Calcium in PDB 1b08: Lung Surfactant Protein D (Sp-D) (Fragment)

The structure of Lung Surfactant Protein D (Sp-D) (Fragment), PDB code: 1b08 was solved by K.Hakansson, N.K.Lim, H.-J.Hoppe, K.B.M.Reid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.960, 109.720, 56.090, 90.00, 92.20, 90.00
R / Rfree (%)	20.9 / 27.1

The binding sites of Calcium atom in the Lung Surfactant Protein D (Sp-D) (Fragment) (pdb code 1b08). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Lung Surfactant Protein D (Sp-D) (Fragment), PDB code: 1b08:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Lung Surfactant Protein D (Sp-D) (Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lung Surfactant Protein D (Sp-D) (Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:27.6 occ:1.00 OE1 A:GLU329 2.5 12.8 1.0 OE1 A:GLU321 2.5 21.1 1.0 OD1 A:ASN341 2.6 28.0 1.0 OD1 A:ASN323 2.6 38.5 1.0 OD1 A:ASP342 2.7 31.4 1.0 O A:HOH79 2.7 33.3 1.0 O A:HOH16 2.7 30.8 1.0 O A:ASP342 2.9 20.1 1.0 CD A:GLU321 3.5 26.3 1.0 CG A:ASP342 3.5 25.9 1.0 CG A:ASN341 3.6 18.6 1.0 CD A:GLU329 3.6 17.8 1.0 CG A:ASN323 3.6 28.7 1.0 ND2 A:ASN341 3.8 20.9 1.0 C A:ASP342 3.8 13.9 1.0 OE2 A:GLU321 3.9 32.5 1.0 N A:ASP342 3.9 15.7 1.0 OE2 A:GLU329 4.0 22.7 1.0 ND2 A:ASN323 4.0 32.6 1.0 OD2 A:ASP342 4.1 28.8 1.0 CA A:ASP342 4.3 15.3 1.0 CB A:ASP342 4.4 22.2 1.0 N A:ASN323 4.5 23.8 1.0 CB A:ASP325 4.5 22.8 1.0 CG A:GLU321 4.7 20.1 1.0 CB A:ASN323 4.7 24.7 1.0 CG A:GLU329 4.8 13.5 1.0 C A:ASN341 4.8 14.4 1.0 CB A:ASN341 4.9 15.9 1.0 N A:ARG343 4.9 16.9 1.0 N A:ASP325 4.9 17.3 1.0 CB A:GLU329 5.0 15.7 1.0

Calcium binding site 2 out of 9 in the Lung Surfactant Protein D (Sp-D) (Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lung Surfactant Protein D (Sp-D) (Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:26.1 occ:1.00 O A:HOH70 2.6 35.0 1.0 OD2 A:ASP297 2.6 26.9 1.0 OE2 A:GLU301 2.6 23.8 1.0 OE1 A:GLU301 2.6 26.8 1.0 O A:GLU329 2.6 17.3 1.0 OD1 A:ASP324 2.7 33.1 1.0 OD1 A:ASP297 2.7 27.4 1.0 OD1 A:ASP330 2.9 22.0 1.0 CD A:GLU301 3.0 27.1 1.0 CG A:ASP297 3.0 23.8 1.0 C A:GLU329 3.4 17.5 1.0 CG A:ASP324 3.6 26.6 1.0 CA A:ASP330 4.0 22.2 1.0 CG A:ASP330 4.0 27.3 1.0 N A:ASP330 4.1 16.8 1.0 CB A:ASP324 4.1 23.0 1.0 CA A:CA3 4.1 31.8 1.0 CA A:GLU329 4.4 16.8 1.0 N A:GLU329 4.4 19.4 1.0 OD2 A:ASP324 4.5 37.6 1.0 CG A:GLU301 4.5 24.9 1.0 CZ A:PHE304 4.5 16.6 1.0 CB A:ASP330 4.5 25.2 1.0 CA A:ASP324 4.5 21.1 1.0 CB A:ASP297 4.5 23.1 1.0 O A:HOH66 4.6 47.5 1.0 OD2 A:ASP342 4.6 28.8 1.0 O A:HOH98 4.7 52.2 1.0 N A:GLY302 4.8 26.5 1.0 CB A:GLU329 4.9 15.7 1.0 O A:ASP297 5.0 22.6 1.0 O A:HOH164 5.0 55.7 1.0

Calcium binding site 3 out of 9 in the Lung Surfactant Protein D (Sp-D) (Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lung Surfactant Protein D (Sp-D) (Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:31.8 occ:1.00 OE1 A:GLU301 2.5 26.8 1.0 O A:HOH66 2.6 47.5 1.0 O A:HOH174 2.6 54.6 1.0 OD1 A:ASP330 2.7 22.0 1.0 OD2 A:ASP330 3.2 32.4 1.0 CG A:ASP330 3.3 27.3 1.0 CD A:GLU301 3.7 27.1 1.0 CA A:CA2 4.1 26.1 1.0 OD1 A:ASP324 4.2 33.1 1.0 CB A:GLU301 4.2 22.6 1.0 CG A:GLU301 4.3 24.9 1.0 O A:ASP297 4.5 22.6 1.0 OE2 A:GLU301 4.6 23.8 1.0 OD1 A:ASP297 4.7 27.4 1.0 CA A:GLU301 4.8 26.6 1.0 CB A:ASP330 4.8 25.2 1.0 OD2 A:ASP324 4.8 37.6 1.0 CG A:ASP324 4.9 26.6 1.0 CA A:SER298 5.0 27.0 1.0

Calcium binding site 4 out of 9 in the Lung Surfactant Protein D (Sp-D) (Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lung Surfactant Protein D (Sp-D) (Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4 b:21.4 occ:1.00 OD1 B:ASP1342 2.4 9.0 1.0 OE1 B:GLU1329 2.5 18.3 1.0 OD1 B:ASN1341 2.5 30.4 1.0 OD1 B:ASN1323 2.6 24.0 1.0 OE1 B:GLU1321 2.6 18.0 1.0 O B:HOH1373 2.6 27.0 1.0 O B:HOH1374 2.7 26.6 1.0 O B:ASP1342 2.8 14.0 1.0 CD B:GLU1329 3.4 14.1 1.0 CD B:GLU1321 3.5 9.9 1.0 CG B:ASP1342 3.6 16.4 1.0 CG B:ASN1323 3.6 17.1 1.0 CG B:ASN1341 3.6 22.6 1.0 OE2 B:GLU1329 3.6 21.4 1.0 C B:ASP1342 3.8 13.3 1.0 OE2 B:GLU1321 3.8 17.8 1.0 N B:ASP1342 3.9 16.9 1.0 ND2 B:ASN1341 3.9 25.0 1.0 ND2 B:ASN1323 4.0 16.8 1.0 CA B:ASP1342 4.3 12.6 1.0 OD2 B:ASP1342 4.4 7.7 1.0 N B:ASN1323 4.4 18.7 1.0 CB B:ASP1342 4.5 9.6 1.0 CB B:ASP1325 4.6 20.6 1.0 CG B:GLU1329 4.7 7.5 1.0 C B:ASN1341 4.7 15.3 1.0 CG B:GLU1321 4.7 6.8 1.0 CB B:ASN1323 4.7 13.8 1.0 N B:ASP1325 4.9 15.6 1.0 CB B:ASN1341 4.9 16.7 1.0 CB B:GLU1329 4.9 8.4 1.0 N B:ARG1343 4.9 16.8 1.0 N B:ASP1324 4.9 15.4 1.0 CA B:ASN1323 4.9 17.6 1.0

Calcium binding site 5 out of 9 in the Lung Surfactant Protein D (Sp-D) (Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Lung Surfactant Protein D (Sp-D) (Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5 b:26.5 occ:1.00 O B:GLU1329 2.5 19.9 1.0 O B:HOH1358 2.6 16.0 1.0 OD2 B:ASP1297 2.7 32.1 1.0 OE1 B:GLU1301 2.7 26.7 1.0 OD1 B:ASP1330 2.8 36.1 1.0 OD1 B:ASP1324 2.8 22.6 1.0 OD1 B:ASP1297 2.8 31.9 1.0 OE2 B:GLU1301 2.8 33.3 1.0 CG B:ASP1297 3.1 27.9 1.0 CD B:GLU1301 3.1 31.6 1.0 C B:GLU1329 3.5 18.0 1.0 CG B:ASP1324 3.6 16.7 1.0 O B:HOH1381 3.7 33.3 1.0 CG B:ASP1330 3.8 32.4 1.0 CA B:ASP1330 3.9 19.4 1.0 CB B:ASP1324 4.0 13.5 1.0 O B:HOH1430 4.1 65.1 1.0 N B:ASP1330 4.1 18.5 1.0 CA B:CA6 4.1 30.8 1.0 CB B:ASP1330 4.4 25.4 1.0 OD2 B:ASP1324 4.4 28.8 1.0 N B:GLU1329 4.5 23.4 1.0 OD2 B:ASP1342 4.5 7.7 1.0 CA B:GLU1329 4.5 13.1 1.0 CA B:ASP1324 4.6 14.4 1.0 CB B:ASP1297 4.6 26.4 1.0 CG B:GLU1301 4.6 25.4 1.0 CZ B:PHE1304 4.7 12.6 1.0 OD2 B:ASP1330 4.8 33.8 1.0 N B:GLY1302 5.0 25.6 1.0

Calcium binding site 6 out of 9 in the Lung Surfactant Protein D (Sp-D) (Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Lung Surfactant Protein D (Sp-D) (Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca6 b:30.8 occ:1.00 O B:HOH1382 2.5 40.3 1.0 O B:HOH1381 2.5 33.3 1.0 OE1 B:GLU1301 2.6 26.7 1.0 O B:HOH1421 2.7 33.3 1.0 OD1 B:ASP1330 2.7 36.1 1.0 O B:HOH1388 2.8 48.0 1.0 OD2 B:ASP1330 2.9 33.8 1.0 CG B:ASP1330 3.2 32.4 1.0 CD B:GLU1301 3.7 31.6 1.0 CA B:CA5 4.1 26.5 1.0 O B:HOH1408 4.4 46.1 1.0 CG B:GLU1301 4.4 25.4 1.0 CB B:GLU1301 4.4 29.5 1.0 O B:ASP1297 4.4 33.0 1.0 OD1 B:ASP1324 4.6 22.6 1.0 OE2 B:GLU1301 4.7 33.3 1.0 CB B:ASP1330 4.7 25.4 1.0 O B:GLY1327 4.9 23.3 1.0 CA B:GLU1301 4.9 31.9 1.0 OD1 B:ASP1297 5.0 31.9 1.0

Calcium binding site 7 out of 9 in the Lung Surfactant Protein D (Sp-D) (Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Lung Surfactant Protein D (Sp-D) (Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca7 b:27.2 occ:1.00 OD1 C:ASN2323 2.5 25.3 1.0 OD1 C:ASN2341 2.5 30.8 1.0 OE1 C:GLU2329 2.6 22.7 1.0 OD1 C:ASP2342 2.6 20.8 1.0 OE1 C:GLU2321 2.6 33.3 1.0 O C:ASP2342 2.8 24.6 1.0 O C:HOH2375 2.8 40.9 1.0 O C:HOH2373 2.9 42.7 1.0 CD C:GLU2329 3.4 24.1 1.0 CG C:ASN2341 3.5 28.4 1.0 CD C:GLU2321 3.5 31.8 1.0 OE2 C:GLU2329 3.5 25.5 1.0 CG C:ASN2323 3.6 27.4 1.0 ND2 C:ASN2341 3.7 29.2 1.0 CG C:ASP2342 3.7 15.0 1.0 OE2 C:GLU2321 3.8 34.9 1.0 C C:ASP2342 3.9 24.3 1.0 N C:ASP2342 4.0 13.9 1.0 ND2 C:ASN2323 4.1 23.7 1.0 OD2 C:ASP2342 4.3 16.0 1.0 CA C:ASP2342 4.4 17.3 1.0 N C:ASN2323 4.5 23.1 1.0 CB C:ASP2342 4.6 8.1 1.0 CB C:ASP2325 4.6 30.3 1.0 CG C:GLU2321 4.7 24.2 1.0 N C:ASP2325 4.7 19.6 1.0 N C:ASP2324 4.7 26.4 1.0 CG C:GLU2329 4.7 18.1 1.0 CB C:ASN2323 4.8 24.5 1.0 CB C:ASN2341 4.8 21.1 1.0 C C:ASN2341 4.9 17.1 1.0

Calcium binding site 8 out of 9 in the Lung Surfactant Protein D (Sp-D) (Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Lung Surfactant Protein D (Sp-D) (Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca8 b:31.5 occ:1.00 O C:GLU2329 2.5 26.0 1.0 OD2 C:ASP2297 2.6 28.0 1.0 OD1 C:ASP2297 2.6 26.6 1.0 O C:HOH2365 2.6 51.9 1.0 OE1 C:GLU2301 2.6 37.2 1.0 OE2 C:GLU2301 2.6 37.1 1.0 OD1 C:ASP2324 2.7 31.5 1.0 OD1 C:ASP2330 2.7 36.8 1.0 CG C:ASP2297 3.0 25.9 1.0 CD C:GLU2301 3.0 34.0 1.0 CG C:ASP2324 3.4 24.8 1.0 C C:GLU2329 3.4 25.7 1.0 CG C:ASP2330 3.8 29.6 1.0 CA C:ASP2330 3.9 22.1 1.0 CB C:ASP2324 4.0 22.3 1.0 N C:ASP2330 4.0 24.2 1.0 O C:HOH2374 4.1 28.8 1.0 OD2 C:ASP2324 4.1 29.2 1.0 CA C:CA9 4.2 45.5 1.0 CB C:ASP2330 4.4 27.4 1.0 CZ C:PHE2304 4.4 16.8 1.0 CG C:GLU2301 4.5 35.6 1.0 OD2 C:ASP2342 4.5 16.0 1.0 CB C:ASP2297 4.5 29.2 1.0 CA C:GLU2329 4.5 25.2 1.0 O C:HOH2360 4.6 34.6 1.0 CA C:ASP2324 4.6 22.9 1.0 N C:GLU2329 4.6 34.1 1.0 OD2 C:ASP2330 4.8 38.0 1.0 N C:GLY2302 4.9 37.5 1.0 CA C:GLU2301 4.9 41.0 1.0 CE1 C:PHE2304 4.9 15.1 1.0 O C:HOH2402 4.9 59.9 1.0 CB C:GLU2329 5.0 25.0 1.0

Calcium binding site 9 out of 9 in the Lung Surfactant Protein D (Sp-D) (Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Lung Surfactant Protein D (Sp-D) (Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca9 b:45.5 occ:1.00 O C:HOH2374 2.6 28.8 1.0 O C:HOH2402 2.6 59.9 1.0 OE1 C:GLU2301 2.6 37.2 1.0 OD1 C:ASP2330 2.7 36.8 1.0 OD2 C:ASP2330 2.7 38.0 1.0 CG C:ASP2330 3.1 29.6 1.0 CD C:GLU2301 3.8 34.0 1.0 CA C:CA8 4.2 31.5 1.0 CB C:GLU2301 4.4 35.2 1.0 CG C:GLU2301 4.4 35.6 1.0 CB C:ASP2330 4.6 27.4 1.0 OD1 C:ASP2324 4.6 31.5 1.0 O C:ASP2297 4.7 37.1 1.0 OE2 C:GLU2301 4.8 37.1 1.0 O C:GLY2327 4.9 38.0 1.0 OD1 C:ASP2297 4.9 26.6 1.0 CA C:GLU2301 4.9 41.0 1.0 CA C:SER2298 5.0 46.8 1.0

K.Hakansson, N.K.Lim, H.J.Hoppe, K.B.Reid. Crystal Structure of the Trimeric Alpha-Helical Coiled-Coil and the Three Lectin Domains of Human Lung Surfactant Protein D. Structure Fold.Des. V. 7 255 1999.
ISSN: ISSN 0969-2126
PubMed: 10368295
DOI: 10.1016/S0969-2126(99)80036-7