Calcium in PDB 5oxs: Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide

The structure of Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide, PDB code: 5oxs was solved by A.K.Shrive, T.J.Greenhough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.10 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.679, 108.510, 56.170, 90.00, 92.89, 90.00
R / Rfree (%)	16.5 / 18.7

The binding sites of Calcium atom in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide (pdb code 5oxs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide, PDB code: 5oxs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide


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 Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:17.6 occ:1.00 O4 A:GLC406 2.4 20.2 1.0 O3 A:GLC406 2.4 20.8 1.0 OE1 A:GLU329 2.4 16.5 1.0 OD1 A:ASN323 2.5 20.2 1.0 OD1 A:ASP342 2.5 15.5 1.0 OD1 A:ASN341 2.5 16.6 1.0 O A:ASP342 2.6 15.1 1.0 OE1 A:GLU321 2.6 19.8 1.0 C4 A:GLC406 3.3 21.7 1.0 C3 A:GLC406 3.4 22.0 1.0 CG A:ASN323 3.4 22.4 1.0 CD A:GLU329 3.4 16.1 1.0 CD A:GLU321 3.4 21.0 1.0 CG A:ASP342 3.5 16.6 1.0 CG A:ASN341 3.5 17.1 1.0 C A:ASP342 3.6 16.4 1.0 OE2 A:GLU321 3.7 21.2 1.0 OE2 A:GLU329 3.7 16.9 1.0 ND2 A:ASN341 3.8 17.1 1.0 ND2 A:ASN323 3.8 26.2 1.0 N A:ASP342 3.9 16.1 1.0 CA A:ASP342 4.1 16.3 1.0 OD2 A:ASP342 4.2 16.1 1.0 N A:ASN323 4.2 19.7 1.0 CB A:ASP342 4.4 15.9 1.0 CB A:ASN323 4.6 20.3 1.0 CB A:ASP325 4.6 19.4 1.0 C A:ASN341 4.6 17.1 1.0 CG A:GLU321 4.7 21.4 1.0 CG A:GLU329 4.7 16.4 1.0 C5 A:GLC406 4.8 22.7 1.0 N A:ASP325 4.8 17.4 1.0 CB A:ASN341 4.8 17.1 1.0 C2 A:GLC406 4.8 23.5 1.0 N A:ASP324 4.8 17.8 1.0 N A:ARG343 4.8 16.5 1.0 CA A:ASN323 4.8 19.2 1.0 CA A:ASN341 4.9 16.9 1.0 CB A:GLU329 5.0 16.2 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide


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 Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:16.5 occ:1.00 OD1 A:ASP330 2.4 17.7 1.0 OD2 A:ASP297 2.5 17.9 1.0 OD1 A:ASP324 2.5 16.7 1.0 O A:GLU329 2.5 15.6 1.0 O A:HOH525 2.5 16.1 1.0 OE1 A:GLU301 2.5 17.8 1.0 OE2 A:GLU301 2.6 16.9 1.0 OD1 A:ASP297 2.6 16.6 1.0 CD A:GLU301 2.9 17.9 1.0 CG A:ASP297 2.9 17.5 1.0 CG A:ASP324 3.4 18.0 1.0 C A:GLU329 3.4 15.8 1.0 CG A:ASP330 3.5 17.4 1.0 O A:HOH503 3.8 18.9 1.0 CA A:ASP330 3.9 16.0 1.0 CB A:ASP324 4.0 17.5 1.0 N A:ASP330 4.0 15.8 1.0 OD2 A:ASP324 4.1 17.8 1.0 CB A:ASP330 4.2 15.9 1.0 N A:GLU329 4.3 17.2 1.0 OD2 A:ASP330 4.4 17.9 1.0 CG A:GLU301 4.4 18.1 1.0 O A:HOH571 4.5 20.6 1.0 CB A:ASP297 4.5 17.3 1.0 CA A:GLU329 4.5 17.0 1.0 CZ A:PHE304 4.6 18.8 1.0 CA A:ASP324 4.6 17.3 1.0 OD2 A:ASP342 4.7 16.1 1.0 O A:HOH642 4.7 25.8 1.0 O A:HOH588 4.7 24.7 1.0 N A:GLY302 4.8 20.4 1.0 O A:ASP297 4.9 19.4 1.0 O A:HOH517 4.9 29.9 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide


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 Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:14.4 occ:1.00 O6 B:GMH404 2.3 15.8 1.0 O7 B:GMH404 2.4 15.6 1.0 OD1 B:ASP342 2.4 13.2 1.0 OD1 B:ASN323 2.4 12.6 1.0 OD1 B:ASN341 2.4 14.2 1.0 OE1 B:GLU329 2.5 17.3 1.0 O B:ASP342 2.6 15.4 1.0 OE1 B:GLU321 2.6 14.1 1.0 C7 B:GMH404 3.3 15.6 1.0 C6 B:GMH404 3.4 16.2 1.0 CG B:ASP342 3.4 13.6 1.0 CG B:ASN341 3.4 15.0 1.0 CG B:ASN323 3.5 12.9 1.0 CD B:GLU329 3.5 17.2 1.0 CD B:GLU321 3.5 13.8 1.0 C B:ASP342 3.6 15.2 1.0 OE2 B:GLU321 3.8 14.0 1.0 OE2 B:GLU329 3.8 16.9 1.0 N B:ASP342 3.8 14.5 1.0 ND2 B:ASN341 3.8 14.7 1.0 CA B:ASP342 4.0 14.5 1.0 ND2 B:ASN323 4.0 13.7 1.0 OD2 B:ASP342 4.2 13.8 1.0 N B:ASN323 4.2 12.9 1.0 CB B:ASP342 4.3 14.0 1.0 C B:ASN341 4.6 15.7 1.0 CB B:ASN323 4.6 13.3 1.0 N B:ASP324 4.7 14.8 1.0 CB B:ASP325 4.7 17.6 1.0 N B:ASP325 4.7 16.4 1.0 CB B:ASN341 4.7 14.8 1.0 C5 B:GMH404 4.7 17.5 1.0 N B:ARG343 4.7 15.8 1.0 CG B:GLU329 4.7 18.5 1.0 CG B:GLU321 4.7 13.8 1.0 CA B:ASN323 4.8 13.1 1.0 CA B:ASN341 4.9 14.8 1.0 CB B:GLU329 4.9 18.9 1.0 O5 B:GMH404 4.9 17.1 1.0 C B:ASN323 5.0 13.9 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide


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 Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:33.9 occ:1.00 O B:HOH520 2.1 20.6 1.0 O B:GLU329 2.5 18.2 1.0 OD1 B:ASP330 2.7 26.4 1.0 OD2 B:ASP297 2.7 37.2 1.0 OE1 B:GLU301 2.7 44.6 1.0 OD1 B:ASP297 2.8 37.7 1.0 OD1 B:ASP324 2.9 21.7 1.0 OE2 B:GLU301 3.0 46.5 1.0 CG B:ASP297 3.1 37.8 1.0 CD B:GLU301 3.2 47.6 1.0 C B:GLU329 3.4 19.6 1.0 O B:HOH506 3.6 42.3 1.0 CG B:ASP324 3.6 19.7 1.0 CG B:ASP330 3.8 24.6 1.0 CA B:ASP330 3.9 20.2 1.0 N B:ASP330 4.0 19.5 1.0 O B:HOH552 4.1 32.8 1.0 OD2 B:ASP324 4.3 20.5 1.0 N B:GLU329 4.3 22.6 1.0 CB B:ASP324 4.3 16.9 1.0 CA B:GLU329 4.3 19.9 1.0 O B:HOH602 4.4 36.0 1.0 CZ B:PHE304 4.4 24.5 1.0 CB B:ASP330 4.4 22.7 1.0 OD2 B:ASP342 4.4 13.8 1.0 CB B:ASP297 4.7 35.0 1.0 CG B:GLU301 4.7 46.6 1.0 CB B:GLU329 4.8 18.9 1.0 OD2 B:ASP330 4.9 29.5 1.0 CE1 B:PHE304 4.9 24.1 1.0 CA B:ASP324 4.9 16.2 1.0 N B:GLY302 4.9 46.6 1.0 O B:ASP297 5.0 40.3 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide


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 Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R5 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:17.5 occ:1.00 O7 C:GMH404 2.3 19.0 1.0 O6 C:GMH404 2.3 18.9 1.0 OD1 C:ASP342 2.4 17.1 1.0 OD1 C:ASN341 2.4 16.5 1.0 OE1 C:GLU329 2.4 18.3 1.0 OD1 C:ASN323 2.5 19.3 1.0 OE1 C:GLU321 2.6 17.0 1.0 O C:ASP342 2.6 16.9 1.0 C7 C:GMH404 3.3 19.9 1.0 C6 C:GMH404 3.3 20.1 1.0 CD C:GLU321 3.4 17.4 1.0 CG C:ASN323 3.4 20.5 1.0 CG C:ASN341 3.4 18.1 1.0 CG C:ASP342 3.4 17.3 1.0 CD C:GLU329 3.5 18.9 1.0 C C:ASP342 3.6 17.1 1.0 OE2 C:GLU321 3.7 18.6 1.0 OE2 C:GLU329 3.8 19.9 1.0 ND2 C:ASN341 3.8 16.6 1.0 N C:ASP342 3.9 17.1 1.0 ND2 C:ASN323 4.0 19.4 1.0 CA C:ASP342 4.1 17.6 1.0 N C:ASN323 4.2 19.8 1.0 OD2 C:ASP342 4.2 17.3 1.0 CB C:ASP342 4.4 17.4 1.0 CB C:ASN323 4.6 20.0 1.0 C C:ASN341 4.6 17.7 1.0 N C:ASP324 4.7 20.5 1.0 CG C:GLU321 4.7 18.1 1.0 CB C:ASP325 4.7 25.3 1.0 C5 C:GMH404 4.7 21.8 1.0 N C:ASP325 4.7 21.7 1.0 CB C:ASN341 4.7 17.2 1.0 CG C:GLU329 4.7 20.6 1.0 N C:ARG343 4.8 17.9 1.0 CA C:ASN323 4.8 19.6 1.0 O5 C:GMH404 4.9 23.3 1.0 CA C:ASN341 4.9 17.1 1.0 CB C:GLU329 4.9 20.4 1.0

J.R.Littlejohn, R.F.Da Silva, W.A.Neale, C.C.Smallcombe, H.W.Clark, R.A.Mackay, A.S.Watson, J.Madsen, D.W.Hood, I.Burns, T.J.Greenhough, A.K.Shrive. Structural Definition of Hsp-D Recognition of Salmonella Enterica Lps Inner Core Oligosaccharides Reveals Alternative Binding Modes For the Same Lps. Plos One V. 13 99175 2018.
ISSN: ESSN 1932-6203
PubMed: 29912941
DOI: 10.1371/JOURNAL.PONE.0199175