Calcium in PDB 3g83: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
Protein crystallography data
The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose., PDB code: 3g83
was solved by
J.F.Head,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.23 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.754,
108.774,
56.011,
90.00,
91.58,
90.00
|
R / Rfree (%)
|
18.9 /
21.5
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
(pdb code 3g83). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the
Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose., PDB code: 3g83:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Calcium binding site 1 out
of 9 in 3g83
Go back to
Calcium Binding Sites List in 3g83
Calcium binding site 1 out
of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:20.5
occ:1.00
|
OD1
|
A:ASP342
|
2.4
|
18.3
|
1.0
|
OD1
|
A:ASN341
|
2.5
|
18.3
|
1.0
|
OD1
|
A:ASN323
|
2.5
|
19.5
|
1.0
|
OE1
|
A:GLU329
|
2.5
|
19.6
|
1.0
|
O3
|
A:MAN500
|
2.6
|
21.2
|
1.0
|
OE1
|
A:GLU321
|
2.7
|
19.6
|
1.0
|
O
|
A:ASP342
|
2.7
|
18.5
|
1.0
|
O4
|
A:MAN500
|
2.7
|
18.5
|
1.0
|
CG
|
A:ASP342
|
3.4
|
19.4
|
1.0
|
C4
|
A:MAN500
|
3.4
|
21.1
|
1.0
|
CG
|
A:ASN323
|
3.4
|
24.5
|
1.0
|
CD
|
A:GLU321
|
3.4
|
22.5
|
1.0
|
CD
|
A:GLU329
|
3.5
|
20.6
|
1.0
|
C3
|
A:MAN500
|
3.5
|
23.3
|
1.0
|
CG
|
A:ASN341
|
3.5
|
20.0
|
1.0
|
C
|
A:ASP342
|
3.7
|
19.3
|
1.0
|
OE2
|
A:GLU321
|
3.7
|
21.3
|
1.0
|
OE2
|
A:GLU329
|
3.8
|
18.2
|
1.0
|
N
|
A:ASP342
|
3.9
|
16.6
|
1.0
|
ND2
|
A:ASN323
|
3.9
|
25.9
|
1.0
|
ND2
|
A:ASN341
|
4.0
|
21.9
|
1.0
|
OD2
|
A:ASP342
|
4.0
|
20.6
|
1.0
|
CA
|
A:ASP342
|
4.1
|
18.6
|
1.0
|
N
|
A:ASN323
|
4.2
|
21.8
|
1.0
|
CB
|
A:ASP342
|
4.3
|
17.1
|
1.0
|
C
|
A:ASN341
|
4.6
|
18.1
|
1.0
|
CB
|
A:ASN323
|
4.6
|
19.4
|
1.0
|
CG
|
A:GLU321
|
4.7
|
20.4
|
1.0
|
N
|
A:ASP324
|
4.7
|
17.7
|
1.0
|
N
|
A:ASP325
|
4.7
|
21.3
|
1.0
|
CB
|
A:ASP325
|
4.7
|
23.8
|
1.0
|
CG
|
A:GLU329
|
4.8
|
19.3
|
1.0
|
CB
|
A:ASN341
|
4.8
|
17.0
|
1.0
|
CA
|
A:ASN323
|
4.8
|
21.5
|
1.0
|
N
|
A:ARG343
|
4.8
|
17.1
|
1.0
|
C2
|
A:MAN500
|
4.8
|
26.8
|
1.0
|
C5
|
A:MAN500
|
4.9
|
23.6
|
1.0
|
CB
|
A:GLU329
|
4.9
|
19.0
|
1.0
|
CA
|
A:ASN341
|
4.9
|
18.8
|
1.0
|
O2
|
A:MAN500
|
5.0
|
25.6
|
1.0
|
|
Calcium binding site 2 out
of 9 in 3g83
Go back to
Calcium Binding Sites List in 3g83
Calcium binding site 2 out
of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:20.4
occ:1.00
|
O
|
A:HOH95
|
2.5
|
22.1
|
1.0
|
OD1
|
A:ASP324
|
2.5
|
21.3
|
1.0
|
O
|
A:GLU329
|
2.5
|
16.8
|
1.0
|
OD1
|
A:ASP330
|
2.6
|
20.1
|
1.0
|
OD2
|
A:ASP297
|
2.6
|
20.4
|
1.0
|
OE1
|
A:GLU301
|
2.6
|
20.4
|
1.0
|
OE2
|
A:GLU301
|
2.6
|
21.5
|
1.0
|
OD1
|
A:ASP297
|
2.7
|
19.2
|
1.0
|
CD
|
A:GLU301
|
2.9
|
23.5
|
1.0
|
CG
|
A:ASP297
|
3.0
|
21.1
|
1.0
|
C
|
A:GLU329
|
3.4
|
18.6
|
1.0
|
CG
|
A:ASP324
|
3.4
|
23.3
|
1.0
|
CG
|
A:ASP330
|
3.6
|
22.3
|
1.0
|
CA
|
A:ASP330
|
3.8
|
19.3
|
1.0
|
CA
|
A:CA403
|
4.0
|
26.5
|
1.0
|
N
|
A:ASP330
|
4.0
|
15.9
|
1.0
|
CB
|
A:ASP324
|
4.0
|
19.4
|
1.0
|
OD2
|
A:ASP324
|
4.2
|
20.4
|
1.0
|
N
|
A:GLU329
|
4.3
|
20.4
|
1.0
|
CB
|
A:ASP330
|
4.3
|
18.6
|
1.0
|
CA
|
A:GLU329
|
4.4
|
21.9
|
1.0
|
O
|
A:HOH375
|
4.4
|
36.0
|
1.0
|
CG
|
A:GLU301
|
4.4
|
22.6
|
1.0
|
CZ
|
A:PHE304
|
4.5
|
21.0
|
1.0
|
CB
|
A:ASP297
|
4.5
|
18.2
|
1.0
|
OD2
|
A:ASP330
|
4.6
|
27.5
|
1.0
|
CA
|
A:ASP324
|
4.6
|
21.0
|
1.0
|
O
|
A:HOH32
|
4.6
|
24.2
|
1.0
|
OD2
|
A:ASP342
|
4.6
|
20.6
|
1.0
|
N
|
A:GLY302
|
4.6
|
22.8
|
1.0
|
O
|
A:HOH38
|
4.7
|
24.1
|
1.0
|
O
|
A:ASP297
|
4.8
|
26.6
|
1.0
|
CB
|
A:GLU329
|
5.0
|
19.0
|
1.0
|
|
Calcium binding site 3 out
of 9 in 3g83
Go back to
Calcium Binding Sites List in 3g83
Calcium binding site 3 out
of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:26.5
occ:1.00
|
O
|
A:HOH145
|
2.5
|
28.2
|
1.0
|
OE1
|
A:GLU301
|
2.5
|
20.4
|
1.0
|
O
|
A:HOH426
|
2.6
|
38.7
|
1.0
|
OD2
|
A:ASP330
|
2.6
|
27.5
|
1.0
|
OD1
|
A:ASP330
|
2.7
|
20.1
|
1.0
|
O
|
A:HOH375
|
2.7
|
36.0
|
1.0
|
O
|
A:HOH1
|
2.8
|
43.7
|
1.0
|
CG
|
A:ASP330
|
3.0
|
22.3
|
1.0
|
CD
|
A:GLU301
|
3.7
|
23.5
|
1.0
|
CA
|
A:CA402
|
4.0
|
20.4
|
1.0
|
CB
|
A:GLU301
|
4.2
|
28.1
|
1.0
|
OD1
|
A:ASP324
|
4.3
|
21.3
|
1.0
|
O
|
A:ASP297
|
4.4
|
26.6
|
1.0
|
CG
|
A:GLU301
|
4.4
|
22.6
|
1.0
|
CB
|
A:ASP330
|
4.5
|
18.6
|
1.0
|
O
|
A:HOH431
|
4.5
|
39.0
|
1.0
|
OE2
|
A:GLU301
|
4.6
|
21.5
|
1.0
|
CA
|
A:GLU301
|
4.7
|
25.8
|
1.0
|
OD1
|
A:ASP297
|
4.8
|
19.2
|
1.0
|
O
|
A:GLY327
|
4.8
|
27.0
|
1.0
|
OD2
|
A:ASP324
|
4.9
|
20.4
|
1.0
|
O
|
A:HOH466
|
4.9
|
36.6
|
1.0
|
|
Calcium binding site 4 out
of 9 in 3g83
Go back to
Calcium Binding Sites List in 3g83
Calcium binding site 4 out
of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:18.5
occ:1.00
|
OD1
|
B:ASP342
|
2.4
|
15.6
|
1.0
|
OE1
|
B:GLU329
|
2.4
|
17.8
|
1.0
|
OD1
|
B:ASN341
|
2.5
|
17.7
|
1.0
|
OD1
|
B:ASN323
|
2.5
|
18.8
|
1.0
|
O3
|
B:MAN500
|
2.6
|
18.2
|
1.0
|
OE1
|
B:GLU321
|
2.6
|
16.9
|
1.0
|
O
|
B:ASP342
|
2.6
|
15.2
|
1.0
|
O4
|
B:MAN500
|
2.7
|
23.5
|
1.0
|
CD
|
B:GLU329
|
3.3
|
23.1
|
1.0
|
CG
|
B:ASP342
|
3.4
|
16.3
|
1.0
|
CG
|
B:ASN341
|
3.4
|
21.6
|
1.0
|
CD
|
B:GLU321
|
3.4
|
18.8
|
1.0
|
C4
|
B:MAN500
|
3.4
|
25.9
|
1.0
|
C3
|
B:MAN500
|
3.5
|
25.1
|
1.0
|
CG
|
B:ASN323
|
3.5
|
19.5
|
1.0
|
OE2
|
B:GLU329
|
3.6
|
21.5
|
1.0
|
C
|
B:ASP342
|
3.6
|
18.3
|
1.0
|
OE2
|
B:GLU321
|
3.7
|
18.8
|
1.0
|
N
|
B:ASP342
|
3.8
|
18.2
|
1.0
|
ND2
|
B:ASN341
|
3.8
|
20.9
|
1.0
|
ND2
|
B:ASN323
|
4.1
|
19.0
|
1.0
|
CA
|
B:ASP342
|
4.1
|
17.8
|
1.0
|
OD2
|
B:ASP342
|
4.1
|
19.8
|
1.0
|
N
|
B:ASN323
|
4.2
|
16.9
|
1.0
|
CB
|
B:ASP342
|
4.3
|
16.5
|
1.0
|
C
|
B:ASN341
|
4.5
|
18.8
|
1.0
|
N
|
B:ASP324
|
4.6
|
18.0
|
1.0
|
CB
|
B:ASP325
|
4.6
|
25.7
|
1.0
|
CG
|
B:GLU321
|
4.6
|
19.1
|
1.0
|
CG
|
B:GLU329
|
4.6
|
22.9
|
1.0
|
CB
|
B:ASN323
|
4.6
|
17.7
|
1.0
|
CB
|
B:ASN341
|
4.7
|
17.0
|
1.0
|
N
|
B:ASP325
|
4.7
|
21.4
|
1.0
|
N
|
B:ARG343
|
4.8
|
19.1
|
1.0
|
CA
|
B:ASN323
|
4.8
|
19.3
|
1.0
|
C2
|
B:MAN500
|
4.8
|
32.6
|
1.0
|
CB
|
B:GLU329
|
4.8
|
20.7
|
1.0
|
CA
|
B:ASN341
|
4.8
|
17.3
|
1.0
|
C5
|
B:MAN500
|
4.9
|
34.1
|
1.0
|
O2
|
B:MAN500
|
5.0
|
32.9
|
1.0
|
C
|
B:ASN323
|
5.0
|
19.7
|
1.0
|
|
Calcium binding site 5 out
of 9 in 3g83
Go back to
Calcium Binding Sites List in 3g83
Calcium binding site 5 out
of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:23.8
occ:1.00
|
O
|
B:GLU329
|
2.5
|
17.6
|
1.0
|
OD1
|
B:ASP330
|
2.5
|
21.4
|
1.0
|
O
|
B:HOH400
|
2.5
|
17.9
|
1.0
|
OD2
|
B:ASP297
|
2.6
|
24.4
|
1.0
|
OD1
|
B:ASP324
|
2.6
|
22.6
|
1.0
|
OE1
|
B:GLU301
|
2.6
|
20.4
|
1.0
|
OE2
|
B:GLU301
|
2.7
|
23.5
|
1.0
|
OD1
|
B:ASP297
|
2.8
|
21.1
|
1.0
|
CD
|
B:GLU301
|
3.0
|
27.4
|
1.0
|
CG
|
B:ASP297
|
3.0
|
23.6
|
1.0
|
CG
|
B:ASP324
|
3.4
|
26.8
|
1.0
|
C
|
B:GLU329
|
3.4
|
20.8
|
1.0
|
CG
|
B:ASP330
|
3.6
|
27.1
|
1.0
|
CA
|
B:ASP330
|
3.8
|
22.3
|
1.0
|
CA
|
B:CA403
|
3.9
|
28.7
|
1.0
|
CB
|
B:ASP324
|
3.9
|
20.8
|
1.0
|
N
|
B:ASP330
|
4.0
|
19.3
|
1.0
|
O
|
B:HOH437
|
4.0
|
30.4
|
1.0
|
OD2
|
B:ASP324
|
4.2
|
23.4
|
1.0
|
CB
|
B:ASP330
|
4.3
|
22.1
|
1.0
|
N
|
B:GLU329
|
4.4
|
22.2
|
1.0
|
CA
|
B:GLU329
|
4.4
|
22.7
|
1.0
|
OD2
|
B:ASP342
|
4.5
|
19.8
|
1.0
|
OD2
|
B:ASP330
|
4.5
|
21.6
|
1.0
|
CG
|
B:GLU301
|
4.5
|
26.1
|
1.0
|
CA
|
B:ASP324
|
4.5
|
20.9
|
1.0
|
CB
|
B:ASP297
|
4.5
|
22.9
|
1.0
|
CZ
|
B:PHE304
|
4.6
|
22.6
|
1.0
|
N
|
B:GLY302
|
4.8
|
23.2
|
1.0
|
O
|
B:ASP297
|
4.9
|
25.6
|
1.0
|
C
|
B:ASP330
|
5.0
|
20.2
|
1.0
|
CB
|
B:GLU329
|
5.0
|
20.7
|
1.0
|
|
Calcium binding site 6 out
of 9 in 3g83
Go back to
Calcium Binding Sites List in 3g83
Calcium binding site 6 out
of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca403
b:28.7
occ:1.00
|
OE1
|
B:GLU301
|
2.5
|
20.4
|
1.0
|
O
|
B:HOH405
|
2.5
|
24.3
|
1.0
|
O
|
B:HOH440
|
2.5
|
27.2
|
1.0
|
O
|
B:HOH437
|
2.6
|
30.4
|
1.0
|
OD2
|
B:ASP330
|
2.6
|
21.6
|
1.0
|
OD1
|
B:ASP330
|
2.7
|
21.4
|
1.0
|
O
|
B:HOH414
|
2.7
|
33.4
|
1.0
|
CG
|
B:ASP330
|
3.0
|
27.1
|
1.0
|
CD
|
B:GLU301
|
3.7
|
27.4
|
1.0
|
CA
|
B:CA402
|
3.9
|
23.8
|
1.0
|
O
|
B:HOH374
|
4.1
|
28.9
|
1.0
|
CB
|
B:GLU301
|
4.2
|
29.8
|
1.0
|
O
|
B:ASP297
|
4.3
|
25.6
|
1.0
|
CG
|
B:GLU301
|
4.4
|
26.1
|
1.0
|
OD1
|
B:ASP324
|
4.4
|
22.6
|
1.0
|
O
|
B:HOH426
|
4.4
|
40.6
|
1.0
|
CB
|
B:ASP330
|
4.5
|
22.1
|
1.0
|
OE2
|
B:GLU301
|
4.6
|
23.5
|
1.0
|
CA
|
B:GLU301
|
4.6
|
26.8
|
1.0
|
O
|
B:HOH452
|
4.7
|
41.8
|
1.0
|
OD1
|
B:ASP297
|
4.7
|
21.1
|
1.0
|
OD2
|
B:ASP297
|
4.9
|
24.4
|
1.0
|
OD2
|
B:ASP324
|
4.9
|
23.4
|
1.0
|
O
|
B:HOH552
|
4.9
|
42.4
|
1.0
|
O
|
B:GLY327
|
5.0
|
27.2
|
1.0
|
O
|
B:HOH174
|
5.0
|
26.8
|
1.0
|
|
Calcium binding site 7 out
of 9 in 3g83
Go back to
Calcium Binding Sites List in 3g83
Calcium binding site 7 out
of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca401
b:20.6
occ:1.00
|
OD1
|
C:ASP342
|
2.3
|
17.3
|
1.0
|
OE1
|
C:GLU329
|
2.4
|
21.2
|
1.0
|
OD1
|
C:ASN341
|
2.4
|
21.1
|
1.0
|
OD1
|
C:ASN323
|
2.6
|
23.3
|
1.0
|
O
|
C:ASP342
|
2.6
|
18.9
|
1.0
|
O3
|
C:MAN500
|
2.6
|
24.5
|
1.0
|
O4
|
C:MAN500
|
2.7
|
22.0
|
1.0
|
OE1
|
C:GLU321
|
2.7
|
18.5
|
1.0
|
CG
|
C:ASN341
|
3.4
|
22.8
|
1.0
|
CG
|
C:ASP342
|
3.4
|
20.1
|
1.0
|
CD
|
C:GLU329
|
3.4
|
22.4
|
1.0
|
C3
|
C:MAN500
|
3.5
|
28.6
|
1.0
|
C4
|
C:MAN500
|
3.5
|
30.4
|
1.0
|
CD
|
C:GLU321
|
3.5
|
19.9
|
1.0
|
CG
|
C:ASN323
|
3.5
|
23.3
|
1.0
|
C
|
C:ASP342
|
3.6
|
20.0
|
1.0
|
ND2
|
C:ASN341
|
3.8
|
22.3
|
1.0
|
N
|
C:ASP342
|
3.8
|
20.5
|
1.0
|
OE2
|
C:GLU329
|
3.8
|
26.0
|
1.0
|
OE2
|
C:GLU321
|
3.8
|
23.8
|
1.0
|
CA
|
C:ASP342
|
4.0
|
20.9
|
1.0
|
ND2
|
C:ASN323
|
4.1
|
24.2
|
1.0
|
OD2
|
C:ASP342
|
4.1
|
18.1
|
1.0
|
N
|
C:ASN323
|
4.2
|
21.6
|
1.0
|
CB
|
C:ASP342
|
4.3
|
18.8
|
1.0
|
C
|
C:ASN341
|
4.5
|
23.1
|
1.0
|
CB
|
C:ASP325
|
4.6
|
26.8
|
1.0
|
N
|
C:ASP325
|
4.6
|
22.2
|
1.0
|
CB
|
C:ASN341
|
4.7
|
17.6
|
1.0
|
N
|
C:ASP324
|
4.7
|
20.2
|
1.0
|
CB
|
C:ASN323
|
4.7
|
18.6
|
1.0
|
CG
|
C:GLU329
|
4.7
|
22.7
|
1.0
|
CG
|
C:GLU321
|
4.7
|
19.0
|
1.0
|
N
|
C:ARG343
|
4.8
|
24.0
|
1.0
|
CA
|
C:ASN323
|
4.8
|
22.6
|
1.0
|
CA
|
C:ASN341
|
4.8
|
18.6
|
1.0
|
CB
|
C:GLU329
|
4.9
|
22.5
|
1.0
|
C2
|
C:MAN500
|
4.9
|
35.6
|
1.0
|
C5
|
C:MAN500
|
4.9
|
38.1
|
1.0
|
C
|
C:ASN323
|
5.0
|
21.4
|
1.0
|
|
Calcium binding site 8 out
of 9 in 3g83
Go back to
Calcium Binding Sites List in 3g83
Calcium binding site 8 out
of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca402
b:26.8
occ:1.00
|
O
|
C:GLU329
|
2.4
|
24.4
|
1.0
|
O
|
C:HOH104
|
2.5
|
20.3
|
1.0
|
OD1
|
C:ASP330
|
2.5
|
25.6
|
1.0
|
OD2
|
C:ASP297
|
2.6
|
30.8
|
1.0
|
OD1
|
C:ASP324
|
2.7
|
25.3
|
1.0
|
OE2
|
C:GLU301
|
2.7
|
26.6
|
1.0
|
OE1
|
C:GLU301
|
2.7
|
32.5
|
1.0
|
OD1
|
C:ASP297
|
2.7
|
25.9
|
1.0
|
CD
|
C:GLU301
|
3.0
|
32.1
|
1.0
|
CG
|
C:ASP297
|
3.1
|
32.0
|
1.0
|
C
|
C:GLU329
|
3.3
|
22.2
|
1.0
|
CG
|
C:ASP324
|
3.5
|
30.5
|
1.0
|
CG
|
C:ASP330
|
3.7
|
29.3
|
1.0
|
CA
|
C:ASP330
|
3.8
|
25.8
|
1.0
|
N
|
C:ASP330
|
3.9
|
22.9
|
1.0
|
O
|
C:HOH417
|
4.0
|
30.5
|
1.0
|
CA
|
C:CA403
|
4.0
|
32.4
|
1.0
|
CB
|
C:ASP324
|
4.0
|
23.9
|
1.0
|
CB
|
C:ASP330
|
4.3
|
25.6
|
1.0
|
N
|
C:GLU329
|
4.3
|
23.9
|
1.0
|
OD2
|
C:ASP324
|
4.3
|
26.6
|
1.0
|
CA
|
C:GLU329
|
4.3
|
22.4
|
1.0
|
OD2
|
C:ASP342
|
4.4
|
18.1
|
1.0
|
CZ
|
C:PHE304
|
4.4
|
24.7
|
1.0
|
CG
|
C:GLU301
|
4.5
|
33.6
|
1.0
|
CA
|
C:ASP324
|
4.5
|
21.9
|
1.0
|
CB
|
C:ASP297
|
4.6
|
30.7
|
1.0
|
OD2
|
C:ASP330
|
4.7
|
26.8
|
1.0
|
N
|
C:GLY302
|
4.8
|
33.8
|
1.0
|
O
|
C:ASP297
|
4.8
|
33.5
|
1.0
|
CB
|
C:GLU329
|
4.9
|
22.5
|
1.0
|
CE1
|
C:PHE304
|
4.9
|
25.4
|
1.0
|
C
|
C:ASP330
|
5.0
|
22.4
|
1.0
|
|
Calcium binding site 9 out
of 9 in 3g83
Go back to
Calcium Binding Sites List in 3g83
Calcium binding site 9 out
of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca403
b:32.4
occ:1.00
|
OE1
|
C:GLU301
|
2.5
|
32.5
|
1.0
|
O
|
C:HOH404
|
2.5
|
30.1
|
1.0
|
O
|
C:HOH417
|
2.6
|
30.5
|
1.0
|
OD1
|
C:ASP330
|
2.6
|
25.6
|
1.0
|
OD2
|
C:ASP330
|
2.7
|
26.8
|
1.0
|
O
|
C:HOH433
|
2.7
|
34.4
|
1.0
|
O
|
C:HOH449
|
2.8
|
38.8
|
1.0
|
CG
|
C:ASP330
|
3.0
|
29.3
|
1.0
|
CD
|
C:GLU301
|
3.6
|
32.1
|
1.0
|
CA
|
C:CA402
|
4.0
|
26.8
|
1.0
|
O
|
C:HOH434
|
4.1
|
37.0
|
1.0
|
O
|
C:ASP297
|
4.2
|
33.5
|
1.0
|
CB
|
C:GLU301
|
4.2
|
35.7
|
1.0
|
CG
|
C:GLU301
|
4.4
|
33.6
|
1.0
|
OD1
|
C:ASP324
|
4.4
|
25.3
|
1.0
|
CB
|
C:ASP330
|
4.5
|
25.6
|
1.0
|
OE2
|
C:GLU301
|
4.5
|
26.6
|
1.0
|
O
|
C:HOH420
|
4.5
|
41.6
|
1.0
|
CA
|
C:GLU301
|
4.6
|
38.8
|
1.0
|
OD1
|
C:ASP297
|
4.8
|
25.9
|
1.0
|
OD2
|
C:ASP324
|
4.9
|
26.6
|
1.0
|
O
|
C:HOH361
|
5.0
|
32.7
|
1.0
|
|
Reference:
E.Crouch,
K.Hartshorn,
T.Horlacher,
B.Mcdonald,
K.Smith,
T.Cafarella,
B.Seaton,
P.H.Seeberger,
J.Head.
Recognition of Mannosylated Ligands and Influenza A Virus By Human Surfactant Protein D: Contributions of An Extended Site and Residue 343. Biochemistry V. 48 3335 2009.
ISSN: ISSN 0006-2960
PubMed: 19249874
DOI: 10.1021/BI8022703
Page generated: Sat Jul 13 10:30:48 2024
|