Calcium in PDB 6bbe: Structure of N-Glycosylated Porcine Surfactant Protein-D

The structure of Structure of N-Glycosylated Porcine Surfactant Protein-D, PDB code: 6bbe 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)	14.70 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	66.015, 66.015, 64.658, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 25

The binding sites of Calcium atom in the Structure of N-Glycosylated Porcine Surfactant Protein-D (pdb code 6bbe). 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, PDB code: 6bbe:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:41.7 occ:0.91 OD1 A:ASP345 2.3 42.5 1.0 OD1 A:ASN323 2.4 51.1 1.0 OE1 A:GLU332 2.4 42.8 1.0 OD1 A:ASN344 2.4 37.6 1.0 OE1 A:GLU321 2.4 48.4 1.0 O A:ASP345 2.5 40.5 1.0 CG A:ASP345 3.2 42.5 1.0 CD A:GLU332 3.3 42.8 1.0 CD A:GLU321 3.4 48.4 1.0 CG A:ASN323 3.5 51.1 1.0 CG A:ASN344 3.5 37.6 1.0 C A:ASP345 3.5 40.5 1.0 OE2 A:GLU332 3.6 42.8 1.0 OE2 A:GLU321 3.8 48.4 1.0 N A:ASP345 3.8 40.5 1.0 OD2 A:ASP345 3.9 42.5 1.0 ND2 A:ASN344 3.9 37.6 1.0 CA A:ASP345 4.0 40.5 1.0 ND2 A:ASN323 4.0 51.1 1.0 CB A:ASP345 4.2 42.5 1.0 N A:ASN323 4.3 49.6 1.0 N A:ASN324 4.5 52.7 1.0 C A:ASN344 4.5 41.5 1.0 CG A:GLU332 4.6 42.8 1.0 CG A:GLU321 4.6 48.4 1.0 CB A:ASN323 4.7 51.1 1.0 N A:ASN325 4.7 42.4 1.0 N A:LYS346 4.7 40.6 1.0 CB A:ASN344 4.7 37.6 1.0 O A:ASN325 4.8 42.4 1.0 CB A:GLU332 4.8 42.8 1.0 CA A:ASN323 4.9 49.6 1.0 CA A:ASN344 4.9 41.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:40.9 occ:0.91 O A:HOH541 2.3 38.5 1.0 OD1 A:ASN324 2.4 62.3 1.0 OE2 A:GLU301 2.4 43.1 1.0 OD2 A:ASP297 2.4 37.1 1.0 O A:GLU332 2.4 38.1 1.0 OD1 A:ASN333 2.5 39.6 1.0 OD1 A:ASP297 2.6 37.1 1.0 CG A:ASP297 2.8 37.1 1.0 OE1 A:GLU301 2.8 43.1 1.0 CD A:GLU301 2.9 43.1 1.0 C A:GLU332 3.4 38.1 1.0 CG A:ASN324 3.4 62.3 1.0 CG A:ASN333 3.6 39.6 1.0 CA A:ASN333 3.7 30.8 1.0 CB A:ASN324 3.9 62.3 1.0 N A:ASN333 3.9 30.8 1.0 CB A:ASN333 4.2 39.6 1.0 CB A:ASP297 4.3 37.1 1.0 CZ A:PHE304 4.4 40.2 1.0 CG A:GLU301 4.4 43.1 1.0 N A:GLU332 4.4 38.1 1.0 CA A:GLU332 4.5 38.1 1.0 O A:HOH565 4.5 42.5 1.0 ND2 A:ASN324 4.5 62.3 1.0 CA A:ASN324 4.7 52.7 1.0 N A:GLY302 4.7 43.2 1.0 ND2 A:ASN333 4.8 39.6 1.0 OD2 A:ASP345 4.8 42.5 1.0 C A:ASN333 4.9 30.8 1.0 CE2 A:PHE304 4.9 40.2 1.0 O A:ASP297 5.0 43.7 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