Calcium in PDB 3g84: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of R343V Mutant 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 R343V Mutant of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose., PDB code: 3g84 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)	49.42 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.605, 108.066, 55.595, 90.00, 91.47, 90.00
R / Rfree (%)	15.2 / 19.1

The binding sites of Calcium atom in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of R343V Mutant of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose. (pdb code 3g84). 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 R343V Mutant of Human Surfactant Protein D in Complex with Alpha 1,2 Dimannose., PDB code: 3g84:
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 R343V Mutant 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 R343V Mutant 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:33.8 occ:1.00 OD1 A:ASN341 2.6 30.4 1.0 OD1 A:ASP342 2.6 30.8 1.0 OD1 A:ASN323 2.7 33.4 1.0 OE1 A:GLU329 2.8 34.1 1.0 O3 A:MAN501 2.8 37.3 1.0 OE1 A:GLU321 2.9 33.0 1.0 O4 A:MAN501 3.0 36.4 1.0 O A:ASP342 3.0 37.3 1.0 CG A:ASP342 3.3 31.6 1.0 CG A:ASN341 3.5 30.0 1.0 CG A:ASN323 3.5 30.2 1.0 CD A:GLU321 3.6 30.4 1.0 CD A:GLU329 3.6 32.3 1.0 OD2 A:ASP342 3.7 32.4 1.0 N A:ASP342 3.7 30.1 1.0 C3 A:MAN501 3.7 33.6 1.0 C4 A:MAN501 3.7 36.5 1.0 OE2 A:GLU321 3.7 29.3 1.0 OE2 A:GLU329 3.8 28.7 1.0 ND2 A:ASN341 3.8 28.1 1.0 C A:ASP342 3.9 31.7 1.0 N A:ASN323 4.0 29.2 1.0 ND2 A:ASN323 4.0 27.5 1.0 CA A:ASP342 4.1 32.1 1.0 CB A:ASP342 4.3 32.4 1.0 N A:ASP324 4.5 32.1 1.0 N A:ASP325 4.6 31.8 1.0 CB A:ASN323 4.6 29.9 1.0 C A:ASN341 4.6 31.5 1.0 CB A:ASP325 4.7 31.0 1.0 CA A:ASN323 4.7 29.7 1.0 CB A:ASN341 4.7 30.7 1.0 CA A:ASN341 4.8 28.5 1.0 CG A:GLU321 4.9 31.4 1.0 C A:ASN323 4.9 32.7 1.0 CA A:PRO322 4.9 29.5 1.0 C A:PRO322 4.9 29.2 1.0 CG A:GLU329 4.9 31.4 1.0

Calcium binding site 2 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of R343V Mutant 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 R343V Mutant 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:34.6 occ:1.00 O A:GLU329 2.7 31.6 1.0 OE1 A:GLU301 2.7 41.2 1.0 OD2 A:ASP297 2.8 34.3 1.0 OD1 A:ASP324 2.8 35.2 1.0 OE2 A:GLU301 2.9 37.2 1.0 OD1 A:ASP297 2.9 35.1 1.0 CD A:GLU301 3.2 34.9 1.0 CG A:ASP297 3.2 36.2 1.0 OD1 A:ASP330 3.3 40.4 1.0 CG A:ASP324 3.3 34.5 1.0 C A:GLU329 3.4 32.9 1.0 CB A:ASP324 3.9 33.9 1.0 OD2 A:ASP324 3.9 33.4 1.0 N A:GLU329 4.0 42.4 1.0 CA A:ASP330 4.0 36.9 1.0 CA A:CA403 4.0 36.2 1.0 N A:ASP330 4.0 35.2 1.0 CA A:GLU329 4.3 34.4 1.0 CG A:ASP330 4.3 40.2 1.0 CA A:ASP324 4.5 32.1 1.0 CZ A:PHE304 4.6 36.2 1.0 CB A:ASP297 4.7 38.0 1.0 CG A:GLU301 4.7 31.7 1.0 CB A:ASP330 4.8 42.3 1.0 N A:GLY302 4.8 38.5 1.0 OD2 A:ASP342 4.8 32.4 1.0 CB A:GLU329 4.8 31.7 1.0 O A:ASP297 4.9 39.9 1.0 O A:HOH65 4.9 34.1 1.0

Calcium binding site 3 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of R343V Mutant 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 R343V Mutant 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:36.2 occ:1.00 O A:HOH65 2.7 34.1 1.0 OE1 A:GLU301 2.9 41.2 1.0 OD1 A:ASP330 2.9 40.4 1.0 O A:HOH75 2.9 37.5 1.0 CG A:ASP330 3.6 40.2 1.0 CD A:GLU301 3.7 34.9 1.0 OD2 A:ASP330 3.7 39.3 1.0 CA A:CA402 4.0 34.6 1.0 CG A:GLU301 4.3 31.7 1.0 CB A:GLU301 4.3 36.8 1.0 OE2 A:GLU301 4.4 37.2 1.0 OD1 A:ASP324 4.6 35.2 1.0 O A:ASP297 4.6 39.9 1.0 OD2 A:ASP324 4.7 33.4 1.0 CA A:GLU301 4.8 34.5 1.0 OD1 A:ASP297 4.8 35.1 1.0

Calcium binding site 4 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of R343V Mutant 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 R343V Mutant 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:25.4 occ:1.00 OD1 B:ASP342 2.5 29.6 1.0 OD1 B:ASN341 2.6 30.3 1.0 OE1 B:GLU329 2.6 27.3 1.0 O B:ASP342 2.6 33.5 1.0 OE1 B:GLU321 2.7 25.2 1.0 OD1 B:ASN323 2.7 28.6 1.0 O3 B:MAN501 2.9 30.1 1.0 O4 B:MAN501 2.9 37.7 1.0 CD B:GLU321 3.4 26.7 1.0 CG B:ASN323 3.5 28.0 1.0 OE2 B:GLU321 3.5 30.2 1.0 CD B:GLU329 3.5 28.8 1.0 CG B:ASP342 3.6 29.4 1.0 CG B:ASN341 3.7 28.5 1.0 C B:ASP342 3.7 29.5 1.0 C4 B:MAN501 3.7 33.6 1.0 C3 B:MAN501 3.7 33.0 1.0 N B:ASP342 3.8 26.4 1.0 ND2 B:ASN323 3.9 33.6 1.0 OE2 B:GLU329 3.9 29.2 1.0 N B:ASN323 4.1 27.6 1.0 CA B:ASP342 4.1 28.0 1.0 ND2 B:ASN341 4.2 27.9 1.0 OD2 B:ASP342 4.4 26.6 1.0 CB B:ASP342 4.5 32.0 1.0 N B:ASP324 4.5 24.8 1.0 C B:ASN341 4.6 25.4 1.0 CB B:ASN323 4.7 30.0 1.0 N B:ASP325 4.7 30.6 1.0 CA B:ASN323 4.8 28.2 1.0 CG B:GLU329 4.8 32.0 1.0 CG B:GLU321 4.8 27.2 1.0 CB B:ASP325 4.8 33.3 1.0 N B:VAL343 4.8 29.3 1.0 OD1 B:ASP325 4.9 41.7 1.0 CB B:ASN341 4.9 29.9 1.0 CB B:GLU329 4.9 31.2 1.0 CA B:ASN341 4.9 27.7 1.0 CA B:PRO322 5.0 26.1 1.0 C B:ASN323 5.0 29.0 1.0

Calcium binding site 5 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of R343V Mutant 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 R343V Mutant 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:34.5 occ:1.00 OE2 B:GLU301 2.7 39.6 1.0 OE1 B:GLU301 2.7 34.4 1.0 OD2 B:ASP297 2.8 37.8 1.0 O B:GLU329 2.8 35.4 1.0 OD1 B:ASP330 2.9 37.8 1.0 OD1 B:ASP297 2.9 36.9 1.0 OD1 B:ASP324 3.0 32.4 1.0 CD B:GLU301 3.1 37.6 1.0 CG B:ASP297 3.2 34.4 1.0 CG B:ASP324 3.3 31.8 1.0 C B:GLU329 3.5 33.8 1.0 CA B:ASP330 3.7 37.2 1.0 CB B:ASP324 3.7 31.4 1.0 CG B:ASP330 3.8 36.5 1.0 OD2 B:ASP324 3.9 35.5 1.0 N B:ASP330 3.9 36.0 1.0 OD2 B:ASP342 4.1 26.6 1.0 CA B:CA403 4.3 41.0 1.0 CB B:ASP330 4.3 34.5 1.0 CZ B:PHE304 4.3 29.6 1.0 CA B:ASP324 4.4 27.0 1.0 CA B:GLU329 4.5 32.5 1.0 CG B:GLU301 4.6 35.5 1.0 N B:GLY302 4.6 32.5 1.0 N B:GLU329 4.6 37.6 1.0 CB B:ASP297 4.7 28.9 1.0 OD2 B:ASP330 4.8 41.1 1.0 O B:ASP297 4.8 33.6 1.0 C B:ASP330 4.8 38.0 1.0 CE1 B:PHE304 4.8 27.9 1.0

Calcium binding site 6 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of R343V Mutant 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 R343V Mutant 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:41.0 occ:1.00 OD1 B:ASP330 2.7 37.8 1.0 OE1 B:GLU301 2.8 34.4 1.0 OD2 B:ASP330 3.0 41.1 1.0 CG B:ASP330 3.2 36.5 1.0 CD B:GLU301 3.7 37.6 1.0 CA B:CA402 4.3 34.5 1.0 OD1 B:ASP324 4.4 32.4 1.0 CG B:GLU301 4.4 35.5 1.0 OD2 B:ASP324 4.5 35.5 1.0 CB B:GLU301 4.5 36.2 1.0 O B:GLY327 4.5 40.8 1.0 OE2 B:GLU301 4.5 39.6 1.0 CB B:ASP330 4.7 34.5 1.0 CG B:ASP324 4.8 31.8 1.0 O B:ASP297 4.8 33.6 1.0

Calcium binding site 7 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of R343V Mutant 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 R343V Mutant 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:28.4 occ:1.00 OD1 C:ASP342 2.5 25.1 1.0 OE1 C:GLU329 2.5 25.4 1.0 OD1 C:ASN341 2.6 30.1 1.0 OE1 C:GLU321 2.6 26.5 1.0 O3 C:MAN501 2.7 32.5 1.0 O C:ASP342 2.7 31.6 1.0 O4 C:MAN501 2.7 29.1 1.0 OD1 C:ASN323 2.8 31.0 1.0 CD C:GLU321 3.4 27.3 1.0 CG C:ASP342 3.4 27.2 1.0 C4 C:MAN501 3.4 32.8 1.0 C3 C:MAN501 3.5 34.5 1.0 CG C:ASN323 3.5 28.1 1.0 OE2 C:GLU321 3.5 29.7 1.0 CD C:GLU329 3.6 27.3 1.0 CG C:ASN341 3.7 28.2 1.0 C C:ASP342 3.7 28.4 1.0 ND2 C:ASN323 3.8 29.9 1.0 N C:ASP342 4.0 24.6 1.0 OD2 C:ASP342 4.0 25.2 1.0 OE2 C:GLU329 4.1 29.1 1.0 N C:ASN323 4.1 30.4 1.0 ND2 C:ASN341 4.2 27.4 1.0 CA C:ASP342 4.2 26.1 1.0 CB C:ASP325 4.2 34.7 1.0 CB C:ASP342 4.4 24.6 1.0 N C:ASP325 4.4 30.2 1.0 N C:ASP324 4.6 30.7 1.0 C C:ASN341 4.6 26.2 1.0 CB C:ASN323 4.7 30.3 1.0 CA C:ASN323 4.8 29.4 1.0 N C:VAL343 4.8 26.9 1.0 CG C:GLU321 4.8 24.4 1.0 CG C:GLU329 4.8 26.3 1.0 CB C:GLU329 4.8 24.3 1.0 C2 C:MAN501 4.9 36.5 1.0 C5 C:MAN501 4.9 33.3 1.0 C C:ASN323 4.9 28.4 1.0 CB C:ASN341 4.9 26.3 1.0 CA C:ASN341 5.0 26.9 1.0 O2 C:MAN501 5.0 34.8 1.0

Calcium binding site 8 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of R343V Mutant 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 R343V Mutant 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:30.3 occ:1.00 O C:GLU329 2.6 29.6 1.0 OE2 C:GLU301 2.6 36.0 1.0 OD1 C:ASP330 2.7 35.6 1.0 OE1 C:GLU301 2.7 36.6 1.0 OD1 C:ASP324 2.8 32.6 1.0 OD2 C:ASP297 3.0 37.3 1.0 CD C:GLU301 3.0 35.6 1.0 OD1 C:ASP297 3.0 38.3 1.0 C C:GLU329 3.4 31.0 1.0 CG C:ASP324 3.4 30.7 1.0 CG C:ASP297 3.4 38.0 1.0 CA C:ASP330 3.7 34.8 1.0 CG C:ASP330 3.7 35.4 1.0 CB C:ASP324 3.7 30.5 1.0 N C:ASP330 3.9 33.6 1.0 CZ C:PHE304 4.0 28.6 1.0 CB C:ASP330 4.1 35.2 1.0 OD2 C:ASP342 4.2 25.2 1.0 CA C:ASP324 4.2 29.3 1.0 OD2 C:ASP324 4.2 34.7 1.0 N C:GLU329 4.4 30.1 1.0 CA C:GLU329 4.4 28.9 1.0 CA C:CA403 4.5 41.1 1.0 CE1 C:PHE304 4.5 35.9 1.0 CG C:GLU301 4.5 34.0 1.0 N C:GLY302 4.7 41.9 1.0 OD2 C:ASP330 4.7 37.1 1.0 CE2 C:PHE304 4.9 31.0 1.0 C C:ASP330 4.9 29.9 1.0 CB C:ASP297 4.9 37.4 1.0 N C:ASP324 4.9 30.7 1.0 CB C:GLU329 5.0 24.3 1.0 O C:ASP297 5.0 40.9 1.0

Calcium binding site 9 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of R343V Mutant 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 R343V Mutant 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:41.1 occ:1.00 O C:HOH66 2.8 29.1 1.0 O C:HOH53 2.8 28.7 1.0 OD2 C:ASP330 2.8 37.1 1.0 OD1 C:ASP330 2.8 35.6 1.0 OE1 C:GLU301 3.0 36.6 1.0 CG C:ASP330 3.2 35.4 1.0 CD C:GLU301 3.7 35.6 1.0 O C:GLY327 4.2 38.4 1.0 OD1 C:ASP324 4.2 32.6 1.0 CB C:GLU301 4.3 37.0 1.0 CG C:GLU301 4.3 34.0 1.0 OE2 C:GLU301 4.4 36.0 1.0 OD2 C:ASP324 4.5 34.7 1.0 CA C:CA402 4.5 30.3 1.0 O C:HOH61 4.6 29.6 1.0 CB C:ASP330 4.6 35.2 1.0 CG C:ASP324 4.7 30.7 1.0 CA C:SER328 4.9 31.0 1.0 CA C:GLU301 4.9 40.4 1.0 O C:HOH108 5.0 35.7 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