2 A:GLU293 4.8 32.2 1.0
HA A:GLU285 4.9 37.7 1.0
CA A:ASN307 4.9 25.4 1.0
CB A:GLU285 4.9 28.6 1.0
HB3 A:ASP308 4.9 30.8 1.0
HB3 A:ASN287 4.9 44.6 1.0
N A:ALA289 4.9 40.5 1.0
CB A:GLU293 5.0 26.8 1.0
C02 A:YJM1327 5.0 51.2 1.0
HA A:ASP308 5.0 28.9 1.0

Calcium binding site 2 out of 4 in 5g6u

Go back to Calcium Binding Sites List in 5g6u
Calcium binding site 2 out of 4 in the Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1328

b:24.4
occ:0.70
EU B:EU1327 0.2 28.8 0.3
OE1 B:GLU285 2.5 27.4 1.0
OD1 B:ASP308 2.5 29.0 1.0
OD1 B:ASN307 2.5 23.4 1.0
OD1 B:ASN287 2.5 30.9 1.0
O B:ASP308 2.7 20.5 1.0
OE1 B:GLU293 2.7 28.2 1.0
O08 B:YJM1326 2.7 43.6 1.0
O09 B:YJM1326 2.8 41.9 1.0
CD B:GLU285 3.3 26.4 1.0
H B:ASN287 3.4 36.6 1.0
CG B:ASN287 3.5 33.9 1.0
C03 B:YJM1326 3.5 51.9 1.0
H B:ASP308 3.5 27.2 1.0
CG B:ASN307 3.5 26.1 1.0
CG B:ASP308 3.5 30.2 1.0
HD22 B:ASN307 3.5 31.4 1.0
C04 B:YJM1326 3.5 48.1 1.0
CD B:GLU293 3.6 26.6 1.0
OE2 B:GLU285 3.6 28.0 1.0
HD22 B:ASN287 3.7 40.9 1.0
C B:ASP308 3.7 22.5 1.0
ND2 B:ASN307 3.9 26.2 1.0
OE2 B:GLU293 3.9 27.7 1.0
N B:ASP308 3.9 22.7 1.0
ND2 B:ASN287 3.9 34.1 1.0
H B:ALA289 4.1 38.0 1.0
OD2 B:ASP308 4.2 29.0 1.0
CA B:ASP308 4.2 23.1 1.0
N B:ASN287 4.2 30.5 1.0
H B:ASN288 4.2 39.2 1.0
HA B:PRO286 4.3 35.5 1.0
HB3 B:ALA289 4.4 36.7 1.0
CB B:ASP308 4.4 24.4 1.0
HB3 B:GLU285 4.5 28.6 1.0
HA B:ASN307 4.5 27.0 1.0
CG B:GLU285 4.6 25.9 1.0
HB3 B:GLU293 4.6 29.7 1.0
HA B:ALA309 4.6 28.0 1.0
CB B:ASN287 4.6 33.9 1.0
HG3 B:GLU285 4.7 31.1 1.0
HB1 B:ALA289 4.7 36.7 1.0
HD21 B:ASN307 4.7 31.4 1.0
N B:ASN288 4.7 32.7 1.0
HD21 B:ASN287 4.7 40.9 1.0
CB B:ASN307 4.8 22.7 1.0
C B:ASN307 4.8 20.6 1.0
C02 B:YJM1326 4.8 63.2 1.0
CA B:ASN287 4.8 31.5 1.0
N B:ALA309 4.9 22.5 1.0
HB3 B:ASN287 4.9 40.6 1.0
HA B:GLU285 4.9 31.9 1.0
CG B:GLU293 4.9 25.4 1.0
HB2 B:GLU293 4.9 29.7 1.0
O B:HOH2101 4.9 29.1 1.0
N B:ALA289 4.9 31.7 1.0
CA B:ASN307 4.9 22.5 1.0
C05 B:YJM1326 4.9 53.1 1.0
HB2 B:ASP308 5.0 29.3 1.0
CB B:GLU285 5.0 23.9 1.0
CB B:ALA289 5.0 30.6 1.0

Calcium binding site 3 out of 4 in 5g6u

Go back to Calcium Binding Sites List in 5g6u
Calcium binding site 3 out of 4 in the Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1327

b:34.4
occ:0.70
EU C:EU1328 0.2 34.8 0.3
OD1 C:ASP308 2.4 30.6 1.0
OE1 C:GLU285 2.5 34.0 1.0
OD1 C:ASN287 2.6 37.1 1.0
OD1 C:ASN307 2.6 28.9 1.0
O C:ASP308 2.6 25.4 1.0
OE1 C:GLU293 2.6 34.4 1.0
O08 C:YJM1326 2.8 52.1 1.0
O09 C:YJM1326 2.9 51.2 1.0
H C:ASP308 3.2 28.9 1.0
CG C:ASP308 3.3 32.5 1.0
CD C:GLU285 3.4 33.9 1.0
H C:ASN287 3.4 48.5 1.0
HD22 C:ASN307 3.4 36.8 1.0
CG C:ASN307 3.5 27.4 1.0
CD C:GLU293 3.5 35.1 1.0
CG C:ASN287 3.6 43.0 1.0
C C:ASP308 3.6 24.7 1.0
C04 C:YJM1326 3.6 56.8 1.0
C03 C:YJM1326 3.6 58.4 1.0
OE2 C:GLU285 3.7 35.5 1.0
N C:ASP308 3.8 24.1 1.0
HD22 C:ASN287 3.8 52.8 1.0
OE2 C:GLU293 3.8 35.5 1.0
ND2 C:ASN307 3.8 30.7 1.0
OD2 C:ASP308 3.9 35.4 1.0
H C:ALA289 4.0 52.9 1.0
ND2 C:ASN287 4.0 44.0 1.0
CA C:ASP308 4.1 24.1 1.0
CB C:ASP308 4.2 26.4 1.0
N C:ASN287 4.2 40.4 1.0
H C:ASN288 4.3 47.2 1.0
HA C:PRO286 4.3 42.0 1.0
HB3 C:GLU285 4.4 39.4 1.0
HB3 C:ALA289 4.5 58.1 1.0
HB1 C:ALA289 4.5 58.1 1.0
HB3 C:GLU293 4.5 35.5 1.0
CG C:GLU285 4.5 34.5 1.0
HA C:ASN307 4.6 26.5 1.0
HD21 C:ASN307 4.6 36.8 1.0
HA C:ALA309 4.6 26.6 1.0
HG3 C:GLU285 4.6 41.4 1.0
C C:ASN307 4.7 21.4 1.0
N C:ASN288 4.7 39.3 1.0
HB2 C:ASP308 4.7 31.7 1.0
CB C:ASN287 4.7 43.0 1.0
N C:ALA309 4.8 21.4 1.0
CB C:ASN307 4.8 22.6 1.0
CG C:GLU293 4.8 33.9 1.0
HB2 C:GLU293 4.8 35.5 1.0
N C:ALA289 4.8 44.1 1.0
HD21 C:ASN287 4.9 52.8 1.0
HA C:GLU285 4.9 42.3 1.0
CA C:ASN287 4.9 42.9 1.0
CA C:ASN307 4.9 22.1 1.0
HB3 C:ASP308 4.9 31.7 1.0
CB C:GLU285 4.9 32.9 1.0
CB C:ALA289 4.9 48.4 1.0
CB C:GLU293 5.0 29.6 1.0
C02 C:YJM1326 5.0 66.6 1.0

Calcium binding site 4 out of 4 in 5g6u

Go back to Calcium Binding Sites List in 5g6u
Calcium binding site 4 out of 4 in the Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Langerin Carbohydrate Recognition Domain with GLCNS6S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1326

b:23.0
occ:1.00
OE1 D:GLU293 2.3 34.0 1.0
OD1 D:ASP308 2.3 29.6 1.0
OE1 D:GLU285 2.3 28.4 1.0
OD1 D:ASN287 2.4 36.2 1.0
O D:ASP308 2.5 26.6 1.0
O08 D:YJM1325 2.5 50.1 1.0
O09 D:YJM1325 2.5 49.2 1.0
OD1 D:ASN307 2.5 36.3 1.0
CD D:GLU293 3.2 35.1 1.0
C04 D:YJM1325 3.3 52.0 1.0
CD D:GLU285 3.3 31.8 1.0
C03 D:YJM1325 3.3 53.5 1.0
CG D:ASP308 3.3 31.4 1.0
H D:ASP308 3.4 31.3 1.0
H D:ASN287 3.4 40.9 1.0
HD22 D:ASN307 3.4 37.5 1.0
CG D:ASN287 3.4 36.6 1.0
CG D:ASN307 3.5 30.2 1.0
C D:ASP308 3.5 25.7 1.0
OE2 D:GLU293 3.6 34.9 1.0
OE2 D:GLU285 3.7 31.9 1.0
HD22 D:ASN287 3.7 48.0 1.0
ND2 D:ASN307 3.8 31.3 1.0
N D:ASP308 3.9 26.1 1.0
H D:ALA289 3.9 46.6 1.0
ND2 D:ASN287 4.0 40.0 1.0
OD2 D:ASP308 4.0 33.0 1.0
CA D:ASP308 4.1 26.8 1.0
H D:ASN288 4.1 42.2 1.0
N D:ASN287 4.2 34.1 1.0
HB3 D:ALA289 4.3 49.5 1.0
CB D:ASP308 4.3 28.0 1.0
HB3 D:GLU293 4.4 38.0 1.0
HB3 D:GLU285 4.4 37.8 1.0
HA D:PRO286 4.4 38.3 1.0
HA D:ALA309 4.5 32.4 1.0
HB1 D:ALA289 4.5 49.5 1.0
CG D:GLU285 4.5 32.1 1.0
CG D:GLU293 4.5 34.9 1.0
N D:ASN288 4.6 35.2 1.0
CB D:ASN287 4.6 37.2 1.0
HD21 D:ASN307 4.6 37.5 1.0
HB2 D:GLU293 4.6 38.0 1.0
C02 D:YJM1325 4.7 60.3 1.0
N D:ALA309 4.7 25.3 1.0
HG3 D:GLU285 4.7 38.5 1.0
C05 D:YJM1325 4.7 53.8 1.0
HA D:ASN307 4.8 29.9 1.0
N D:ALA289 4.8 38.8 1.0
CB D:GLU293 4.8 31.6 1.0
HD21 D:ASN287 4.8 48.0 1.0
C D:ASN307 4.8 24.2 1.0
CA D:ASN287 4.8 34.9 1.0
CB D:ASN307 4.8 27.5 1.0
HB2 D:ASP308 4.8 33.6 1.0
CB D:ALA289 4.9 41.3 1.0
HB3 D:ASN287 4.9 44.6 1.0
C D:ASN287 4.9 35.5 1.0
CB D:GLU285 5.0 31.5 1.0
HB3 D:ASP308 5.0 33.6 1.0

Reference:

V.Porkolab, E.Chabrol, N.Varga, S.Ordanini, I.Sutkeviciu Te, M.Thepaut, M.J.Garcia-Jimenez, E.Girard, P.M.Nieto, A.Bernardi, F.Fieschi. Rational-Differential Design of Highly Specific Glycomimetic Ligands: Targeting Dc-Sign and Excluding Langerin Recognition. Acs Chem. Biol. V. 13 600 2018.
ISSN: ESSN 1554-8937
PubMed: 29272097
DOI: 10.1021/ACSCHEMBIO.7B00958
Page generated: Sat Dec 12 05:26:23 2020

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