Calcium in PDB 2orj: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with N-Acetyl Mannosamine

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with N-Acetyl Mannosamine, PDB code: 2orj 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)	26.47 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.630, 108.330, 55.970, 90.00, 91.51, 90.00
R / Rfree (%)	17.8 / 20.5

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 N-Acetyl Mannosamine (pdb code 2orj). 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 N-Acetyl Mannosamine, PDB code: 2orj:
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 N-Acetyl Mannosamine


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 N-Acetyl Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:17.2 occ:1.00 OD1 A:ASN341 2.4 16.2 1.0 OD1 A:ASP342 2.4 15.4 1.0 OE1 A:GLU329 2.5 15.4 1.0 OE1 A:GLU321 2.5 17.4 1.0 OD1 A:ASN323 2.5 15.4 1.0 O3 A:BM31 2.6 24.9 1.0 O4 A:BM31 2.6 19.5 1.0 O A:ASP342 2.6 14.6 1.0 C4 A:BM31 3.3 23.4 1.0 CD A:GLU321 3.4 19.3 1.0 CG A:ASN341 3.4 17.1 1.0 CG A:ASN323 3.4 19.1 1.0 C3 A:BM31 3.4 24.5 1.0 CG A:ASP342 3.4 16.6 1.0 CD A:GLU329 3.4 16.0 1.0 C A:ASP342 3.6 15.7 1.0 OE2 A:GLU321 3.6 19.7 1.0 OE2 A:GLU329 3.8 17.3 1.0 N A:ASP342 3.8 16.0 1.0 ND2 A:ASN341 3.8 19.2 1.0 ND2 A:ASN323 3.9 18.3 1.0 CA A:ASP342 4.1 15.5 1.0 OD2 A:ASP342 4.2 16.6 1.0 N A:ASN323 4.2 18.3 1.0 CB A:ASP342 4.4 15.2 1.0 CB A:ASP325 4.5 19.1 1.0 C A:ASN341 4.6 16.6 1.0 CG A:GLU321 4.6 18.7 1.0 CB A:ASN323 4.6 17.7 1.0 CB A:ASN341 4.7 16.1 1.0 N A:ASP325 4.7 18.4 1.0 N A:ASP324 4.7 16.4 1.0 CG A:GLU329 4.7 16.9 1.0 C5 A:BM31 4.8 24.3 1.0 N A:ARG343 4.8 15.7 1.0 C2 A:BM31 4.8 26.4 1.0 CA A:ASN323 4.8 17.4 1.0 CA A:ASN341 4.9 16.6 1.0 CB A:GLU329 4.9 18.0 1.0 N2 A:BM31 5.0 27.1 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 N-Acetyl Mannosamine


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 N-Acetyl Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:17.5 occ:1.00 O A:HOH427 2.4 16.2 1.0 OD2 A:ASP297 2.4 19.6 1.0 OD1 A:ASP330 2.5 20.1 1.0 O A:GLU329 2.5 17.6 1.0 OD1 A:ASP324 2.5 17.0 1.0 OE2 A:GLU301 2.5 17.3 1.0 OE1 A:GLU301 2.5 19.2 1.0 OD1 A:ASP297 2.6 18.2 1.0 CD A:GLU301 2.9 18.1 1.0 CG A:ASP297 2.9 19.1 1.0 CG A:ASP324 3.3 18.9 1.0 C A:GLU329 3.4 18.2 1.0 CG A:ASP330 3.6 19.2 1.0 CA A:ASP330 3.8 17.4 1.0 CA A:CA403 3.9 26.3 1.0 CB A:ASP324 3.9 17.3 1.0 N A:ASP330 4.0 17.5 1.0 O A:HOH452 4.0 26.6 1.0 OD2 A:ASP324 4.1 18.8 1.0 CB A:ASP330 4.3 17.6 1.0 N A:GLU329 4.3 19.6 1.0 CG A:GLU301 4.4 21.1 1.0 CA A:GLU329 4.4 18.4 1.0 CB A:ASP297 4.4 19.6 1.0 CZ A:PHE304 4.5 21.2 1.0 OD2 A:ASP330 4.5 21.5 1.0 CA A:ASP324 4.5 17.7 1.0 OD2 A:ASP342 4.5 16.6 1.0 N A:GLY302 4.6 22.4 1.0 O A:HOH434 4.7 24.7 1.0 O A:HOH443 4.8 21.7 1.0 O A:HOH448 4.8 20.9 1.0 O A:ASP297 4.9 21.6 1.0 CB A:GLU329 4.9 18.0 1.0 CE1 A:PHE304 4.9 20.0 1.0 CA A:GLU301 5.0 22.5 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 N-Acetyl Mannosamine


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 N-Acetyl Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:26.3 occ:1.00 O A:HOH580 2.3 38.5 1.0 O A:HOH448 2.3 20.9 1.0 O A:HOH452 2.4 26.6 1.0 OE1 A:GLU301 2.4 19.2 1.0 OD2 A:ASP330 2.4 21.5 1.0 OD1 A:ASP330 2.5 20.1 1.0 O A:HOH573 2.5 30.2 1.0 CG A:ASP330 2.8 19.2 1.0 CD A:GLU301 3.6 18.1 1.0 CA A:CA402 3.9 17.5 1.0 OD1 A:ASP324 4.2 17.0 1.0 CB A:ASP330 4.3 17.6 1.0 CB A:GLU301 4.4 22.1 1.0 CG A:GLU301 4.4 21.1 1.0 O A:ASP297 4.5 21.6 1.0 OE2 A:GLU301 4.5 17.3 1.0 O A:GLY327 4.6 22.9 1.0 OD1 A:ASP297 4.7 18.2 1.0 OD2 A:ASP324 4.7 18.8 1.0 O A:HOH553 4.8 41.1 1.0 CA A:GLU301 4.9 22.5 1.0 CG A:ASP324 4.9 18.9 1.0 O A:HOH436 4.9 22.8 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 N-Acetyl Mannosamine


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 N-Acetyl Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:14.3 occ:1.00 OD1 B:ASP342 2.4 13.4 1.0 OD1 B:ASN341 2.4 13.9 1.0 OE1 B:GLU329 2.4 16.7 1.0 OD1 B:ASN323 2.5 13.3 1.0 OE1 B:GLU321 2.5 12.5 1.0 O3 B:BM31 2.6 17.6 1.0 O B:ASP342 2.6 13.8 1.0 O4 B:BM31 2.7 17.4 1.0 CD B:GLU321 3.4 14.9 1.0 CG B:ASP342 3.4 14.2 1.0 C3 B:BM31 3.4 19.7 1.0 C4 B:BM31 3.4 19.0 1.0 CG B:ASN341 3.4 14.3 1.0 CG B:ASN323 3.4 12.5 1.0 CD B:GLU329 3.4 16.1 1.0 C B:ASP342 3.6 14.6 1.0 OE2 B:GLU321 3.7 14.7 1.0 N B:ASP342 3.8 14.1 1.0 OE2 B:GLU329 3.8 15.8 1.0 ND2 B:ASN341 3.8 13.2 1.0 ND2 B:ASN323 3.9 13.9 1.0 CA B:ASP342 4.1 14.1 1.0 OD2 B:ASP342 4.1 14.0 1.0 N B:ASN323 4.2 14.5 1.0 CB B:ASP342 4.3 14.2 1.0 CB B:ASP325 4.5 17.3 1.0 C B:ASN341 4.6 14.1 1.0 CB B:ASN323 4.6 13.9 1.0 CG B:GLU321 4.6 15.2 1.0 N B:ASP325 4.7 16.4 1.0 CB B:ASN341 4.7 13.9 1.0 CG B:GLU329 4.7 16.1 1.0 CA B:ASN323 4.8 14.1 1.0 N B:ASP324 4.8 14.6 1.0 N B:ARG343 4.8 14.3 1.0 C2 B:BM31 4.8 21.1 1.0 CA B:ASN341 4.9 13.8 1.0 C5 B:BM31 4.9 23.3 1.0 CB B:GLU329 4.9 16.9 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 N-Acetyl Mannosamine


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 N-Acetyl Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:18.2 occ:1.00 OD1 B:ASP330 2.4 17.9 1.0 O B:HOH421 2.4 17.9 1.0 O B:GLU329 2.4 15.9 1.0 OD2 B:ASP297 2.4 20.9 1.0 OE1 B:GLU301 2.5 18.9 1.0 OD1 B:ASP324 2.5 16.1 1.0 OE2 B:GLU301 2.6 18.8 1.0 OD1 B:ASP297 2.7 17.9 1.0 CD B:GLU301 2.9 21.4 1.0 CG B:ASP297 2.9 19.4 1.0 C B:GLU329 3.4 16.5 1.0 CG B:ASP324 3.4 18.1 1.0 CG B:ASP330 3.5 18.9 1.0 CA B:ASP330 3.8 16.4 1.0 CA B:CA403 3.9 28.9 1.0 O B:HOH447 3.9 26.8 1.0 CB B:ASP324 4.0 16.0 1.0 N B:ASP330 4.0 16.0 1.0 OD2 B:ASP324 4.2 18.1 1.0 CB B:ASP330 4.2 17.7 1.0 N B:GLU329 4.4 18.5 1.0 CG B:GLU301 4.4 23.1 1.0 CB B:ASP297 4.4 19.1 1.0 CA B:GLU329 4.4 17.0 1.0 O B:HOH562 4.5 32.4 1.0 OD2 B:ASP330 4.5 20.5 1.0 CZ B:PHE304 4.5 19.7 1.0 CA B:ASP324 4.5 16.1 1.0 OD2 B:ASP342 4.6 14.0 1.0 N B:GLY302 4.8 24.1 1.0 O B:ASP297 4.8 20.9 1.0 O B:HOH433 4.9 19.8 1.0 CB B:GLU329 5.0 16.9 1.0 CE1 B:PHE304 5.0 19.5 1.0 O B:HOH475 5.0 30.0 1.0 CA B:GLU301 5.0 24.7 1.0 C B:ASP330 5.0 16.3 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 N-Acetyl Mannosamine


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 N-Acetyl Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:28.9 occ:1.00 O B:HOH433 2.3 19.8 1.0 O B:HOH521 2.4 32.3 1.0 O B:HOH447 2.4 26.8 1.0 O B:HOH465 2.4 25.1 1.0 OE1 B:GLU301 2.5 18.9 1.0 OD2 B:ASP330 2.5 20.5 1.0 OD1 B:ASP330 2.5 17.9 1.0 CG B:ASP330 2.9 18.9 1.0 CD B:GLU301 3.7 21.4 1.0 CA B:CA402 3.9 18.2 1.0 O B:HOH479 4.1 27.5 1.0 CB B:GLU301 4.3 24.8 1.0 O B:ASP297 4.3 20.9 1.0 OD1 B:ASP324 4.3 16.1 1.0 CB B:ASP330 4.4 17.7 1.0 CG B:GLU301 4.4 23.1 1.0 OE2 B:GLU301 4.6 18.8 1.0 O B:HOH550 4.6 47.3 1.0 O B:HOH572 4.7 34.5 1.0 CA B:GLU301 4.7 24.7 1.0 OD1 B:ASP297 4.7 17.9 1.0 O B:GLY327 4.8 22.3 1.0 O B:HOH430 4.9 23.0 1.0 OD2 B:ASP297 4.9 20.9 1.0 OD2 B:ASP324 4.9 18.1 1.0 CG B:ASP324 5.0 18.1 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 N-Acetyl Mannosamine


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 N-Acetyl Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:14.7 occ:1.00 OD1 C:ASP342 2.3 13.7 1.0 OE1 C:GLU329 2.4 13.7 1.0 OD1 C:ASN341 2.4 15.2 1.0 OD1 C:ASN323 2.4 15.2 1.0 O C:ASP342 2.6 14.4 1.0 O3 C:BM31 2.6 17.3 1.0 OE1 C:GLU321 2.6 14.6 1.0 O4 C:BM31 2.6 18.7 1.0 CG C:ASP342 3.3 14.2 1.0 CD C:GLU329 3.4 13.2 1.0 CG C:ASN341 3.4 15.4 1.0 CD C:GLU321 3.4 14.3 1.0 C3 C:BM31 3.4 17.6 1.0 C4 C:BM31 3.4 19.3 1.0 CG C:ASN323 3.5 15.9 1.0 C C:ASP342 3.6 15.0 1.0 OE2 C:GLU321 3.7 15.7 1.0 OE2 C:GLU329 3.8 14.8 1.0 N C:ASP342 3.8 14.5 1.0 ND2 C:ASN341 3.8 15.1 1.0 CA C:ASP342 4.0 14.8 1.0 ND2 C:ASN323 4.0 16.8 1.0 OD2 C:ASP342 4.1 12.7 1.0 N C:ASN323 4.2 15.3 1.0 CB C:ASP342 4.3 14.2 1.0 CB C:ASP325 4.5 16.5 1.0 C C:ASN341 4.5 14.8 1.0 CB C:ASN323 4.7 15.0 1.0 CB C:ASN341 4.7 13.6 1.0 CG C:GLU329 4.7 15.1 1.0 CG C:GLU321 4.7 14.5 1.0 N C:ASP325 4.7 15.0 1.0 N C:ARG343 4.7 15.0 1.0 N C:ASP324 4.7 15.1 1.0 CA C:ASN323 4.8 14.7 1.0 CB C:GLU329 4.8 16.2 1.0 C2 C:BM31 4.8 19.0 1.0 CA C:ASN341 4.8 13.9 1.0 C5 C:BM31 4.9 21.8 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 N-Acetyl Mannosamine


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 N-Acetyl Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:18.7 occ:1.00 O C:GLU329 2.4 16.0 1.0 O C:HOH422 2.4 17.7 1.0 OD1 C:ASP330 2.5 20.1 1.0 OE2 C:GLU301 2.5 16.2 1.0 OE1 C:GLU301 2.6 17.8 1.0 OD2 C:ASP297 2.6 20.1 1.0 OD1 C:ASP297 2.6 19.7 1.0 OD1 C:ASP324 2.6 15.9 1.0 CD C:GLU301 2.9 18.8 1.0 CG C:ASP297 3.0 21.5 1.0 C C:GLU329 3.4 16.6 1.0 CG C:ASP324 3.4 17.7 1.0 CG C:ASP330 3.6 20.5 1.0 CA C:ASP330 3.8 17.4 1.0 O C:HOH441 3.8 25.8 1.0 CA C:CA403 3.9 27.6 1.0 CB C:ASP324 3.9 15.4 1.0 N C:ASP330 4.0 16.7 1.0 OD2 C:ASP324 4.2 15.7 1.0 CB C:ASP330 4.3 17.7 1.0 N C:GLU329 4.4 17.9 1.0 CG C:GLU301 4.4 22.5 1.0 CZ C:PHE304 4.4 19.0 1.0 CA C:GLU329 4.4 16.8 1.0 CB C:ASP297 4.5 21.8 1.0 OD2 C:ASP342 4.5 12.7 1.0 CA C:ASP324 4.5 15.4 1.0 OD2 C:ASP330 4.6 23.4 1.0 N C:GLY302 4.7 24.6 1.0 O C:HOH478 4.7 26.9 1.0 O C:ASP297 4.8 24.7 1.0 CE1 C:PHE304 4.8 19.4 1.0 CA C:GLU301 5.0 25.4 1.0 CB C:GLU329 5.0 16.2 1.0 O C:HOH428 5.0 22.1 1.0 O C:HOH443 5.0 21.8 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 N-Acetyl Mannosamine


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 N-Acetyl Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:27.6 occ:1.00 O C:HOH443 2.2 21.8 1.0 OE1 C:GLU301 2.3 17.8 1.0 O C:HOH504 2.4 39.3 1.0 O C:HOH545 2.4 27.1 1.0 O C:HOH441 2.4 25.8 1.0 OD1 C:ASP330 2.5 20.1 1.0 OD2 C:ASP330 2.6 23.4 1.0 CG C:ASP330 2.9 20.5 1.0 CD C:GLU301 3.6 18.8 1.0 CA C:CA402 3.9 18.7 1.0 O C:HOH544 4.1 26.9 1.0 O C:ASP297 4.2 24.7 1.0 CB C:GLU301 4.2 25.5 1.0 CG C:GLU301 4.3 22.5 1.0 OD1 C:ASP324 4.4 15.9 1.0 CB C:ASP330 4.4 17.7 1.0 OE2 C:GLU301 4.5 16.2 1.0 OD1 C:ASP297 4.5 19.7 1.0 CA C:GLU301 4.6 25.4 1.0 O C:HOH533 4.6 35.8 1.0 OD2 C:ASP324 4.8 15.7 1.0 O C:HOH440 4.9 25.4 1.0 O C:GLY327 4.9 20.4 1.0 CG C:ASP297 5.0 21.5 1.0 OD2 C:ASP297 5.0 20.1 1.0 CG C:ASP324 5.0 17.7 1.0

E.Crouch, B.Mcdonald, K.Smith, M.Roberts, T.Mealy, B.Seaton, J.Head. Critical Role of Arg/LYS343 in the Species-Dependent Recognition of Phosphatidylinositol By Pulmonary Surfactant Protein D. Biochemistry V. 46 5160 2007.
ISSN: ISSN 0006-2960
PubMed: 17417879
DOI: 10.1021/BI700037X