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Calcium in PDB 3p5h: Structure of the Carbohydrate-Recognition Domain of Human Langerin with Laminaritriose

Protein crystallography data

The structure of Structure of the Carbohydrate-Recognition Domain of Human Langerin with Laminaritriose, PDB code: 3p5h was solved by H.Feinberg, M.E.Taylor, N.Razi, R.Mcbride, Y.A.Knirel, S.A.Graham, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.32 / 1.61
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 80.110, 80.110, 90.720, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Laminaritriose (pdb code 3p5h). 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 Human Langerin with Laminaritriose, PDB code: 3p5h:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3p5h

Go back to Calcium Binding Sites List in 3p5h
Calcium binding site 1 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Laminaritriose


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 Human Langerin with Laminaritriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:23.4
occ:1.00
 OD1 A:ASP308 2.4 20.6 1.0
OE1 A:GLU293 2.4 22.2 1.0
O A:ASP308 2.4 19.8 1.0
OD1 A:ASN307 2.5 22.7 1.0
OD1 A:ASN287 2.5 26.3 1.0
OE1 A:GLU285 2.5 25.7 1.0
O2 A:BGC400 2.5 27.5 1.0
O1 A:BGC400 2.5 23.3 1.0
CG A:ASP308 3.3 22.6 1.0
CD A:GLU285 3.3 21.1 1.0
CD A:GLU293 3.3 13.1 1.0
C2 A:BGC400 3.4 21.3 1.0
CG A:ASN287 3.4 52.2 1.0
C1 A:BGC400 3.4 31.2 1.0
CG A:ASN307 3.5 21.4 1.0
C A:ASP308 3.5 15.5 1.0
OE2 A:GLU285 3.6 29.7 1.0
OE2 A:GLU293 3.6 25.9 1.0
N A:ASP308 3.8 17.9 1.0
ND2 A:ASN307 3.8 17.1 1.0
ND2 A:ASN287 3.9 33.9 1.0
OD2 A:ASP308 4.0 25.8 1.0
CA A:ASP308 4.0 15.4 1.0
CB A:ASP308 4.2 18.5 1.0
N A:ASN287 4.3 29.4 1.0
N A:ASN288 4.4 28.0 1.0
CB A:ASN287 4.5 36.8 1.0
N A:ALA289 4.5 53.0 1.0
CG A:GLU285 4.6 23.9 1.0
CG A:GLU293 4.6 26.9 1.0
CB A:ALA289 4.6 38.8 1.0
N A:ALA309 4.6 16.1 1.0
O5 A:BGC400 4.7 28.5 1.0
C A:ASN307 4.7 29.1 1.0
C3 A:BGC400 4.8 24.6 1.0
CB A:ASN307 4.8 20.7 1.0
CA A:ASN287 4.8 31.5 1.0
CB A:GLU293 4.8 18.4 1.0
C A:ASN287 5.0 28.1 1.0

Calcium binding site 2 out of 4 in 3p5h

Go back to Calcium Binding Sites List in 3p5h
Calcium binding site 2 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Laminaritriose


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 Human Langerin with Laminaritriose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca500

b:20.5
occ:1.00
 OD1 B:ASP308 2.4 17.8 1.0
OD1 B:ASN287 2.4 22.6 1.0
OE1 B:GLU293 2.5 20.1 1.0
OD1 B:ASN307 2.5 20.5 1.0
O B:ASP308 2.5 20.6 1.0
O1 B:BGC400 2.5 21.9 1.0
O2 B:BGC400 2.5 20.0 1.0
OE1 B:GLU285 2.5 21.6 1.0
C2 B:BGC400 3.3 23.2 1.0
C1 B:BGC400 3.3 21.4 1.0
CG B:ASP308 3.3 26.5 1.0
CG B:ASN287 3.4 27.3 1.0
CD B:GLU293 3.4 14.3 1.0
CD B:GLU285 3.4 22.4 1.0
CG B:ASN307 3.5 15.7 1.0
C B:ASP308 3.5 16.3 1.0
OE2 B:GLU293 3.7 20.6 1.0
OE2 B:GLU285 3.7 27.3 1.0
N B:ASP308 3.8 18.7 1.0
ND2 B:ASN307 3.8 16.5 1.0
ND2 B:ASN287 3.9 25.2 1.0
CA B:ASP308 4.0 14.4 1.0
OD2 B:ASP308 4.0 21.2 1.0
N B:ASN287 4.1 20.9 1.0
CB B:ASP308 4.3 17.6 1.0
CB B:ASN287 4.5 25.9 1.0
O5 B:BGC400 4.6 28.1 1.0
N B:ASN288 4.6 24.8 1.0
CG B:GLU285 4.6 15.8 1.0
C3 B:BGC400 4.7 30.9 1.0
N B:ALA309 4.7 14.0 1.0
CA B:ASN287 4.7 32.4 1.0
CG B:GLU293 4.7 21.1 1.0
C B:ASN307 4.7 24.4 1.0
CB B:ASN307 4.8 18.8 1.0
N B:ALA289 4.8 28.1 1.0
CB B:GLU293 4.9 17.1 1.0
C B:ASN287 4.9 27.8 1.0
CB B:ALA289 5.0 23.4 1.0
CA B:ASN307 5.0 19.1 1.0

Calcium binding site 3 out of 4 in 3p5h

Go back to Calcium Binding Sites List in 3p5h
Calcium binding site 3 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Laminaritriose


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 Human Langerin with Laminaritriose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca500

b:20.1
occ:1.00
 OD1 C:ASP308 2.4 18.4 1.0
OD1 C:ASN307 2.4 18.4 1.0
OD1 C:ASN287 2.4 22.4 1.0
OE1 C:GLU293 2.5 18.3 1.0
O C:ASP308 2.5 20.8 1.0
O4 C:BGC402 2.5 21.9 1.0
OE1 C:GLU285 2.5 21.6 1.0
O3 C:BGC402 2.5 22.7 1.0
C4 C:BGC402 3.3 20.8 1.0
C3 C:BGC402 3.3 24.8 1.0
CG C:ASP308 3.3 22.0 1.0
CD C:GLU293 3.4 18.1 1.0
CG C:ASN307 3.4 13.9 1.0
CG C:ASN287 3.4 31.0 1.0
CD C:GLU285 3.4 25.8 1.0
C C:ASP308 3.5 15.6 1.0
OE2 C:GLU293 3.7 19.8 1.0
ND2 C:ASN307 3.7 20.6 1.0
OE2 C:GLU285 3.8 23.2 1.0
N C:ASP308 3.8 19.5 1.0
ND2 C:ASN287 3.9 26.5 1.0
OD2 C:ASP308 4.0 24.0 1.0
CA C:ASP308 4.0 14.7 1.0
N C:ASN287 4.2 20.8 1.0
CB C:ASP308 4.3 15.2 1.0
CB C:ASN287 4.5 23.9 1.0
N C:ASN288 4.6 20.9 1.0
CG C:GLU285 4.6 19.8 1.0
CG C:GLU293 4.7 19.5 1.0
N C:ALA309 4.7 13.9 1.0
C5 C:BGC402 4.7 24.8 1.0
C2 C:BGC402 4.7 25.1 1.0
CB C:ASN307 4.7 16.5 1.0
C C:ASN307 4.7 19.9 1.0
CA C:ASN287 4.8 25.2 1.0
N C:ALA289 4.8 20.4 1.0
CB C:GLU293 4.9 20.3 1.0
CB C:ALA289 4.9 25.4 1.0
CA C:ASN307 5.0 15.8 1.0
C C:ASN287 5.0 27.0 1.0

Calcium binding site 4 out of 4 in 3p5h

Go back to Calcium Binding Sites List in 3p5h
Calcium binding site 4 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Laminaritriose


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 Human Langerin with Laminaritriose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca500

b:19.6
occ:1.00
 OD1 D:ASP308 2.4 16.6 1.0
OD1 D:ASN287 2.4 20.4 1.0
OD1 D:ASN307 2.5 20.0 1.0
OE1 D:GLU293 2.5 17.9 1.0
OE1 D:GLU285 2.5 19.9 1.0
O1 D:BGC400 2.5 19.7 1.0
O2 D:BGC400 2.5 21.7 1.0
O D:ASP308 2.5 19.0 1.0
C2 D:BGC400 3.2 15.4 1.0
C1 D:BGC400 3.3 22.7 1.0
CG D:ASP308 3.4 23.1 1.0
CD D:GLU285 3.4 24.6 1.0
CD D:GLU293 3.4 14.0 1.0
CG D:ASN287 3.4 19.0 1.0
CG D:ASN307 3.4 14.4 1.0
C D:ASP308 3.6 15.3 1.0
OE2 D:GLU293 3.7 22.3 1.0
OE2 D:GLU285 3.7 25.2 1.0
ND2 D:ASN307 3.8 18.1 1.0
N D:ASP308 3.8 16.1 1.0
ND2 D:ASN287 4.0 30.7 1.0
CA D:ASP308 4.0 13.4 1.0
OD2 D:ASP308 4.1 18.7 1.0
N D:ASN287 4.1 17.1 1.0
CB D:ASP308 4.3 15.7 1.0
CB D:ASN287 4.5 20.8 1.0
O5 D:BGC400 4.6 26.4 1.0
CG D:GLU285 4.6 16.1 1.0
N D:ASN288 4.6 18.7 1.0
CG D:GLU293 4.7 17.3 1.0
C3 D:BGC400 4.7 21.7 1.0
C D:ASN307 4.7 18.6 1.0
CA D:ASN287 4.7 18.2 1.0
N D:ALA309 4.7 15.5 1.0
CB D:ASN307 4.8 15.0 1.0
N D:ALA289 4.8 23.4 1.0
CB D:GLU293 4.8 17.2 1.0
CB D:ALA289 4.9 23.5 1.0
C D:ASN287 5.0 28.5 1.0
CA D:ASN307 5.0 17.1 1.0

Reference:

H.Feinberg, M.E.Taylor, N.Razi, R.Mcbride, Y.A.Knirel, S.A.Graham, K.Drickamer, W.I.Weis. Structural Basis For Langerin Recognition of Diverse Pathogen and Mammalian Glycans Through A Single Binding Site. J.Mol.Biol. V. 405 1027 2011.
ISSN: ISSN 0022-2836
PubMed: 21112338
DOI: 10.1016/J.JMB.2010.11.039
Page generated: Tue Jul 8 15:18:35 2025

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