Calcium in PDB 6bbd: Structure of N-Glycosylated Porcine Surfactant Protein-D Complexed with Glycerol

The structure of Structure of N-Glycosylated Porcine Surfactant Protein-D Complexed with Glycerol, PDB code: 6bbd was solved by M.Van Eijk, M.J.Rynkiewicz, K.Khatri, N.Leymarie, J.Zaia, M.R.White, K.L.Hartshorn, T.R.Cafarella, I.Van Die, M.Hessing, B.A.Seaton, H.P.Haagsman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.85 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	66.798, 66.798, 64.974, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 24.7

The binding sites of Calcium atom in the Structure of N-Glycosylated Porcine Surfactant Protein-D Complexed with Glycerol (pdb code 6bbd). 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 N-Glycosylated Porcine Surfactant Protein-D Complexed with Glycerol, PDB code: 6bbd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of N-Glycosylated Porcine Surfactant Protein-D Complexed with Glycerol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of N-Glycosylated Porcine Surfactant Protein-D Complexed with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:36.0 occ:0.77 OD1 A:ASP345 2.3 42.6 1.0 OD1 A:ASN344 2.3 42.6 1.0 O3 A:GOL403 2.3 44.8 1.0 OD1 A:ASN323 2.4 50.6 1.0 OE1 A:GLU332 2.4 48.3 1.0 OE1 A:GLU321 2.5 47.1 1.0 O2 A:GOL403 2.5 47.8 1.0 O A:ASP345 2.5 49.1 1.0 C3 A:GOL403 3.3 46.2 1.0 C2 A:GOL403 3.3 45.9 1.0 CG A:ASP345 3.3 39.1 1.0 CD A:GLU321 3.3 50.2 1.0 CG A:ASN344 3.3 43.9 1.0 CG A:ASN323 3.4 53.3 1.0 CD A:GLU332 3.4 48.7 1.0 C A:ASP345 3.6 47.3 1.0 OE2 A:GLU321 3.7 52.6 1.0 ND2 A:ASN344 3.7 47.3 1.0 OE2 A:GLU332 3.8 49.3 1.0 N A:ASP345 3.8 41.1 1.0 ND2 A:ASN323 3.9 55.0 1.0 OD2 A:ASP345 4.0 38.5 1.0 CA A:ASP345 4.0 40.4 1.0 N A:ASN323 4.1 51.8 1.0 CB A:ASP345 4.2 37.2 1.0 N A:ASN324 4.5 46.3 1.0 CB A:ASN323 4.6 52.9 1.0 C A:ASN344 4.6 40.6 1.0 CG A:GLU321 4.6 50.4 1.0 CB A:ASN344 4.6 40.7 1.0 C1 A:GOL403 4.7 46.2 1.0 CG A:GLU332 4.7 48.7 1.0 CA A:ASN323 4.7 51.5 1.0 N A:LYS346 4.8 45.0 1.0 CB A:GLU332 4.8 47.2 1.0 O A:ASN325 4.8 51.1 1.0 N A:ASN325 4.8 50.8 1.0 CA A:ASN344 4.9 43.4 1.0 C A:ASN323 5.0 48.5 1.0 CB A:GLU321 5.0 49.9 1.0

Calcium binding site 2 out of 2 in the Structure of N-Glycosylated Porcine Surfactant Protein-D Complexed with Glycerol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of N-Glycosylated Porcine Surfactant Protein-D Complexed with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:33.0 occ:0.74 O A:HOH522 2.1 37.1 1.0 OD1 A:ASN333 2.4 41.7 1.0 OE1 A:GLU301 2.4 53.2 1.0 OD2 A:ASP297 2.4 43.4 1.0 O A:GLU332 2.4 38.8 1.0 OE2 A:GLU301 2.4 53.0 1.0 OD1 A:ASN324 2.5 44.6 1.0 OD1 A:ASP297 2.6 42.3 1.0 CD A:GLU301 2.7 53.2 1.0 CG A:ASP297 2.9 43.9 1.0 CG A:ASN324 3.2 49.5 1.0 C A:GLU332 3.4 40.1 1.0 CG A:ASN333 3.5 36.6 1.0 CA A:ASN333 3.8 36.7 1.0 N A:ASN333 4.0 40.8 1.0 CB A:ASN324 4.0 48.8 1.0 ND2 A:ASN324 4.0 55.5 1.0 CB A:ASN333 4.1 32.8 1.0 CG A:GLU301 4.2 53.4 1.0 CB A:ASP297 4.4 44.6 1.0 N A:GLU332 4.4 40.8 1.0 CZ A:PHE304 4.4 43.1 1.0 CA A:GLU332 4.5 43.8 1.0 ND2 A:ASN333 4.6 35.5 1.0 CA A:ASN324 4.6 46.8 1.0 N A:GLY302 4.7 48.1 1.0 OD2 A:ASP345 4.8 38.5 1.0 O A:ASP297 4.9 41.0 1.0 CA A:GLU301 4.9 48.4 1.0 O A:HOH530 4.9 58.2 1.0 CB A:GLU301 4.9 52.4 1.0 CE1 A:PHE304 4.9 44.7 1.0

M.Van Eijk, M.J.Rynkiewicz, K.Khatri, N.Leymarie, J.Zaia, M.R.White, K.L.Hartshorn, T.R.Cafarella, I.Van Die, M.Hessing, B.A.Seaton, H.P.Haagsman. Lectin-Mediated Binding and Sialoglycans of Porcine Surfactant Protein D Synergistically Neutralize Influenza A Virus. J. Biol. Chem. V. 293 10646 2018.
ISSN: ESSN 1083-351X
PubMed: 29769321
DOI: 10.1074/JBC.RA117.001430