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Calcium in PDB 4ak8: Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain.

Protein crystallography data

The structure of Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain., PDB code: 4ak8 was solved by E.Chabrol, M.Thepaut, C.Dezutter-Dambuyant, C.Vives, J.Marcoux, R.Kahn, J.Valadeau-Guilemond, P.Vachette, D.Durand, F.Fieschi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.52 / 1.40
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 79.959, 79.959, 90.419, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.9

Other elements in 4ak8:

The structure of Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain. also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain. (pdb code 4ak8). 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 F241L Mutant of Langerin Carbohydrate Recognition Domain., PDB code: 4ak8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4ak8

Go back to Calcium Binding Sites List in 4ak8
Calcium binding site 1 out of 4 in the Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1326

b:16.1
occ:1.00
 OD1 A:ASN287 2.4 16.3 1.0
OD1 A:ASP308 2.4 12.8 1.0
O A:HOH2180 2.4 16.4 1.0
OE1 A:GLU293 2.5 12.8 1.0
OD1 A:ASN307 2.5 13.3 1.0
OE1 A:GLU285 2.5 15.2 1.0
O A:ASP308 2.6 14.0 1.0
O A:HOH2151 2.6 15.5 1.0
CG A:ASP308 3.3 13.0 1.0
CD A:GLU293 3.4 11.5 1.0
CG A:ASN287 3.4 16.6 1.0
CG A:ASN307 3.4 14.8 1.0
CD A:GLU285 3.5 13.8 1.0
C A:ASP308 3.6 10.5 1.0
OE2 A:GLU293 3.7 16.2 1.0
ND2 A:ASN307 3.7 16.9 1.0
OE2 A:GLU285 3.9 17.7 1.0
N A:ASP308 3.9 12.2 1.0
OD2 A:ASP308 4.1 16.1 1.0
ND2 A:ASN287 4.1 18.1 1.0
CA A:ASP308 4.1 11.9 1.0
N A:ASN287 4.2 14.7 1.0
CB A:ASP308 4.3 13.3 1.0
CB A:ASN287 4.5 16.5 1.0
O A:HOH2191 4.5 28.4 1.0
N A:ASN288 4.6 18.6 1.0
CG A:GLU285 4.6 14.0 1.0
CG A:GLU293 4.6 13.2 1.0
CB A:ASN307 4.7 11.3 1.0
N A:ALA289 4.7 17.3 1.0
N A:ALA309 4.7 10.4 1.0
CB A:ALA289 4.8 18.3 1.0
CA A:ASN287 4.8 18.4 1.0
C A:ASN307 4.8 13.1 1.0
CB A:GLU293 4.9 15.1 1.0
C A:ASN287 4.9 19.6 1.0
O A:HOH2182 4.9 33.6 1.0
O A:HOH2152 4.9 21.5 1.0
CA A:ASN307 5.0 11.1 1.0

Calcium binding site 2 out of 4 in 4ak8

Go back to Calcium Binding Sites List in 4ak8
Calcium binding site 2 out of 4 in the Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1326

b:20.0
occ:1.00
 OD1 B:ASP308 2.3 16.8 1.0
O B:HOH2137 2.4 21.9 1.0
OD1 B:ASN307 2.4 14.8 1.0
OD1 B:ASN287 2.5 22.4 1.0
OE1 B:GLU293 2.5 20.8 1.0
O B:HOH2161 2.5 20.1 1.0
OE1 B:GLU285 2.5 19.4 1.0
O B:ASP308 2.6 16.9 1.0
CG B:ASP308 3.2 14.2 1.0
CD B:GLU285 3.4 16.9 1.0
CG B:ASN287 3.4 29.7 1.0
CG B:ASN307 3.4 15.8 1.0
CD B:GLU293 3.4 15.6 1.0
C B:ASP308 3.6 13.7 1.0
ND2 B:ASN307 3.7 21.0 1.0
OE2 B:GLU293 3.7 19.1 1.0
OE2 B:GLU285 3.7 22.0 1.0
N B:ASP308 3.8 13.5 1.0
ND2 B:ASN287 3.9 32.1 1.0
CA B:ASP308 4.0 11.0 1.0
OD2 B:ASP308 4.1 22.1 1.0
N B:ASN287 4.1 26.8 1.0
CB B:ASP308 4.2 14.6 1.0
CB B:ASN287 4.5 29.6 1.0
O B:HOH2182 4.5 40.9 1.0
CG B:GLU285 4.5 17.6 1.0
CG B:GLU293 4.7 18.4 1.0
C B:ASN307 4.7 14.6 1.0
N B:ALA309 4.7 11.5 1.0
CB B:ASN307 4.8 11.8 1.0
N B:ALA289 4.8 32.7 1.0
O B:HOH2167 4.8 30.7 1.0
CA B:ASN287 4.8 28.9 1.0
CB B:ALA289 4.8 34.2 1.0
CB B:GLU293 4.9 18.8 1.0
N B:ASN288 4.9 31.4 1.0

Calcium binding site 3 out of 4 in 4ak8

Go back to Calcium Binding Sites List in 4ak8
Calcium binding site 3 out of 4 in the Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1326

b:19.4
occ:1.00
 OD1 C:ASP308 2.3 15.1 1.0
OD1 C:ASN307 2.4 19.0 1.0
OD1 C:ASN287 2.4 19.6 1.0
O C:HOH2123 2.5 22.7 1.0
OE1 C:GLU293 2.5 16.8 1.0
OE1 C:GLU285 2.5 19.3 1.0
O C:HOH2148 2.5 22.2 1.0
O C:ASP308 2.6 15.8 1.0
CG C:ASP308 3.4 15.3 1.0
CG C:ASN287 3.4 18.5 1.0
CG C:ASN307 3.4 19.3 1.0
CD C:GLU285 3.4 22.3 1.0
CD C:GLU293 3.4 13.7 1.0
C C:ASP308 3.7 12.7 1.0
OE2 C:GLU285 3.8 25.9 1.0
ND2 C:ASN307 3.8 23.3 1.0
OE2 C:GLU293 3.8 19.7 1.0
N C:ASP308 3.9 13.9 1.0
ND2 C:ASN287 4.0 21.2 1.0
N C:ASN287 4.1 16.3 1.0
OD2 C:ASP308 4.1 16.0 1.0
CA C:ASP308 4.2 13.3 1.0
CB C:ASP308 4.4 13.1 1.0
CB C:ASN287 4.5 19.4 1.0
CG C:GLU285 4.6 16.6 1.0
N C:ASN288 4.7 20.9 1.0
CA C:ASN287 4.7 21.2 1.0
CG C:GLU293 4.7 14.8 1.0
CB C:ASN307 4.7 13.6 1.0
N C:ALA289 4.8 21.3 1.0
O C:HOH2153 4.8 32.4 1.0
N C:ALA309 4.8 12.9 1.0
C C:ASN307 4.8 13.9 1.0
CB C:GLU293 5.0 14.7 1.0
CA C:ASN307 5.0 11.8 1.0
CB C:ALA289 5.0 20.4 1.0
C C:ASN287 5.0 22.3 1.0

Calcium binding site 4 out of 4 in 4ak8

Go back to Calcium Binding Sites List in 4ak8
Calcium binding site 4 out of 4 in the Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of F241L Mutant of Langerin Carbohydrate Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1330

b:16.7
occ:1.00
 OD1 D:ASP308 2.3 14.8 1.0
OD1 D:ASN307 2.4 13.8 1.0
OD1 D:ASN287 2.4 18.3 1.0
O D:HOH2160 2.4 20.9 1.0
OE1 D:GLU293 2.5 16.5 1.0
O D:ASP308 2.5 14.3 1.0
O D:HOH2126 2.5 20.6 1.0
OE1 D:GLU285 2.6 19.1 1.0
CG D:ASP308 3.3 14.8 1.0
CG D:ASN307 3.4 13.8 1.0
CD D:GLU293 3.4 12.1 1.0
CG D:ASN287 3.4 23.1 1.0
CD D:GLU285 3.5 15.7 1.0
C D:ASP308 3.6 11.1 1.0
OE2 D:GLU293 3.7 16.9 1.0
ND2 D:ASN307 3.7 24.9 1.0
N D:ASP308 3.8 13.1 1.0
ND2 D:ASN287 4.0 20.6 1.0
OE2 D:GLU285 4.0 22.0 1.0
OD2 D:ASP308 4.1 16.0 1.0
CA D:ASP308 4.1 12.5 1.0
N D:ASN287 4.1 17.0 1.0
CB D:ASP308 4.3 13.8 1.0
O D:HOH2163 4.5 34.5 1.0
CB D:ASN287 4.5 20.0 1.0
N D:ASN288 4.6 19.5 1.0
CG D:GLU285 4.7 13.7 1.0
CG D:GLU293 4.7 15.6 1.0
CB D:ASN307 4.7 12.9 1.0
CA D:ASN287 4.7 20.7 1.0
N D:ALA309 4.7 11.4 1.0
C D:ASN307 4.7 11.0 1.0
N D:ALA289 4.9 22.6 1.0
CB D:GLU293 4.9 15.4 1.0
O D:HOH2127 4.9 27.1 1.0
O D:HOH2167 4.9 31.5 1.0
CB D:ALA289 4.9 24.4 1.0
C D:ASN287 5.0 21.9 1.0
CA D:ASN307 5.0 10.8 1.0

Reference:

E.Chabrol, M.Thepaut, C.Dezutter-Dambuyant, C.Vives, J.Marcoux, R.Kahn, J.Valladeau-Guilemond, P.Vachette, D.Durand, F.Fieschi. Alteration of the Langerin Oligomerization State Affects Birbeck Granule Formation. Biophys.J. V. 108 666 2015.
ISSN: ISSN 0006-3495
PubMed: 25650933
DOI: 10.1016/J.BPJ.2014.10.075
Page generated: Tue Jul 8 18:31:30 2025

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