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.

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

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 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 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 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 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 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 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 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 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 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

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