Calcium in PDB 3dbz: Human Surfactant Protein D

The structure of Human Surfactant Protein D, PDB code: 3dbz 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)	50.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.260, 107.600, 55.600, 90.00, 91.80, 90.00
R / Rfree (%)	18 / 20.2

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

Calcium binding site 1 out of 9 in the Human Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Surfactant Protein D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:14.2 occ:1.00 OD1 A:ASP342 2.3 13.7 1.0 OD1 A:ASN341 2.4 14.4 1.0 OD1 A:ASN323 2.4 16.7 1.0 OE1 A:GLU329 2.4 14.2 1.0 OE1 A:GLU321 2.5 16.4 1.0 O A:ASP342 2.7 12.1 1.0 O2 A:MPD901 2.7 24.0 1.0 O4 A:MPD901 3.1 29.7 1.0 CG A:ASP342 3.3 12.4 1.0 CD A:GLU321 3.4 17.8 1.0 CG A:ASN341 3.4 15.0 1.0 CD A:GLU329 3.4 13.8 1.0 C2 A:MPD901 3.6 28.9 1.0 CG A:ASN323 3.6 22.5 1.0 OE2 A:GLU321 3.7 20.6 1.0 C A:ASP342 3.7 12.1 1.0 OE2 A:GLU329 3.7 13.3 1.0 C1 A:MPD901 3.8 30.9 1.0 N A:ASP342 3.8 12.4 1.0 C3 A:MPD901 3.8 29.1 1.0 ND2 A:ASN341 3.8 16.2 1.0 OD2 A:ASP342 4.0 13.2 1.0 C4 A:MPD901 4.1 28.4 1.0 CA A:ASP342 4.1 12.1 1.0 N A:ASN323 4.2 16.4 1.0 CB A:ASP342 4.3 11.3 1.0 ND2 A:ASN323 4.4 25.3 1.0 CG A:GLU321 4.6 16.5 1.0 CB A:ASN323 4.6 18.4 1.0 CB A:ASP325 4.6 17.0 1.0 C A:ASN341 4.6 14.1 1.0 N A:ASP325 4.7 15.0 1.0 N A:ASP324 4.7 14.7 1.0 CB A:ASN341 4.7 14.8 1.0 CG A:GLU329 4.7 14.4 1.0 CA A:ASN323 4.8 16.0 1.0 N A:ARG343 4.9 12.4 1.0 CA A:ASN341 4.9 12.9 1.0 CB A:GLU329 5.0 13.6 1.0 CM A:MPD901 5.0 31.3 1.0

Calcium binding site 2 out of 9 in the Human Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Surfactant Protein D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:14.3 occ:1.00 O A:HOH992 2.4 15.8 1.0 OD1 A:ASP330 2.4 14.6 1.0 OD2 A:ASP297 2.4 15.4 1.0 OE2 A:GLU301 2.5 13.1 1.0 OD1 A:ASP324 2.5 13.5 1.0 OE1 A:GLU301 2.5 14.1 1.0 O A:GLU329 2.5 13.5 1.0 OD1 A:ASP297 2.7 13.6 1.0 CD A:GLU301 2.8 14.3 1.0 CG A:ASP297 2.9 12.7 1.0 CG A:ASP324 3.3 15.9 1.0 C A:GLU329 3.4 14.0 1.0 CG A:ASP330 3.5 15.7 1.0 CA A:ASP330 3.8 14.0 1.0 CA A:CA403 3.9 16.4 1.0 CB A:ASP324 3.9 15.3 1.0 N A:ASP330 4.0 13.9 1.0 OD2 A:ASP324 4.1 14.8 1.0 CB A:ASP330 4.2 12.3 1.0 O A:HOH993 4.3 23.6 1.0 CG A:GLU301 4.3 15.2 1.0 N A:GLU329 4.3 16.1 1.0 CZ A:PHE304 4.4 16.5 1.0 CB A:ASP297 4.4 14.6 1.0 CA A:GLU329 4.4 14.5 1.0 OD2 A:ASP330 4.4 17.3 1.0 CA A:ASP324 4.5 14.7 1.0 N A:GLY302 4.6 17.9 1.0 OD2 A:ASP342 4.7 13.2 1.0 O A:HOH913 4.7 15.6 1.0 O A:ASP297 4.8 16.5 1.0 O A:HOH910 4.9 19.1 1.0 O A:HOH1008 4.9 16.7 1.0 CE1 A:PHE304 4.9 15.5 1.0 CB A:GLU329 4.9 13.6 1.0 CA A:GLU301 5.0 18.4 1.0

Calcium binding site 3 out of 9 in the Human Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Surfactant Protein D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:16.4 occ:1.00 O A:HOH1008 2.3 16.7 1.0 OE1 A:GLU301 2.3 14.1 1.0 O A:HOH990 2.3 36.5 1.0 O A:HOH989 2.3 19.2 1.0 O A:HOH993 2.4 23.6 1.0 OD2 A:ASP330 2.5 17.3 1.0 OD1 A:ASP330 2.6 14.6 1.0 CG A:ASP330 2.9 15.7 1.0 CD A:GLU301 3.5 14.3 1.0 CA A:CA402 3.9 14.3 1.0 OD1 A:ASP324 4.2 13.5 1.0 CG A:GLU301 4.2 15.2 1.0 CB A:GLU301 4.3 17.6 1.0 CB A:ASP330 4.4 12.3 1.0 OE2 A:GLU301 4.4 13.1 1.0 O A:ASP297 4.5 16.5 1.0 OD1 A:ASP297 4.7 13.6 1.0 OD2 A:ASP324 4.7 14.8 1.0 O A:GLY327 4.8 19.0 1.0 CA A:GLU301 4.8 18.4 1.0 O A:HOH1050 4.8 46.2 1.0 CG A:ASP324 4.8 15.9 1.0 OD2 A:ASP297 4.9 15.4 1.0 O A:HOH939 4.9 21.9 1.0

Calcium binding site 4 out of 9 in the Human Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Surfactant Protein D within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:13.5 occ:1.00 OD1 B:ASP342 2.4 13.3 1.0 OD1 B:ASN341 2.4 15.1 1.0 OD1 B:ASN323 2.5 13.9 1.0 O B:HOH405 2.5 15.3 1.0 OE1 B:GLU329 2.5 13.2 1.0 O B:HOH500 2.5 14.2 1.0 OE1 B:GLU321 2.6 14.2 1.0 O B:ASP342 2.7 12.6 1.0 CG B:ASN341 3.4 13.7 1.0 CG B:ASP342 3.4 11.8 1.0 CD B:GLU321 3.4 15.6 1.0 CG B:ASN323 3.5 13.7 1.0 CD B:GLU329 3.5 15.3 1.0 C B:ASP342 3.7 13.0 1.0 OE2 B:GLU321 3.8 14.5 1.0 ND2 B:ASN341 3.8 14.5 1.0 N B:ASP342 3.8 13.3 1.0 OE2 B:GLU329 3.8 14.3 1.0 ND2 B:ASN323 4.0 15.3 1.0 OD2 B:ASP342 4.1 13.1 1.0 CA B:ASP342 4.2 12.6 1.0 N B:ASN323 4.2 13.0 1.0 CB B:ASP342 4.4 12.9 1.0 O B:HOH547 4.4 43.8 1.0 CB B:ASP325 4.6 19.6 1.0 C B:ASN341 4.6 11.8 1.0 CB B:ASN323 4.6 13.8 1.0 CG B:GLU321 4.7 14.2 1.0 CB B:ASN341 4.7 13.2 1.0 N B:ASP325 4.7 17.4 1.0 N B:ASP324 4.8 14.1 1.0 CG B:GLU329 4.8 13.0 1.0 CA B:ASN323 4.8 13.3 1.0 N B:ARG343 4.9 14.1 1.0 CA B:ASN341 4.9 12.2 1.0 CB B:GLU329 5.0 14.3 1.0

Calcium binding site 5 out of 9 in the Human Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Surfactant Protein D within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:15.0 occ:1.00 O B:HOH502 2.3 14.2 1.0 OD2 B:ASP297 2.4 20.2 1.0 OD1 B:ASP330 2.4 15.8 1.0 O B:GLU329 2.4 13.8 1.0 OE2 B:GLU301 2.5 18.0 1.0 OE1 B:GLU301 2.6 17.6 1.0 OD1 B:ASP297 2.6 16.2 1.0 OD1 B:ASP324 2.6 16.3 1.0 CG B:ASP297 2.9 18.2 1.0 CD B:GLU301 2.9 18.4 1.0 C B:GLU329 3.4 14.6 1.0 CG B:ASP324 3.4 16.8 1.0 CG B:ASP330 3.5 18.5 1.0 CA B:ASP330 3.8 14.7 1.0 CA B:CA403 3.9 22.6 1.0 O B:HOH501 3.9 19.6 1.0 CB B:ASP324 4.0 16.1 1.0 N B:ASP330 4.0 15.1 1.0 CB B:ASP330 4.2 15.6 1.0 OD2 B:ASP324 4.3 17.1 1.0 O B:HOH513 4.3 32.7 1.0 CB B:ASP297 4.4 17.6 1.0 CG B:GLU301 4.4 19.2 1.0 OD2 B:ASP330 4.5 17.6 1.0 CZ B:PHE304 4.5 16.5 1.0 N B:GLU329 4.5 16.7 1.0 CA B:GLU329 4.5 15.3 1.0 CA B:ASP324 4.5 16.5 1.0 OD2 B:ASP342 4.6 13.1 1.0 O B:ASP297 4.7 19.0 1.0 N B:GLY302 4.7 21.9 1.0 CE1 B:PHE304 4.9 14.9 1.0 O B:HOH467 4.9 31.8 1.0 CA B:GLU301 5.0 22.2 1.0 C B:ASP330 5.0 14.8 1.0

Calcium binding site 6 out of 9 in the Human Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Surfactant Protein D within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:22.6 occ:1.00 O B:HOH498 2.3 17.1 1.0 OE1 B:GLU301 2.4 17.6 1.0 O B:HOH501 2.4 19.6 1.0 O B:HOH509 2.4 23.1 1.0 O B:HOH499 2.4 24.2 1.0 OD2 B:ASP330 2.4 17.6 1.0 OD1 B:ASP330 2.6 15.8 1.0 CG B:ASP330 2.8 18.5 1.0 CD B:GLU301 3.6 18.4 1.0 CA B:CA402 3.9 15.0 1.0 O B:ASP297 4.2 19.0 1.0 O B:HOH469 4.2 28.5 1.0 CB B:GLU301 4.3 22.1 1.0 OD1 B:ASP324 4.3 16.3 1.0 CG B:GLU301 4.3 19.2 1.0 CB B:ASP330 4.3 15.6 1.0 OE2 B:GLU301 4.5 18.0 1.0 O B:HOH518 4.5 36.6 1.0 OD1 B:ASP297 4.7 16.2 1.0 CA B:GLU301 4.7 22.2 1.0 OD2 B:ASP297 4.7 20.2 1.0 O B:HOH592 4.9 43.4 1.0 CG B:ASP297 4.9 18.2 1.0 OD2 B:ASP324 4.9 17.1 1.0 O B:HOH425 4.9 22.5 1.0

Calcium binding site 7 out of 9 in the Human Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human Surfactant Protein D within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:12.0 occ:1.00 OD1 C:ASP342 2.3 12.4 1.0 OE1 C:GLU329 2.4 15.0 1.0 OD1 C:ASN323 2.4 12.8 1.0 OD1 C:ASN341 2.4 14.8 1.0 O C:HOH495 2.5 14.5 1.0 O C:HOH496 2.6 16.8 1.0 OE1 C:GLU321 2.6 14.2 1.0 O C:ASP342 2.6 11.2 1.0 CG C:ASP342 3.4 12.8 1.0 CD C:GLU329 3.4 16.0 1.0 CG C:ASN323 3.4 13.9 1.0 CG C:ASN341 3.4 15.4 1.0 CD C:GLU321 3.5 13.8 1.0 C C:ASP342 3.7 12.4 1.0 OE2 C:GLU329 3.8 13.8 1.0 N C:ASP342 3.8 11.8 1.0 OE2 C:GLU321 3.8 16.0 1.0 ND2 C:ASN341 3.8 15.6 1.0 ND2 C:ASN323 3.9 16.6 1.0 OD2 C:ASP342 4.1 12.2 1.0 CA C:ASP342 4.1 11.9 1.0 N C:ASN323 4.2 12.8 1.0 CB C:ASP342 4.3 12.3 1.0 O C:HOH533 4.4 41.0 1.0 C C:ASN341 4.6 13.4 1.0 CB C:ASP325 4.6 18.9 1.0 CB C:ASN323 4.6 12.4 1.0 CG C:GLU321 4.7 13.6 1.0 CG C:GLU329 4.7 13.4 1.0 N C:ASP325 4.7 14.3 1.0 CB C:ASN341 4.7 12.8 1.0 N C:ASP324 4.8 12.9 1.0 CA C:ASN323 4.8 12.8 1.0 N C:ARG343 4.8 13.2 1.0 CB C:GLU329 4.9 14.5 1.0 CA C:ASN341 4.9 13.2 1.0 C C:ASN323 5.0 13.3 1.0

Calcium binding site 8 out of 9 in the Human Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human Surfactant Protein D within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:15.4 occ:1.00 O C:HOH404 2.4 11.2 1.0 OD1 C:ASP330 2.4 16.5 1.0 OE2 C:GLU301 2.5 15.6 1.0 O C:GLU329 2.5 14.2 1.0 OE1 C:GLU301 2.5 16.3 1.0 OD2 C:ASP297 2.5 19.2 1.0 OD1 C:ASP324 2.5 15.9 1.0 OD1 C:ASP297 2.8 15.8 1.0 CD C:GLU301 2.8 15.7 1.0 CG C:ASP297 3.0 18.7 1.0 CG C:ASP324 3.3 16.3 1.0 C C:GLU329 3.4 15.4 1.0 CG C:ASP330 3.5 19.3 1.0 CA C:ASP330 3.8 15.8 1.0 CB C:ASP324 3.9 13.8 1.0 O C:HOH410 3.9 22.1 1.0 CA C:CA403 3.9 20.1 1.0 N C:ASP330 4.0 15.6 1.0 OD2 C:ASP324 4.2 12.4 1.0 CB C:ASP330 4.2 16.4 1.0 CG C:GLU301 4.3 18.5 1.0 N C:GLU329 4.4 16.7 1.0 CA C:ASP324 4.4 13.1 1.0 CZ C:PHE304 4.4 15.9 1.0 CA C:GLU329 4.5 15.2 1.0 OD2 C:ASP330 4.5 19.4 1.0 CB C:ASP297 4.5 17.2 1.0 OD2 C:ASP342 4.6 12.2 1.0 N C:GLY302 4.8 20.7 1.0 O C:ASP297 4.9 20.9 1.0 CE1 C:PHE304 4.9 14.2 1.0 O C:HOH427 4.9 22.5 1.0 O C:HOH413 4.9 17.2 1.0 CA C:GLU301 5.0 21.1 1.0

Calcium binding site 9 out of 9 in the Human Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Human Surfactant Protein D within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:20.1 occ:1.00 O C:HOH492 2.3 20.3 1.0 OE1 C:GLU301 2.3 16.3 1.0 O C:HOH494 2.4 19.9 1.0 OD2 C:ASP330 2.5 19.4 1.0 O C:HOH493 2.5 25.3 1.0 O C:HOH410 2.5 22.1 1.0 OD1 C:ASP330 2.6 16.5 1.0 CG C:ASP330 2.9 19.3 1.0 CD C:GLU301 3.5 15.7 1.0 CA C:CA402 3.9 15.4 1.0 O C:HOH422 4.1 23.5 1.0 CB C:GLU301 4.1 19.5 1.0 CG C:GLU301 4.2 18.5 1.0 O C:ASP297 4.3 20.9 1.0 OD1 C:ASP324 4.3 15.9 1.0 CB C:ASP330 4.4 16.4 1.0 OE2 C:GLU301 4.5 15.6 1.0 O C:HOH569 4.5 43.3 1.0 O C:HOH530 4.6 36.0 1.0 CA C:GLU301 4.6 21.1 1.0 OD1 C:ASP297 4.7 15.8 1.0 OD2 C:ASP324 4.9 12.4 1.0 OD2 C:ASP297 4.9 19.2 1.0 CG C:ASP324 5.0 16.3 1.0 O C:HOH447 5.0 24.5 1.0

L.Wang, J.W.Brauner, G.Mao, E.Crouch, B.Seaton, J.Head, K.Smith, C.R.Flach, R.Mendelsohn. Interaction of Recombinant Surfactant Protein D with Lipopolysaccharide: Conformation and Orientation of Bound Protein By Irras and Simulations. Biochemistry V. 47 8103 2008.
ISSN: ISSN 0006-2960
PubMed: 18620419
DOI: 10.1021/BI800626H