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 Jul 13 12:38:29 2024
|
