Calcium in PDB 4dn8: Structure of Porcine Surfactant Protein D Neck and Carbohydrate Recognition Domain Complexed with Mannose

The structure of Structure of Porcine Surfactant Protein D Neck and Carbohydrate Recognition Domain Complexed with Mannose, PDB code: 4dn8 was solved by M.Van Eijk, M.J.Rynkiewicz, M.R.White, K.L.Hartshorn, X.Zou, K.Schulten, D.Luo, E.C.Crouch, T.M.Cafarella, J.F.Head, H.P.Haagsman, B.A.Seaton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.76 / 2.20
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	66.024, 66.024, 66.018, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 23.7

The binding sites of Calcium atom in the Structure of Porcine Surfactant Protein D Neck and Carbohydrate Recognition Domain Complexed with Mannose (pdb code 4dn8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Porcine Surfactant Protein D Neck and Carbohydrate Recognition Domain Complexed with Mannose, PDB code: 4dn8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Porcine Surfactant Protein D Neck and Carbohydrate Recognition Domain Complexed with Mannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Porcine Surfactant Protein D Neck and Carbohydrate Recognition Domain Complexed with Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:66.4 occ:1.00 O A:GLU329 2.8 72.1 1.0 OD2 A:ASP297 2.9 57.9 1.0 OE1 A:GLU301 2.9 74.9 1.0 OD1 A:ASN324 3.0 91.4 1.0 OE2 A:GLU301 3.0 68.8 1.0 OD1 A:ASN330 3.1 55.4 1.0 OD1 A:ASP297 3.2 65.3 1.0 CD A:GLU301 3.3 74.0 1.0 CG A:ASN324 3.4 96.3 1.0 CG A:ASP297 3.4 59.6 1.0 C A:GLU329 3.5 69.3 1.0 CA A:ASN330 3.9 55.6 1.0 CB A:ASN324 4.0 99.8 1.0 N A:ASN330 4.1 61.1 1.0 ND2 A:ASN324 4.1 97.7 1.0 CG A:ASN330 4.1 52.4 1.0 N A:GLU329 4.4 75.5 1.0 CA A:GLU329 4.5 73.9 1.0 OD2 A:ASP342 4.5 71.5 1.0 CB A:ASN330 4.5 50.6 1.0 CZ A:PHE304 4.5 66.7 1.0 CA A:ASN324 4.6 97.8 1.0 CG A:GLU301 4.8 74.9 1.0 CB A:ASP297 4.9 58.2 1.0 N A:GLY302 5.0 71.0 1.0 CE1 A:PHE304 5.0 68.6 1.0 CB A:GLU329 5.0 75.7 1.0

Calcium binding site 2 out of 2 in the Structure of Porcine Surfactant Protein D Neck and Carbohydrate Recognition Domain Complexed with Mannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Porcine Surfactant Protein D Neck and Carbohydrate Recognition Domain Complexed with Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:70.8 occ:1.00 OD1 A:ASP342 2.7 76.0 1.0 O3 A:BMA403 2.8 82.5 1.0 OE1 A:GLU329 2.8 78.9 1.0 OD1 A:ASN323 2.8 95.0 1.0 O A:ASP342 2.9 73.4 1.0 O4 A:BMA403 2.9 82.6 1.0 OD1 A:ASN341 2.9 70.9 1.0 OE1 A:GLU321 2.9 87.0 1.0 CG A:ASN323 3.4 1.0 1.0 CG A:ASP342 3.5 74.1 1.0 C3 A:BMA403 3.5 84.9 1.0 CD A:GLU321 3.5 93.8 1.0 OE2 A:GLU321 3.5 98.8 1.0 ND2 A:ASN323 3.5 0.6 1.0 C4 A:BMA403 3.6 84.3 1.0 CD A:GLU329 3.7 76.0 1.0 OD2 A:ASP342 3.8 71.5 1.0 CG A:ASN341 3.9 74.5 1.0 C A:ASP342 3.9 71.6 1.0 OE2 A:GLU329 4.0 71.6 1.0 N A:ASN323 4.2 92.6 1.0 ND2 A:ASN341 4.2 77.8 1.0 N A:ASP342 4.3 72.8 1.0 N A:ASN324 4.4 96.1 1.0 CA A:ASP342 4.5 70.4 1.0 CB A:ASN323 4.5 0.7 1.0 CB A:ASP342 4.6 70.3 1.0 N A:ASN325 4.6 0.7 1.0 O A:ASN325 4.6 1.0 1.0 CA A:ASN323 4.7 0.1 1.0 CG A:GLU321 4.8 91.7 1.0 C2 A:BMA403 4.9 88.3 1.0 C A:ASN341 4.9 72.0 1.0 C A:ASN323 5.0 98.5 1.0

M.Van Eijk, M.J.Rynkiewicz, M.R.White, K.L.Hartshorn, X.Zou, K.Schulten, D.Luo, E.C.Crouch, T.R.Cafarella, J.F.Head, H.P.Haagsman, B.A.Seaton. A Unique Sugar-Binding Site Mediates the Distinct Anti-Influenza Activity of Pig Surfactant Protein D. J.Biol.Chem. V. 287 26666 2012.
ISSN: ISSN 0021-9258
PubMed: 22685299
DOI: 10.1074/JBC.M112.368571