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Calcium in PDB 5oxr: Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide

Protein crystallography data

The structure of Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide, PDB code: 5oxr 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) 55.30 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.329, 108.140, 55.670, 90.00, 91.82, 90.00
R / Rfree (%) 17.3 / 19.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide (pdb code 5oxr). 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 Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide, PDB code: 5oxr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 5oxr

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Calcium binding site 1 out of 9 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 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 R7 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:16.2
occ:1.00
 OD1 A:ASP342 2.3 14.8 1.0
OD1 A:ASN341 2.4 16.5 1.0
O A:HOH503 2.4 20.8 1.0
OD1 A:ASN323 2.5 18.6 1.0
OE1 A:GLU329 2.5 18.2 1.0
O A:ASP342 2.5 13.6 1.0
O A:HOH504 2.6 20.6 1.0
OE1 A:GLU321 2.7 20.6 1.0
CG A:ASP342 3.4 15.6 1.0
CG A:ASN341 3.4 18.1 1.0
CD A:GLU321 3.4 20.5 1.0
O A:HOH648 3.4 21.3 1.0
CG A:ASN323 3.4 21.9 1.0
CD A:GLU329 3.5 17.8 1.0
C A:ASP342 3.6 15.5 1.0
OE2 A:GLU321 3.6 22.0 1.0
OE2 A:GLU329 3.7 18.4 1.0
N A:ASP342 3.8 14.9 1.0
ND2 A:ASN341 3.8 23.2 1.0
ND2 A:ASN323 3.9 22.1 1.0
CA A:ASP342 4.0 14.9 1.0
OD2 A:ASP342 4.1 15.9 1.0
N A:ASN323 4.2 20.5 1.0
CB A:ASP342 4.3 15.5 1.0
C A:ASN341 4.5 15.4 1.0
CB A:ASP325 4.6 25.8 1.0
CB A:ASN341 4.7 16.8 1.0
CB A:ASN323 4.7 21.4 1.0
CG A:GLU321 4.7 19.5 1.0
N A:ASP325 4.7 22.4 1.0
N A:ARG343 4.7 16.5 1.0
CG A:GLU329 4.8 18.5 1.0
N A:ASP324 4.8 20.8 1.0
CA A:ASN341 4.8 15.6 1.0
CA A:ASN323 4.8 20.8 1.0
CB A:GLU329 5.0 18.0 1.0

Calcium binding site 2 out of 9 in 5oxr

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Calcium binding site 2 out of 9 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 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 R7 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:18.4
occ:1.00
 OD1 A:ASP330 2.3 16.4 1.0
O A:HOH557 2.4 16.6 1.0
OD1 A:ASP324 2.4 19.9 1.0
OD2 A:ASP297 2.4 19.7 1.0
O A:GLU329 2.5 17.8 1.0
OE1 A:GLU301 2.5 20.9 1.0
OE2 A:GLU301 2.5 21.4 1.0
OD1 A:ASP297 2.7 17.8 1.0
CD A:GLU301 2.8 22.2 1.0
CG A:ASP297 2.9 17.8 1.0
CG A:ASP324 3.4 24.1 1.0
C A:GLU329 3.4 17.5 1.0
CG A:ASP330 3.4 17.3 1.0
CA A:ASP330 3.8 16.6 1.0
CA A:CA403 3.9 19.9 1.0
N A:ASP330 4.0 16.4 1.0
O A:HOH598 4.0 35.2 1.0
CB A:ASP324 4.0 22.0 1.0
OD2 A:ASP324 4.2 24.5 1.0
CB A:ASP330 4.2 16.5 1.0
OD2 A:ASP330 4.4 17.3 1.0
N A:GLU329 4.4 19.9 1.0
CG A:GLU301 4.4 24.5 1.0
CA A:GLU329 4.4 18.4 1.0
CB A:ASP297 4.4 18.6 1.0
CZ A:PHE304 4.5 20.0 1.0
O A:HOH641 4.5 25.9 1.0
CA A:ASP324 4.6 22.0 1.0
OD2 A:ASP342 4.6 15.9 1.0
N A:GLY302 4.7 24.6 1.0
O A:HOH530 4.8 24.3 1.0
O A:ASP297 4.8 19.8 1.0
CB A:GLU329 5.0 18.0 1.0

Calcium binding site 3 out of 9 in 5oxr

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Calcium binding site 3 out of 9 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 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 R7 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:19.9
occ:1.00
 O A:HOH598 2.2 35.2 1.0
OE1 A:GLU301 2.3 20.9 1.0
O A:HOH600 2.3 37.3 1.0
OD2 A:ASP330 2.4 17.3 1.0
OD1 A:ASP330 2.5 16.4 1.0
CG A:ASP330 2.8 17.3 1.0
CD A:GLU301 3.5 22.2 1.0
CA A:CA402 3.9 18.4 1.0
OD1 A:ASP324 4.2 19.9 1.0
CG A:GLU301 4.2 24.5 1.0
CB A:GLU301 4.3 24.9 1.0
CB A:ASP330 4.4 16.5 1.0
O A:ASP297 4.4 19.8 1.0
OE2 A:GLU301 4.4 21.4 1.0
OD2 A:ASP324 4.7 24.5 1.0
OD1 A:ASP297 4.7 17.8 1.0
O A:HOH544 4.8 32.5 1.0
CG A:ASP324 4.9 24.1 1.0
CA A:GLU301 4.9 25.6 1.0
O A:GLY327 4.9 27.5 1.0
OD2 A:ASP297 5.0 19.7 1.0

Calcium binding site 4 out of 9 in 5oxr

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Calcium binding site 4 out of 9 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 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 R7 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:11.0
occ:1.00
 OD1 B:ASP342 2.3 11.3 1.0
O7 B:GMH405 2.3 13.8 1.0
O6 B:GMH405 2.4 12.4 1.0
OE1 B:GLU329 2.4 15.1 1.0
OD1 B:ASN341 2.4 11.6 1.0
OD1 B:ASN323 2.4 10.7 1.0
O B:ASP342 2.5 11.4 1.0
OE1 B:GLU321 2.6 14.5 1.0
C7 B:GMH405 3.3 13.5 1.0
CG B:ASP342 3.4 11.2 1.0
CG B:ASN341 3.4 11.0 1.0
C6 B:GMH405 3.4 13.5 1.0
CD B:GLU329 3.4 14.1 1.0
CD B:GLU321 3.5 14.5 1.0
CG B:ASN323 3.5 10.8 1.0
C B:ASP342 3.5 12.1 1.0
ND2 B:ASN341 3.7 11.5 1.0
N B:ASP342 3.8 10.9 1.0
OE2 B:GLU329 3.8 15.4 1.0
OE2 B:GLU321 3.8 15.6 1.0
CA B:ASP342 4.0 11.7 1.0
ND2 B:ASN323 4.1 10.7 1.0
OD2 B:ASP342 4.1 11.3 1.0
N B:ASN323 4.2 11.4 1.0
CB B:ASP342 4.3 11.8 1.0
C B:ASN341 4.5 11.2 1.0
CB B:ASN323 4.6 11.1 1.0
CB B:ASN341 4.7 10.9 1.0
CG B:GLU329 4.7 14.3 1.0
N B:ARG343 4.7 13.4 1.0
CG B:GLU321 4.7 14.0 1.0
C5 B:GMH405 4.7 15.0 1.0
CB B:ASP325 4.7 14.8 1.0
N B:ASP324 4.7 12.0 1.0
N B:ASP325 4.8 13.2 1.0
CA B:ASN323 4.8 11.0 1.0
O5 B:GMH405 4.8 15.0 1.0
CA B:ASN341 4.9 10.9 1.0
CB B:GLU329 4.9 14.5 1.0

Calcium binding site 5 out of 9 in 5oxr

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Calcium binding site 5 out of 9 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 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 R7 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:15.2
occ:1.00
 O B:HOH547 2.3 12.1 1.0
O B:GLU329 2.3 14.4 1.0
OD1 B:ASP330 2.4 15.8 1.0
OD2 B:ASP297 2.4 17.4 1.0
OE1 B:GLU301 2.6 19.1 1.0
OE2 B:GLU301 2.6 18.4 1.0
OD1 B:ASP324 2.6 15.7 1.0
OD1 B:ASP297 2.6 16.0 1.0
CG B:ASP297 2.9 17.2 1.0
CD B:GLU301 2.9 20.4 1.0
C B:GLU329 3.4 14.0 1.0
CG B:ASP324 3.4 15.6 1.0
CG B:ASP330 3.6 17.1 1.0
CA B:ASP330 3.8 14.4 1.0
O B:HOH570 3.9 23.8 1.0
CA B:CA403 4.0 20.8 1.0
N B:ASP330 4.0 13.2 1.0
CB B:ASP324 4.0 13.5 1.0
OD2 B:ASP324 4.2 15.2 1.0
CB B:ASP330 4.2 15.3 1.0
O B:HOH643 4.3 27.8 1.0
CZ B:PHE304 4.4 15.0 1.0
CG B:GLU301 4.4 21.0 1.0
CA B:GLU329 4.4 15.2 1.0
N B:GLU329 4.4 16.0 1.0
CB B:ASP297 4.4 16.6 1.0
OD2 B:ASP342 4.5 11.3 1.0
OD2 B:ASP330 4.5 17.4 1.0
CA B:ASP324 4.6 13.2 1.0
N B:GLY302 4.8 19.8 1.0
CE1 B:PHE304 4.9 15.0 1.0
O B:ASP297 4.9 18.6 1.0
O B:HOH574 5.0 19.8 1.0
CB B:GLU329 5.0 14.5 1.0
O B:HOH524 5.0 20.8 1.0

Calcium binding site 6 out of 9 in 5oxr

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Calcium binding site 6 out of 9 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide


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 Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:20.8
occ:1.00
 O B:HOH574 2.3 19.8 1.0
O B:HOH621 2.3 28.8 1.0
O B:HOH570 2.4 23.8 1.0
O B:HOH641 2.4 23.7 1.0
OE1 B:GLU301 2.4 19.1 1.0
OD2 B:ASP330 2.5 17.4 1.0
OD1 B:ASP330 2.5 15.8 1.0
CG B:ASP330 2.8 17.1 1.0
CD B:GLU301 3.6 20.4 1.0
O B:HOH565 4.0 52.6 1.0
CA B:CA402 4.0 15.2 1.0
O B:HOH554 4.3 23.2 1.0
CB B:GLU301 4.3 22.6 1.0
OD1 B:ASP324 4.3 15.7 1.0
O B:ASP297 4.3 18.6 1.0
CB B:ASP330 4.4 15.3 1.0
CG B:GLU301 4.4 21.0 1.0
OE2 B:GLU301 4.6 18.4 1.0
O B:HOH632 4.6 36.1 1.0
OD1 B:ASP297 4.7 16.0 1.0
O B:HOH663 4.7 42.5 1.0
CA B:GLU301 4.8 21.8 1.0
O B:HOH529 4.8 25.3 1.0
OD2 B:ASP297 4.8 17.4 1.0
O B:GLY327 4.9 19.9 1.0
OD2 B:ASP324 4.9 15.2 1.0
CG B:ASP297 5.0 17.2 1.0

Calcium binding site 7 out of 9 in 5oxr

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Calcium binding site 7 out of 9 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide


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 Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:13.1
occ:1.00
 OD1 C:ASP342 2.3 12.4 1.0
O7 C:GMH405 2.3 17.5 1.0
OE1 C:GLU329 2.3 15.8 1.0
O6 C:GMH405 2.4 17.1 1.0
OD1 C:ASN323 2.4 14.0 1.0
OD1 C:ASN341 2.4 14.8 1.0
O C:ASP342 2.5 12.2 1.0
OE1 C:GLU321 2.6 16.2 1.0
C7 C:GMH405 3.3 18.6 1.0
C6 C:GMH405 3.3 18.7 1.0
CG C:ASP342 3.3 12.5 1.0
CD C:GLU329 3.4 17.1 1.0
CG C:ASN323 3.4 16.2 1.0
CG C:ASN341 3.5 14.8 1.0
CD C:GLU321 3.5 15.4 1.0
C C:ASP342 3.5 14.0 1.0
OE2 C:GLU321 3.7 17.3 1.0
OE2 C:GLU329 3.8 17.1 1.0
N C:ASP342 3.8 13.4 1.0
ND2 C:ASN341 3.9 14.4 1.0
ND2 C:ASN323 4.0 15.8 1.0
CA C:ASP342 4.0 13.1 1.0
OD2 C:ASP342 4.1 12.8 1.0
N C:ASN323 4.2 16.2 1.0
CB C:ASP342 4.3 12.9 1.0
C C:ASN341 4.6 14.2 1.0
CB C:ASN323 4.6 15.5 1.0
CG C:GLU329 4.7 16.8 1.0
CB C:ASP325 4.7 21.3 1.0
N C:ARG343 4.7 14.7 1.0
N C:ASP325 4.7 17.1 1.0
C5 C:GMH405 4.7 21.8 1.0
CG C:GLU321 4.7 15.2 1.0
CB C:ASN341 4.7 14.1 1.0
CA C:ASN323 4.8 15.9 1.0
N C:ASP324 4.8 16.2 1.0
CB C:GLU329 4.9 17.3 1.0
CA C:ASN341 4.9 13.9 1.0
O5 C:GMH405 4.9 23.1 1.0

Calcium binding site 8 out of 9 in 5oxr

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Calcium binding site 8 out of 9 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide


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 Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:18.6
occ:1.00
 O C:HOH546 2.3 15.1 1.0
O C:GLU329 2.4 17.3 1.0
OD1 C:ASP330 2.4 19.2 1.0
OD2 C:ASP297 2.4 22.6 1.0
OE2 C:GLU301 2.5 21.4 1.0
OE1 C:GLU301 2.5 22.1 1.0
OD1 C:ASP324 2.6 18.1 1.0
OD1 C:ASP297 2.7 20.4 1.0
CD C:GLU301 2.9 23.6 1.0
CG C:ASP297 3.0 23.2 1.0
C C:GLU329 3.4 17.4 1.0
CG C:ASP324 3.4 19.2 1.0
CG C:ASP330 3.6 19.3 1.0
O C:HOH557 3.8 25.5 1.0
CA C:ASP330 3.8 17.9 1.0
CA C:CA403 3.9 22.8 1.0
N C:ASP330 4.0 16.8 1.0
CB C:ASP324 4.0 17.6 1.0
CB C:ASP330 4.3 18.5 1.0
OD2 C:ASP324 4.3 18.9 1.0
CG C:GLU301 4.4 24.9 1.0
CA C:GLU329 4.4 18.7 1.0
CB C:ASP297 4.5 22.7 1.0
N C:GLU329 4.5 19.3 1.0
OD2 C:ASP330 4.5 20.8 1.0
CZ C:PHE304 4.5 20.4 1.0
CA C:ASP324 4.5 16.4 1.0
OD2 C:ASP342 4.5 12.8 1.0
O C:HOH625 4.6 33.7 1.0
N C:GLY302 4.7 27.0 1.0
O C:ASP297 4.8 27.3 1.0
O C:HOH571 4.9 24.2 1.0
CA C:GLU301 5.0 28.3 1.0
CE1 C:PHE304 5.0 20.2 1.0
O C:HOH565 5.0 18.8 1.0

Calcium binding site 9 out of 9 in 5oxr

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Calcium binding site 9 out of 9 in the Crystal Structure of Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide


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 Human Lung Surfactant Protein D Trimeric Fragment with Bound Ligand Salmonella Enterica Minnesota R7 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:22.8
occ:1.00
 O C:HOH571 2.2 24.2 1.0
O C:HOH594 2.3 36.0 1.0
OE1 C:GLU301 2.3 22.1 1.0
O C:HOH615 2.3 21.5 1.0
O C:HOH557 2.3 25.5 1.0
OD2 C:ASP330 2.4 20.8 1.0
OD1 C:ASP330 2.6 19.2 1.0
CG C:ASP330 2.9 19.3 1.0
CD C:GLU301 3.5 23.6 1.0
CA C:CA402 3.9 18.6 1.0
O C:HOH553 4.1 30.6 1.0
CB C:GLU301 4.2 26.6 1.0
CG C:GLU301 4.2 24.9 1.0
O C:ASP297 4.3 27.3 1.0
OD1 C:ASP324 4.3 18.1 1.0
CB C:ASP330 4.4 18.5 1.0
OE2 C:GLU301 4.5 21.4 1.0
O C:HOH509 4.5 52.5 1.0
O C:HOH596 4.6 56.6 1.0
CA C:GLU301 4.7 28.3 1.0
OD1 C:ASP297 4.7 20.4 1.0
OD2 C:ASP297 4.9 22.6 1.0
O C:HOH537 4.9 28.2 1.0
O C:GLY327 4.9 25.7 1.0
OD2 C:ASP324 5.0 18.9 1.0

Reference:

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
Page generated: Wed Jul 9 09:22:42 2025

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