Calcium in PDB 2rie: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with 2-Deoxy-L- 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 2-Deoxy-L- Glycero-D-Manno-Heptose, PDB code: 2rie 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 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.285, 108.180, 55.543, 90.00, 90.99, 90.00
R / Rfree (%)	19.9 / 21.2

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 2-Deoxy-L- Glycero-D-Manno-Heptose (pdb code 2rie). 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 2-Deoxy-L- Glycero-D-Manno-Heptose, PDB code: 2rie:
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 2-Deoxy-L- 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 2-Deoxy-L- Glycero-D-Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:15.9 occ:1.00 OD1 A:ASN341 2.5 16.9 1.0 OD1 A:ASP342 2.5 15.9 1.0 OE1 A:GLU329 2.5 14.8 1.0 OD1 A:ASN323 2.6 17.4 1.0 O6 A:293356 2.6 20.8 1.0 O A:ASP342 2.6 16.5 1.0 OE1 A:GLU321 2.7 17.2 1.0 O7 A:293356 2.8 19.6 1.0 CG A:ASP342 3.4 16.2 1.0 CG A:ASN323 3.4 19.3 1.0 C7 A:293356 3.5 20.4 1.0 CG A:ASN341 3.5 18.4 1.0 CD A:GLU329 3.5 13.0 1.0 C6 A:293356 3.5 22.5 1.0 CD A:GLU321 3.5 18.5 1.0 C A:ASP342 3.7 16.7 1.0 N A:ASP342 3.8 15.6 1.0 OE2 A:GLU329 3.8 15.9 1.0 OE2 A:GLU321 3.8 19.2 1.0 ND2 A:ASN323 3.8 19.0 1.0 ND2 A:ASN341 3.9 18.6 1.0 OD2 A:ASP342 4.1 14.7 1.0 CA A:ASP342 4.1 16.6 1.0 N A:ASN323 4.2 17.0 1.0 CB A:ASP342 4.3 14.8 1.0 C A:ASN341 4.5 17.4 1.0 CB A:ASP325 4.6 18.8 1.0 N A:ASP325 4.6 16.8 1.0 CB A:ASN323 4.7 17.3 1.0 N A:ASP324 4.7 15.8 1.0 CB A:ASN341 4.7 17.9 1.0 CG A:GLU321 4.7 18.1 1.0 C5 A:293356 4.8 25.4 1.0 CG A:GLU329 4.8 15.4 1.0 O5 A:293356 4.8 29.0 1.0 N A:ARG343 4.8 17.3 1.0 CA A:ASN323 4.8 17.3 1.0 CA A:ASN341 4.9 16.9 1.0 CB A:GLU329 4.9 17.1 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 2-Deoxy-L- 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 2-Deoxy-L- Glycero-D-Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:15.9 occ:1.00 O A:GLU329 2.6 16.6 1.0 OD1 A:ASP330 2.6 21.0 1.0 O A:HOH585 2.6 18.1 1.0 OE1 A:GLU301 2.6 18.9 1.0 OD1 A:ASP324 2.6 19.5 1.0 OD2 A:ASP297 2.6 19.9 1.0 OE2 A:GLU301 2.7 18.3 1.0 OD1 A:ASP297 2.7 17.9 1.0 CD A:GLU301 3.0 20.7 1.0 CG A:ASP297 3.1 19.4 1.0 CG A:ASP324 3.4 20.2 1.0 C A:GLU329 3.4 16.8 1.0 CG A:ASP330 3.7 22.5 1.0 CA A:ASP330 3.8 17.7 1.0 N A:ASP330 3.9 17.4 1.0 CA A:CA403 3.9 18.6 1.0 CB A:ASP324 4.0 16.4 1.0 OD2 A:ASP324 4.1 18.7 1.0 CB A:ASP330 4.2 18.3 1.0 N A:GLU329 4.3 18.0 1.0 CZ A:PHE304 4.4 17.8 1.0 CA A:GLU329 4.4 16.5 1.0 O A:HOH583 4.5 25.5 1.0 CG A:GLU301 4.5 19.7 1.0 OD2 A:ASP342 4.6 14.7 1.0 CB A:ASP297 4.6 19.7 1.0 CA A:ASP324 4.6 16.0 1.0 OD2 A:ASP330 4.6 22.0 1.0 N A:GLY302 4.7 20.1 1.0 O A:HOH488 4.8 23.6 1.0 O A:HOH425 4.9 26.2 1.0 CE1 A:PHE304 4.9 16.8 1.0 O A:ASP297 4.9 20.8 1.0 CB A:GLU329 5.0 17.1 1.0 C A:ASP330 5.0 16.9 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 2-Deoxy-L- 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 2-Deoxy-L- Glycero-D-Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:18.6 occ:1.00 OE1 A:GLU301 2.6 18.9 1.0 OD1 A:ASP330 2.6 21.0 1.0 O A:HOH583 2.6 25.5 1.0 O A:HOH492 2.7 27.5 1.0 O A:HOH584 2.7 24.7 1.0 OD2 A:ASP330 2.7 22.0 1.0 CG A:ASP330 3.0 22.5 1.0 CD A:GLU301 3.7 20.7 1.0 CA A:CA402 3.9 15.9 1.0 OD1 A:ASP324 4.4 19.5 1.0 CB A:GLU301 4.4 20.1 1.0 CG A:GLU301 4.5 19.7 1.0 CB A:ASP330 4.5 18.3 1.0 O A:ASP297 4.6 20.8 1.0 OE2 A:GLU301 4.6 18.3 1.0 OD2 A:ASP324 4.7 18.7 1.0 OD1 A:ASP297 4.8 17.9 1.0 CA A:GLU301 4.8 20.7 1.0 O A:GLY327 4.9 22.4 1.0 O A:HOH424 4.9 23.6 1.0 CG A:ASP324 4.9 20.2 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 2-Deoxy-L- 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 2-Deoxy-L- Glycero-D-Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:12.1 occ:1.00 OD1 B:ASP342 2.5 13.7 1.0 OE1 B:GLU329 2.5 13.5 1.0 OD1 B:ASN341 2.5 14.3 1.0 OD1 B:ASN323 2.5 13.9 1.0 O B:ASP342 2.6 12.4 1.0 OE1 B:GLU321 2.6 14.6 1.0 O6 B:293356 2.6 15.3 1.0 O7 B:293356 2.7 14.3 1.0 CG B:ASP342 3.4 12.9 1.0 C7 B:293356 3.4 15.0 1.0 CD B:GLU321 3.4 14.3 1.0 CD B:GLU329 3.4 13.3 1.0 CG B:ASN341 3.5 15.3 1.0 CG B:ASN323 3.5 14.5 1.0 C6 B:293356 3.5 16.6 1.0 C B:ASP342 3.6 13.1 1.0 OE2 B:GLU329 3.7 15.2 1.0 OE2 B:GLU321 3.7 16.0 1.0 N B:ASP342 3.7 12.2 1.0 ND2 B:ASN341 3.8 15.3 1.0 ND2 B:ASN323 3.9 15.2 1.0 CA B:ASP342 4.1 12.7 1.0 OD2 B:ASP342 4.1 14.4 1.0 N B:ASN323 4.2 14.3 1.0 CB B:ASP342 4.3 12.1 1.0 C B:ASN341 4.5 13.5 1.0 CB B:ASP325 4.6 16.7 1.0 CB B:ASN323 4.6 14.1 1.0 CG B:GLU321 4.6 13.7 1.0 N B:ASP325 4.7 15.9 1.0 N B:ASP324 4.7 14.8 1.0 CB B:ASN341 4.7 13.3 1.0 CG B:GLU329 4.7 15.4 1.0 N B:ARG343 4.8 13.5 1.0 C5 B:293356 4.8 20.2 1.0 CA B:ASN323 4.8 13.8 1.0 CA B:ASN341 4.9 14.1 1.0 O5 B:293356 4.9 21.5 1.0 CB B:GLU329 4.9 16.0 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 2-Deoxy-L- 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 2-Deoxy-L- Glycero-D-Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:15.4 occ:1.00 O B:GLU329 2.5 14.5 1.0 O B:HOH578 2.6 17.9 1.0 OD1 B:ASP330 2.6 17.0 1.0 OE1 B:GLU301 2.6 21.3 1.0 OD2 B:ASP297 2.6 20.4 1.0 OD1 B:ASP324 2.7 18.6 1.0 OE2 B:GLU301 2.7 21.4 1.0 OD1 B:ASP297 2.8 17.2 1.0 CD B:GLU301 3.0 22.3 1.0 CG B:ASP297 3.1 19.0 1.0 CG B:ASP324 3.4 19.8 1.0 C B:GLU329 3.4 14.6 1.0 CG B:ASP330 3.7 20.0 1.0 CA B:ASP330 3.8 15.2 1.0 CB B:ASP324 3.9 15.4 1.0 CA B:CA403 4.0 19.4 1.0 N B:ASP330 4.0 15.8 1.0 O B:HOH580 4.0 22.4 1.0 OD2 B:ASP324 4.2 18.7 1.0 CB B:ASP330 4.3 16.9 1.0 O B:HOH502 4.3 31.3 1.0 N B:GLU329 4.4 16.9 1.0 CA B:ASP324 4.5 15.6 1.0 CA B:GLU329 4.5 15.3 1.0 CG B:GLU301 4.5 22.7 1.0 OD2 B:ASP342 4.5 14.4 1.0 CZ B:PHE304 4.5 21.2 1.0 CB B:ASP297 4.6 20.2 1.0 OD2 B:ASP330 4.6 20.0 1.0 N B:GLY302 4.7 24.4 1.0 O B:ASP297 4.9 23.5 1.0 CE1 B:PHE304 4.9 20.9 1.0 C B:ASP330 5.0 15.3 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 2-Deoxy-L- 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 2-Deoxy-L- Glycero-D-Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:19.4 occ:1.00 OE1 B:GLU301 2.6 21.3 1.0 OD2 B:ASP330 2.6 20.0 1.0 OD1 B:ASP330 2.6 17.0 1.0 O B:HOH580 2.7 22.4 1.0 O B:HOH579 2.7 26.2 1.0 O B:HOH495 2.7 24.7 1.0 O B:HOH581 2.8 32.1 1.0 CG B:ASP330 3.0 20.0 1.0 CD B:GLU301 3.8 22.3 1.0 CA B:CA402 4.0 15.4 1.0 O B:HOH429 4.2 24.5 1.0 CB B:GLU301 4.3 24.5 1.0 O B:ASP297 4.4 23.5 1.0 OD1 B:ASP324 4.4 18.6 1.0 O B:HOH567 4.4 38.3 1.0 CB B:ASP330 4.5 16.9 1.0 CG B:GLU301 4.5 22.7 1.0 O B:HOH463 4.7 33.9 1.0 CA B:GLU301 4.7 24.6 1.0 OE2 B:GLU301 4.7 21.4 1.0 OD1 B:ASP297 4.8 17.2 1.0 O B:HOH426 4.9 26.9 1.0 OD2 B:ASP297 4.9 20.4 1.0 OD2 B:ASP324 5.0 18.7 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 2-Deoxy-L- 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 2-Deoxy-L- Glycero-D-Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:12.8 occ:1.00 OD1 C:ASP342 2.5 14.1 1.0 OD1 C:ASN323 2.5 14.0 1.0 OD1 C:ASN341 2.5 14.1 1.0 OE1 C:GLU329 2.5 13.8 1.0 O C:ASP342 2.6 13.6 1.0 OE1 C:GLU321 2.7 15.1 1.0 O6 C:293356 2.7 16.6 1.0 O7 C:293356 2.7 16.2 1.0 CG C:ASP342 3.4 12.7 1.0 C7 C:293356 3.4 16.9 1.0 CD C:GLU321 3.5 15.0 1.0 CG C:ASN341 3.5 16.2 1.0 CD C:GLU329 3.5 13.6 1.0 CG C:ASN323 3.5 14.8 1.0 C6 C:293356 3.5 18.2 1.0 C C:ASP342 3.6 13.7 1.0 OE2 C:GLU321 3.7 18.3 1.0 N C:ASP342 3.7 12.6 1.0 OE2 C:GLU329 3.8 14.5 1.0 ND2 C:ASN341 3.8 15.8 1.0 OD2 C:ASP342 4.0 14.3 1.0 ND2 C:ASN323 4.0 15.9 1.0 CA C:ASP342 4.1 13.5 1.0 N C:ASN323 4.2 14.0 1.0 CB C:ASP342 4.3 12.4 1.0 C C:ASN341 4.5 15.4 1.0 CB C:ASP325 4.6 17.3 1.0 CB C:ASN323 4.6 13.1 1.0 CG C:GLU321 4.7 15.4 1.0 N C:ASP325 4.7 15.3 1.0 CB C:ASN341 4.7 15.1 1.0 CG C:GLU329 4.8 12.7 1.0 N C:ASP324 4.8 13.8 1.0 N C:ARG343 4.8 13.2 1.0 CA C:ASN323 4.8 13.7 1.0 C5 C:293356 4.8 22.4 1.0 CA C:ASN341 4.9 14.6 1.0 O5 C:293356 4.9 24.7 1.0 CB C:GLU329 4.9 14.6 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 2-Deoxy-L- 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 2-Deoxy-L- Glycero-D-Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:14.3 occ:1.00 O C:GLU329 2.6 15.3 1.0 O C:HOH583 2.6 17.8 1.0 OE1 C:GLU301 2.6 19.9 1.0 OD1 C:ASP330 2.6 19.4 1.0 OD1 C:ASP324 2.6 16.9 1.0 OD2 C:ASP297 2.6 19.3 1.0 OE2 C:GLU301 2.6 20.9 1.0 OD1 C:ASP297 2.7 18.1 1.0 CD C:GLU301 3.0 22.9 1.0 CG C:ASP297 3.0 19.0 1.0 CG C:ASP324 3.4 18.7 1.0 C C:GLU329 3.4 16.2 1.0 CG C:ASP330 3.7 21.9 1.0 CA C:ASP330 3.8 15.8 1.0 CB C:ASP324 3.9 15.8 1.0 CA C:CA403 4.0 19.8 1.0 N C:ASP330 4.0 16.2 1.0 O C:HOH582 4.0 22.7 1.0 OD2 C:ASP324 4.3 18.5 1.0 CB C:ASP330 4.3 17.9 1.0 N C:GLU329 4.4 17.7 1.0 CA C:ASP324 4.4 14.7 1.0 CZ C:PHE304 4.5 18.1 1.0 CG C:GLU301 4.5 21.0 1.0 CA C:GLU329 4.5 16.4 1.0 CB C:ASP297 4.6 20.1 1.0 OD2 C:ASP342 4.6 14.3 1.0 OD2 C:ASP330 4.6 22.1 1.0 O C:HOH511 4.7 33.4 1.0 N C:GLY302 4.8 22.8 1.0 O C:ASP297 4.9 21.8 1.0 CE1 C:PHE304 4.9 20.6 1.0 O C:HOH421 4.9 19.6 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 2-Deoxy-L- 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 2-Deoxy-L- Glycero-D-Manno-Heptose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:19.8 occ:1.00 OE1 C:GLU301 2.5 19.9 1.0 OD2 C:ASP330 2.6 22.1 1.0 O C:HOH581 2.6 26.6 1.0 OD1 C:ASP330 2.7 19.4 1.0 O C:HOH582 2.7 22.7 1.0 O C:HOH580 2.7 23.8 1.0 O C:HOH579 2.9 38.1 1.0 CG C:ASP330 3.0 21.9 1.0 CD C:GLU301 3.7 22.9 1.0 CA C:CA402 4.0 14.3 1.0 O C:HOH435 4.2 25.7 1.0 O C:HOH577 4.3 38.9 1.0 CB C:GLU301 4.3 23.1 1.0 OD1 C:ASP324 4.4 16.9 1.0 O C:ASP297 4.4 21.8 1.0 CG C:GLU301 4.5 21.0 1.0 CB C:ASP330 4.5 17.9 1.0 OE2 C:GLU301 4.6 20.9 1.0 O C:HOH475 4.7 37.0 1.0 OD1 C:ASP297 4.7 18.1 1.0 CA C:GLU301 4.8 23.0 1.0 O C:HOH427 4.8 27.2 1.0 OD2 C:ASP324 5.0 18.5 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