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Calcium in PDB 3kqg: Trimeric Structure of Langerin

Protein crystallography data

The structure of Trimeric Structure of Langerin, PDB code: 3kqg was solved by H.Feinberg, A.S.Powlesland, M.E.Taylor, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.96 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.780, 77.460, 85.920, 90.00, 94.42, 90.00
R / Rfree (%) 18.2 / 23.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Trimeric Structure of Langerin (pdb code 3kqg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Trimeric Structure of Langerin, PDB code: 3kqg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3kqg

Go back to Calcium Binding Sites List in 3kqg
Calcium binding site 1 out of 6 in the Trimeric Structure of Langerin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Trimeric Structure of Langerin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca400

b:41.5
occ:1.00
OD1 A:ASP308 2.4 35.5 1.0
O A:ASP308 2.4 24.2 1.0
OE1 A:GLU285 2.4 52.0 1.0
O A:HOH1 2.4 35.5 1.0
OE1 A:GLU293 2.4 46.8 1.0
OD1 A:ASN287 2.4 50.0 1.0
O A:HOH2 2.4 36.3 1.0
OD1 A:ASN307 2.4 39.0 1.0
CG A:ASN287 3.3 48.3 1.0
CG A:ASP308 3.4 32.2 1.0
CD A:GLU285 3.4 53.1 1.0
CD A:GLU293 3.5 46.0 1.0
C A:ASP308 3.5 28.4 1.0
CG A:ASN307 3.5 36.5 1.0
N A:ASP308 3.6 31.4 1.0
ND2 A:ASN287 3.8 46.0 1.0
OE2 A:GLU293 3.9 46.5 1.0
ND2 A:ASN307 3.9 36.6 1.0
OE2 A:GLU285 3.9 56.5 1.0
CA A:ASP308 4.0 27.2 1.0
OD2 A:ASP308 4.2 33.2 1.0
CB A:ASP308 4.3 30.3 1.0
N A:ASN287 4.3 45.0 1.0
CB A:ASN287 4.5 49.4 1.0
N A:ASN288 4.6 46.2 1.0
C A:ASN307 4.6 33.3 1.0
CG A:GLU285 4.6 48.1 1.0
N A:ALA309 4.6 29.7 1.0
CG A:GLU293 4.7 45.9 1.0
CB A:ASN307 4.7 31.3 1.0
CA A:ASN287 4.8 47.8 1.0
CA A:ASN307 4.9 33.8 1.0
N A:ALA289 4.9 56.8 1.0
O A:HOH360 4.9 45.2 1.0
CB A:GLU293 5.0 44.3 1.0

Calcium binding site 2 out of 6 in 3kqg

Go back to Calcium Binding Sites List in 3kqg
Calcium binding site 2 out of 6 in the Trimeric Structure of Langerin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Trimeric Structure of Langerin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca400

b:27.3
occ:1.00
OD1 B:ASP308 2.3 29.7 1.0
OD1 B:ASN307 2.4 22.1 1.0
OD1 B:ASN287 2.4 26.0 1.0
OE1 B:GLU285 2.4 29.2 1.0
OE1 B:GLU293 2.4 33.2 1.0
O B:HOH3 2.4 27.2 1.0
O B:ASP308 2.4 28.0 1.0
O B:HOH4 2.4 31.4 1.0
CD B:GLU285 3.3 29.4 1.0
CG B:ASP308 3.3 29.1 1.0
CG B:ASN287 3.4 29.8 1.0
CG B:ASN307 3.4 22.5 1.0
CD B:GLU293 3.4 32.3 1.0
C B:ASP308 3.5 27.8 1.0
OE2 B:GLU285 3.6 31.1 1.0
N B:ASP308 3.7 28.8 1.0
OE2 B:GLU293 3.7 34.0 1.0
ND2 B:ASN307 3.8 23.3 1.0
ND2 B:ASN287 3.9 33.5 1.0
CA B:ASP308 4.0 23.7 1.0
OD2 B:ASP308 4.0 30.7 1.0
N B:ASN287 4.1 34.9 1.0
CB B:ASP308 4.3 26.6 1.0
CG B:GLU285 4.5 28.1 1.0
CB B:ASN287 4.5 30.1 1.0
N B:ASN288 4.6 31.0 1.0
C B:ASN307 4.6 31.0 1.0
N B:ALA309 4.7 29.8 1.0
CB B:ASN307 4.7 20.5 1.0
CA B:ASN287 4.7 33.1 1.0
CG B:GLU293 4.8 28.9 1.0
CB B:GLU285 4.8 25.4 1.0
N B:ALA289 4.8 30.3 1.0
CA B:ASN307 4.9 23.6 1.0
O B:HOH92 4.9 27.8 1.0
CB B:ALA289 5.0 27.4 1.0
C B:ASN287 5.0 31.1 1.0

Calcium binding site 3 out of 6 in 3kqg

Go back to Calcium Binding Sites List in 3kqg
Calcium binding site 3 out of 6 in the Trimeric Structure of Langerin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Trimeric Structure of Langerin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca400

b:33.7
occ:1.00
OD1 C:ASP308 2.3 30.9 1.0
O C:HOH6 2.4 38.7 1.0
OE1 C:GLU293 2.4 34.3 1.0
O C:HOH5 2.4 31.2 1.0
OD1 C:ASN307 2.4 34.9 1.0
OD1 C:ASN287 2.4 43.4 1.0
OE1 C:GLU285 2.4 40.1 1.0
O C:ASP308 2.5 38.2 1.0
CG C:ASP308 3.4 31.8 1.0
CD C:GLU293 3.4 31.5 1.0
CG C:ASN307 3.4 32.5 1.0
CD C:GLU285 3.4 39.4 1.0
CG C:ASN287 3.4 44.1 1.0
C C:ASP308 3.5 31.8 1.0
OE2 C:GLU293 3.7 37.0 1.0
ND2 C:ASN307 3.7 26.5 1.0
N C:ASP308 3.8 33.1 1.0
OE2 C:GLU285 3.9 44.9 1.0
ND2 C:ASN287 4.0 43.4 1.0
CA C:ASP308 4.1 29.9 1.0
OD2 C:ASP308 4.1 33.2 1.0
N C:ASN287 4.2 39.9 1.0
CB C:ASP308 4.3 27.7 1.0
N C:ASN288 4.5 40.2 1.0
O C:HOH332 4.5 40.8 1.0
CG C:GLU285 4.6 33.7 1.0
CB C:ASN287 4.7 43.6 1.0
CG C:GLU293 4.7 27.3 1.0
N C:ALA309 4.7 27.2 1.0
C C:ASN307 4.7 36.1 1.0
CB C:ASN307 4.7 31.7 1.0
N C:ALA289 4.7 36.9 1.0
CA C:ASN287 4.8 41.0 1.0
CB C:GLU293 5.0 29.4 1.0
CB C:ALA289 5.0 39.8 1.0
C C:ASN287 5.0 40.2 1.0
CB C:GLU285 5.0 30.5 1.0
CA C:ASN307 5.0 35.2 1.0

Calcium binding site 4 out of 6 in 3kqg

Go back to Calcium Binding Sites List in 3kqg
Calcium binding site 4 out of 6 in the Trimeric Structure of Langerin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Trimeric Structure of Langerin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca400

b:43.9
occ:1.00
OD1 D:ASN287 2.4 51.2 1.0
OD1 D:ASP308 2.4 44.3 1.0
O D:ASP308 2.4 32.0 1.0
O D:HOH8 2.4 56.9 1.0
OE1 D:GLU293 2.4 64.2 1.0
OD1 D:ASN307 2.4 38.0 1.0
OE1 D:GLU285 2.4 45.2 1.0
O D:HOH7 2.4 46.4 1.0
CG D:ASN287 3.3 51.8 1.0
CD D:GLU285 3.3 43.6 1.0
CG D:ASP308 3.4 41.9 1.0
CD D:GLU293 3.5 62.3 1.0
CG D:ASN307 3.5 35.8 1.0
C D:ASP308 3.5 31.3 1.0
OE2 D:GLU285 3.6 44.3 1.0
ND2 D:ASN287 3.7 52.4 1.0
N D:ASP308 3.7 35.0 1.0
OE2 D:GLU293 3.8 65.7 1.0
ND2 D:ASN307 3.9 32.8 1.0
CA D:ASP308 4.0 34.4 1.0
OD2 D:ASP308 4.1 42.4 1.0
CB D:ASP308 4.3 37.7 1.0
N D:ASN287 4.3 43.5 1.0
CB D:ASN287 4.5 49.4 1.0
N D:ALA309 4.6 27.4 1.0
C D:ASN307 4.6 34.0 1.0
N D:ASN288 4.6 42.4 1.0
O D:HOH370 4.7 55.6 1.0
CG D:GLU285 4.7 40.6 1.0
CB D:ASN307 4.7 32.8 1.0
CG D:GLU293 4.8 55.8 1.0
CA D:ASN287 4.9 44.0 1.0
N D:ALA289 4.9 40.5 1.0
CA D:ASN307 4.9 35.4 1.0

Calcium binding site 5 out of 6 in 3kqg

Go back to Calcium Binding Sites List in 3kqg
Calcium binding site 5 out of 6 in the Trimeric Structure of Langerin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Trimeric Structure of Langerin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca400

b:38.7
occ:1.00
OD1 E:ASP308 2.4 41.8 1.0
O E:HOH9 2.4 53.1 1.0
O E:HOH10 2.4 32.7 1.0
OD1 E:ASN287 2.4 54.0 1.0
OE1 E:GLU293 2.4 42.8 1.0
OE1 E:GLU285 2.4 60.0 1.0
O E:ASP308 2.4 34.9 1.0
OD1 E:ASN307 2.4 32.1 1.0
CG E:ASN287 3.3 53.4 1.0
CG E:ASP308 3.3 40.2 1.0
CD E:GLU293 3.3 45.5 1.0
CG E:ASN307 3.3 31.8 1.0
CD E:GLU285 3.4 57.0 1.0
C E:ASP308 3.5 34.9 1.0
OE2 E:GLU293 3.6 47.4 1.0
ND2 E:ASN287 3.7 54.3 1.0
ND2 E:ASN307 3.7 32.6 1.0
N E:ASP308 3.7 34.0 1.0
OE2 E:GLU285 3.8 59.2 1.0
OD2 E:ASP308 3.9 39.9 1.0
CA E:ASP308 4.0 35.5 1.0
CB E:ASP308 4.2 37.7 1.0
N E:ASN287 4.3 47.1 1.0
CB E:ASN287 4.5 51.2 1.0
C E:ASN307 4.6 35.1 1.0
N E:ALA309 4.6 34.8 1.0
CG E:GLU293 4.7 43.5 1.0
CB E:ASN307 4.7 28.9 1.0
CG E:GLU285 4.7 50.3 1.0
CB E:ALA289 4.7 49.6 1.0
N E:ASN288 4.7 40.0 1.0
N E:ALA289 4.8 48.5 1.0
O E:HOH334 4.8 41.2 1.0
CA E:ASN287 4.9 48.9 1.0
CA E:ASN307 4.9 33.0 1.0
CB E:GLU293 5.0 41.0 1.0

Calcium binding site 6 out of 6 in 3kqg

Go back to Calcium Binding Sites List in 3kqg
Calcium binding site 6 out of 6 in the Trimeric Structure of Langerin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Trimeric Structure of Langerin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca400

b:47.4
occ:1.00
OE1 F:GLU293 2.3 45.5 1.0
OD1 F:ASP308 2.3 42.8 1.0
O F:HOH11 2.4 44.6 1.0
OD1 F:ASN307 2.4 45.6 1.0
OE1 F:GLU285 2.4 57.0 1.0
O F:HOH12 2.4 48.0 1.0
OD1 F:ASN287 2.4 64.7 1.0
O F:ASP308 2.6 41.0 1.0
CD F:GLU293 3.2 48.2 1.0
CG F:ASN287 3.3 66.3 1.0
CD F:GLU285 3.4 57.0 1.0
CG F:ASP308 3.4 44.9 1.0
OE2 F:GLU293 3.4 50.6 1.0
CG F:ASN307 3.5 45.6 1.0
C F:ASP308 3.7 39.8 1.0
N F:ASP308 3.8 37.3 1.0
ND2 F:ASN287 3.8 66.2 1.0
OE2 F:GLU285 3.8 60.3 1.0
ND2 F:ASN307 4.0 46.5 1.0
OD2 F:ASP308 4.1 49.9 1.0
CA F:ASP308 4.1 37.6 1.0
N F:ASN287 4.2 64.6 1.0
CB F:ASP308 4.4 40.6 1.0
CG F:GLU285 4.6 54.4 1.0
CB F:ASN287 4.6 67.4 1.0
O F:HOH330 4.6 37.5 1.0
CG F:GLU293 4.6 44.6 1.0
C F:ASN307 4.7 40.7 1.0
CB F:ASN307 4.7 44.1 1.0
N F:ALA309 4.8 37.1 1.0
N F:ASN288 4.8 56.1 1.0
CA F:ASN287 4.9 65.8 1.0
CA F:ASN307 4.9 43.6 1.0
CB F:GLU293 5.0 44.0 1.0
CB F:GLU285 5.0 56.5 1.0

Reference:

H.Feinberg, A.S.Powlesland, M.E.Taylor, W.I.Weis. Trimeric Structure of Langerin. J.Biol.Chem. V. 285 13285 2010.
ISSN: ISSN 0021-9258
PubMed: 20181944
DOI: 10.1074/JBC.M109.086058
Page generated: Sat Dec 12 04:18:00 2020

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