Calcium in PDB 2ria: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with D-Glycero-D- Manno-Heptose

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with D-Glycero-D- Manno-Heptose, PDB code: 2ria was solved by H.Wang, J.Head, P.Kosma, S.Sheikh, B.Mcdonald, K.Smith, T.Cafarella, B.Seaton, E.Crouch, 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 (°)	55.414, 108.606, 55.548, 90.00, 91.03, 90.00
R / Rfree (%)	20.9 / 23.7

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 D-Glycero-D- Manno-Heptose (pdb code 2ria). 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 D-Glycero-D- Manno-Heptose, PDB code: 2ria:
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 D-Glycero-D- Manno-Heptose


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 D-Glycero-D- Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:21.6 occ:1.00 OD1 A:ASN341 2.5 21.8 1.0 OE1 A:GLU329 2.6 20.6 1.0 OD1 A:ASP342 2.6 19.1 1.0 OD1 A:ASN323 2.6 22.3 1.0 OE1 A:GLU321 2.7 21.5 1.0 O A:ASP342 2.7 16.6 1.0 O3 A:289356 2.7 34.5 1.0 O4 A:289356 2.8 34.2 1.0 CG A:ASP342 3.4 24.9 1.0 CG A:ASN323 3.4 24.1 1.0 CD A:GLU321 3.5 22.3 1.0 C3 A:289356 3.5 38.9 1.0 CG A:ASN341 3.5 24.0 1.0 CD A:GLU329 3.5 19.5 1.0 C4 A:289356 3.7 39.4 1.0 C A:ASP342 3.7 20.2 1.0 ND2 A:ASN323 3.7 22.5 1.0 OE2 A:GLU321 3.8 22.3 1.0 N A:ASP342 3.8 20.5 1.0 OE2 A:GLU329 3.8 19.1 1.0 ND2 A:ASN341 3.9 21.6 1.0 OD2 A:ASP342 4.0 23.7 1.0 CA A:ASP342 4.1 20.0 1.0 N A:ASN323 4.2 22.7 1.0 CB A:ASP342 4.4 20.9 1.0 C A:ASN341 4.6 21.0 1.0 CB A:ASP325 4.6 25.9 1.0 CB A:ASN323 4.6 22.1 1.0 N A:ASP324 4.7 21.5 1.0 N A:ASP325 4.7 23.8 1.0 CG A:GLU321 4.7 23.0 1.0 CB A:ASN341 4.8 20.8 1.0 CG A:GLU329 4.8 21.9 1.0 CA A:ASN323 4.8 22.4 1.0 N A:ARG343 4.9 21.8 1.0 CA A:ASN341 4.9 21.6 1.0 CB A:GLU329 5.0 23.8 1.0 C2 A:289356 5.0 41.7 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 D-Glycero-D- Manno-Heptose


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 D-Glycero-D- Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:24.3 occ:1.00 O A:HOH515 2.6 21.3 1.0 OD1 A:ASP330 2.6 22.4 1.0 OD1 A:ASP324 2.6 23.5 1.0 OD2 A:ASP297 2.6 26.4 1.0 OE1 A:GLU301 2.6 23.7 1.0 OE2 A:GLU301 2.7 22.8 1.0 O A:GLU329 2.7 21.6 1.0 OD1 A:ASP297 2.8 24.9 1.0 CD A:GLU301 3.0 25.1 1.0 CG A:ASP297 3.1 24.9 1.0 CG A:ASP324 3.3 25.3 1.0 C A:GLU329 3.4 22.8 1.0 CG A:ASP330 3.7 25.2 1.0 CA A:ASP330 3.8 21.6 1.0 CB A:ASP324 3.9 22.5 1.0 N A:ASP330 4.0 22.9 1.0 CA A:CA403 4.0 26.6 1.0 OD2 A:ASP324 4.1 23.3 1.0 CB A:ASP330 4.3 21.9 1.0 N A:GLU329 4.3 24.9 1.0 CZ A:PHE304 4.4 23.1 1.0 CA A:GLU329 4.5 24.9 1.0 CA A:ASP324 4.5 22.3 1.0 CG A:GLU301 4.5 25.3 1.0 O A:HOH519 4.5 39.8 1.0 OD2 A:ASP342 4.6 23.7 1.0 N A:GLY302 4.6 27.9 1.0 CB A:ASP297 4.6 25.7 1.0 OD2 A:ASP330 4.7 23.1 1.0 O A:HOH478 4.8 27.2 1.0 O A:ASP297 4.8 28.2 1.0 O A:HOH416 4.8 29.6 1.0 CE1 A:PHE304 4.9 22.8 1.0 CA A:GLU301 5.0 28.4 1.0 CB A:GLU329 5.0 23.8 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 D-Glycero-D- Manno-Heptose


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 D-Glycero-D- Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:26.6 occ:1.00 OE1 A:GLU301 2.5 23.7 1.0 OD1 A:ASP330 2.6 22.4 1.0 OD2 A:ASP330 2.7 23.1 1.0 O A:HOH519 2.7 39.8 1.0 O A:HOH520 2.8 41.4 1.0 O A:HOH448 2.8 36.5 1.0 CG A:ASP330 3.0 25.2 1.0 CD A:GLU301 3.7 25.1 1.0 CA A:CA402 4.0 24.3 1.0 OD1 A:ASP324 4.3 23.5 1.0 CB A:GLU301 4.4 28.6 1.0 CG A:GLU301 4.4 25.3 1.0 CB A:ASP330 4.5 21.9 1.0 O A:ASP297 4.5 28.2 1.0 OE2 A:GLU301 4.6 22.8 1.0 OD2 A:ASP324 4.7 23.3 1.0 OD1 A:ASP297 4.8 24.9 1.0 O A:GLY327 4.8 26.9 1.0 CA A:GLU301 4.8 28.4 1.0 O A:HOH424 4.9 33.6 1.0 CG A:ASP324 4.9 25.3 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 D-Glycero-D- Manno-Heptose


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 D-Glycero-D- Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:17.9 occ:1.00 OD1 B:ASP342 2.5 18.0 1.0 OE1 B:GLU329 2.5 17.1 1.0 OD1 B:ASN341 2.6 17.9 1.0 O B:ASP342 2.6 16.1 1.0 OD1 B:ASN323 2.6 20.8 1.0 OE1 B:GLU321 2.6 15.6 1.0 O3 B:289356 2.6 23.8 1.0 O4 B:289356 2.8 23.6 1.0 CG B:ASP342 3.4 15.7 1.0 CD B:GLU321 3.4 16.3 1.0 CD B:GLU329 3.4 19.5 1.0 CG B:ASN341 3.5 18.5 1.0 C4 B:289356 3.5 26.3 1.0 C3 B:289356 3.5 28.0 1.0 CG B:ASN323 3.6 20.8 1.0 C B:ASP342 3.6 16.0 1.0 OE2 B:GLU321 3.7 18.1 1.0 OE2 B:GLU329 3.7 17.6 1.0 N B:ASP342 3.7 16.7 1.0 ND2 B:ASN341 3.8 18.8 1.0 OD2 B:ASP342 4.0 17.3 1.0 ND2 B:ASN323 4.1 19.3 1.0 CA B:ASP342 4.1 15.6 1.0 N B:ASN323 4.2 20.1 1.0 CB B:ASP342 4.3 16.3 1.0 C B:ASN341 4.5 16.7 1.0 CG B:GLU321 4.6 17.8 1.0 CB B:ASP325 4.6 23.8 1.0 CB B:ASN323 4.7 19.2 1.0 CG B:GLU329 4.7 17.6 1.0 N B:ASP325 4.7 20.9 1.0 CB B:ASN341 4.7 17.3 1.0 N B:ASP324 4.8 17.9 1.0 N B:ARG343 4.8 16.4 1.0 CA B:ASN323 4.9 19.4 1.0 CA B:ASN341 4.9 16.6 1.0 C2 B:289356 4.9 29.1 1.0 CB B:GLU329 4.9 19.8 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 D-Glycero-D- Manno-Heptose


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 D-Glycero-D- Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:21.9 occ:1.00 O B:GLU329 2.5 17.1 1.0 OD1 B:ASP330 2.6 19.3 1.0 O B:HOH523 2.6 19.2 1.0 OD2 B:ASP297 2.6 25.0 1.0 OE1 B:GLU301 2.6 23.2 1.0 OD1 B:ASP324 2.7 19.8 1.0 OD1 B:ASP297 2.7 19.7 1.0 OE2 B:GLU301 2.8 26.3 1.0 CG B:ASP297 3.0 23.8 1.0 CD B:GLU301 3.1 26.6 1.0 CG B:ASP324 3.4 23.0 1.0 C B:GLU329 3.4 19.6 1.0 CG B:ASP330 3.6 22.1 1.0 CA B:ASP330 3.8 19.5 1.0 CB B:ASP324 3.9 19.9 1.0 CA B:CA403 3.9 26.3 1.0 N B:ASP330 4.0 19.8 1.0 O B:HOH410 4.0 30.8 1.0 OD2 B:ASP324 4.2 19.6 1.0 CB B:ASP330 4.3 20.1 1.0 O B:HOH493 4.3 35.5 1.0 CA B:ASP324 4.5 20.4 1.0 CZ B:PHE304 4.5 21.1 1.0 N B:GLU329 4.5 22.5 1.0 OD2 B:ASP330 4.5 21.3 1.0 CB B:ASP297 4.5 24.3 1.0 CA B:GLU329 4.5 19.9 1.0 CG B:GLU301 4.6 27.1 1.0 OD2 B:ASP342 4.6 17.3 1.0 O B:ASP297 4.8 28.8 1.0 N B:GLY302 4.8 29.2 1.0 CE1 B:PHE304 5.0 22.0 1.0 C B:ASP330 5.0 19.4 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 D-Glycero-D- Manno-Heptose


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 D-Glycero-D- Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:26.3 occ:1.00 OE1 B:GLU301 2.6 23.2 1.0 OD2 B:ASP330 2.6 21.3 1.0 OD1 B:ASP330 2.7 19.3 1.0 O B:HOH410 2.7 30.8 1.0 O B:HOH524 2.7 28.2 1.0 O B:HOH484 2.7 31.7 1.0 O B:HOH526 2.9 46.6 1.0 CG B:ASP330 3.0 22.1 1.0 CD B:GLU301 3.7 26.6 1.0 CA B:CA402 3.9 21.9 1.0 O B:HOH416 4.1 26.5 1.0 CB B:GLU301 4.3 29.6 1.0 O B:ASP297 4.3 28.8 1.0 OD1 B:ASP324 4.3 19.8 1.0 CG B:GLU301 4.4 27.1 1.0 CB B:ASP330 4.5 20.1 1.0 O B:HOH456 4.6 36.6 1.0 OE2 B:GLU301 4.7 26.3 1.0 CA B:GLU301 4.7 30.4 1.0 OD1 B:ASP297 4.7 19.7 1.0 OD2 B:ASP324 4.9 19.6 1.0 O B:HOH448 4.9 28.1 1.0 OD2 B:ASP297 4.9 25.0 1.0 O B:GLY327 5.0 24.2 1.0 CG B:ASP324 5.0 23.0 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 D-Glycero-D- Manno-Heptose


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 D-Glycero-D- Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:18.1 occ:1.00 OD1 C:ASN341 2.5 17.8 1.0 OE1 C:GLU329 2.5 18.4 1.0 OD1 C:ASP342 2.5 16.3 1.0 OD1 C:ASN323 2.5 18.8 1.0 O C:ASP342 2.6 16.6 1.0 O3 C:289356 2.7 24.8 1.0 OE1 C:GLU321 2.7 18.1 1.0 O4 C:289356 2.8 26.6 1.0 CG C:ASP342 3.4 17.8 1.0 CD C:GLU329 3.5 18.0 1.0 CD C:GLU321 3.5 20.0 1.0 CG C:ASN341 3.5 19.1 1.0 CG C:ASN323 3.5 20.7 1.0 C3 C:289356 3.6 29.5 1.0 C4 C:289356 3.6 31.0 1.0 C C:ASP342 3.6 18.6 1.0 N C:ASP342 3.7 18.1 1.0 OE2 C:GLU329 3.7 17.4 1.0 OE2 C:GLU321 3.7 21.3 1.0 ND2 C:ASN341 3.9 17.8 1.0 ND2 C:ASN323 4.0 20.1 1.0 OD2 C:ASP342 4.1 17.0 1.0 CA C:ASP342 4.1 17.3 1.0 N C:ASN323 4.2 19.5 1.0 CB C:ASP342 4.4 17.2 1.0 C C:ASN341 4.5 19.6 1.0 CB C:ASP325 4.6 25.4 1.0 CG C:GLU321 4.7 20.6 1.0 CB C:ASN323 4.7 19.5 1.0 N C:ASP325 4.7 21.2 1.0 CB C:ASN341 4.7 18.3 1.0 CG C:GLU329 4.7 17.8 1.0 N C:ASP324 4.8 19.8 1.0 N C:ARG343 4.8 18.0 1.0 CA C:ASN323 4.8 19.4 1.0 CA C:ASN341 4.9 19.2 1.0 CB C:GLU329 4.9 19.4 1.0 C2 C:289356 4.9 30.8 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 D-Glycero-D- Manno-Heptose


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 D-Glycero-D- Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:21.5 occ:1.00 O C:HOH515 2.5 21.8 1.0 O C:GLU329 2.6 21.1 1.0 OD1 C:ASP330 2.6 21.0 1.0 OD1 C:ASP324 2.7 20.5 1.0 OE1 C:GLU301 2.7 25.0 1.0 OD2 C:ASP297 2.7 26.4 1.0 OE2 C:GLU301 2.7 25.8 1.0 OD1 C:ASP297 2.8 23.0 1.0 CD C:GLU301 3.1 27.7 1.0 CG C:ASP297 3.1 25.7 1.0 CG C:ASP324 3.4 22.7 1.0 C C:GLU329 3.4 22.0 1.0 CG C:ASP330 3.7 23.6 1.0 CA C:ASP330 3.8 20.9 1.0 CB C:ASP324 3.9 21.8 1.0 N C:ASP330 3.9 22.0 1.0 CA C:CA403 4.0 25.6 1.0 O C:HOH512 4.0 30.1 1.0 OD2 C:ASP324 4.2 22.2 1.0 CB C:ASP330 4.3 20.6 1.0 N C:GLU329 4.4 21.8 1.0 CA C:ASP324 4.4 20.8 1.0 CA C:GLU329 4.4 21.2 1.0 CZ C:PHE304 4.5 24.3 1.0 OD2 C:ASP342 4.5 17.0 1.0 O C:HOH513 4.5 38.4 1.0 CG C:GLU301 4.5 27.6 1.0 CB C:ASP297 4.6 24.8 1.0 OD2 C:ASP330 4.6 24.0 1.0 N C:GLY302 4.8 29.6 1.0 O C:ASP297 4.9 29.9 1.0 CE1 C:PHE304 4.9 24.0 1.0 O C:HOH417 4.9 23.8 1.0 C C:ASP330 5.0 19.8 1.0 CB C:GLU329 5.0 19.4 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 D-Glycero-D- Manno-Heptose


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 D-Glycero-D- Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:25.6 occ:1.00 OE1 C:GLU301 2.5 25.0 1.0 OD1 C:ASP330 2.6 21.0 1.0 OD2 C:ASP330 2.7 24.0 1.0 O C:HOH512 2.7 30.1 1.0 O C:HOH518 2.7 32.5 1.0 O C:HOH482 2.8 30.2 1.0 O C:HOH517 2.9 38.7 1.0 CG C:ASP330 3.0 23.6 1.0 CD C:GLU301 3.7 27.7 1.0 CA C:CA402 4.0 21.5 1.0 O C:HOH415 4.1 23.0 1.0 CB C:GLU301 4.3 28.8 1.0 O C:ASP297 4.4 29.9 1.0 OD1 C:ASP324 4.4 20.5 1.0 CG C:GLU301 4.4 27.6 1.0 CB C:ASP330 4.5 20.6 1.0 OE2 C:GLU301 4.6 25.8 1.0 CA C:GLU301 4.8 29.6 1.0 OD1 C:ASP297 4.8 23.0 1.0 O C:HOH448 4.8 37.8 1.0 O C:GLY327 4.8 24.7 1.0 O C:HOH425 4.9 27.7 1.0 OD2 C:ASP324 4.9 22.2 1.0 OD2 C:ASP297 5.0 26.4 1.0

H.Wang, J.Head, P.Kosma, H.Brade, S.Muller-Loennies, S.Sheikh, B.Mcdonald, K.Smith, T.Cafarella, B.Seaton, E.Crouch. Recognition of Heptoses and the Inner Core of Bacterial Lipopolysaccharides By Surfactant Protein D. Biochemistry V. 47 710 2008.
ISSN: ISSN 0006-2960
PubMed: 18092821
DOI: 10.1021/BI7020553