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Calcium in PDB 4e52: Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D

Protein crystallography data

The structure of Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D, PDB code: 4e52 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) 26.75 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.350, 107.990, 55.650, 90.00, 92.14, 90.00
R / Rfree (%) 19.2 / 21

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D (pdb code 4e52). 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 Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D, PDB code: 4e52:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4e52

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Calcium binding site 1 out of 9 in the Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung 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 Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:17.6
occ:1.00
 OD1 A:ASP342 2.3 16.6 1.0
OD1 A:ASN341 2.4 18.3 1.0
OD1 A:ASN323 2.4 20.4 1.0
OE1 A:GLU329 2.5 18.4 1.0
O A:HOH510 2.5 21.3 1.0
O A:HOH501 2.5 20.6 1.0
OE1 A:GLU321 2.5 20.1 1.0
O A:ASP342 2.7 15.9 1.0
CD A:GLU321 3.4 21.9 1.0
CG A:ASP342 3.4 16.1 1.0
CG A:ASN341 3.4 19.1 1.0
CD A:GLU329 3.4 17.0 1.0
CG A:ASN323 3.6 24.5 1.0
OE2 A:GLU321 3.7 25.4 1.0
C A:ASP342 3.7 15.8 1.0
OE2 A:GLU329 3.8 19.1 1.0
ND2 A:ASN341 3.8 19.9 1.0
N A:ASP342 3.8 16.7 1.0
OD2 A:ASP342 4.1 16.6 1.0
CA A:ASP342 4.2 16.0 1.0
N A:ASN323 4.2 19.7 1.0
CB A:ASP342 4.4 15.4 1.0
ND2 A:ASN323 4.4 26.3 1.0
CB A:ASN323 4.6 19.5 1.0
CG A:GLU321 4.6 20.6 1.0
CB A:ASP325 4.6 20.9 1.0
C A:ASN341 4.6 17.5 1.0
N A:ASP325 4.7 17.6 1.0
CB A:ASN341 4.7 18.6 1.0
N A:ASP324 4.7 17.1 1.0
CG A:GLU329 4.8 17.5 1.0
CA A:ASN323 4.8 19.0 1.0
N A:ARG343 4.8 15.0 1.0
CA A:ASN341 4.9 17.6 1.0
CB A:GLU329 5.0 16.9 1.0

Calcium binding site 2 out of 9 in 4e52

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Calcium binding site 2 out of 9 in the Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:17.1
occ:1.00
 OD1 A:ASP330 2.4 17.8 1.0
OD2 A:ASP297 2.4 19.6 1.0
OD1 A:ASP324 2.5 16.1 1.0
O A:GLU329 2.5 15.9 1.0
OE2 A:GLU301 2.5 15.8 1.0
O A:HOH502 2.5 17.9 1.0
OE1 A:GLU301 2.5 15.6 1.0
OD1 A:ASP297 2.7 18.8 1.0
CD A:GLU301 2.8 17.2 1.0
CG A:ASP297 2.9 17.7 1.0
CG A:ASP324 3.3 19.6 1.0
C A:GLU329 3.3 16.5 1.0
CG A:ASP330 3.5 20.0 1.0
CA A:ASP330 3.7 17.2 1.0
CA A:CA403 3.9 19.5 1.0
CB A:ASP324 3.9 16.9 1.0
N A:ASP330 3.9 16.4 1.0
OD2 A:ASP324 4.1 18.1 1.0
CB A:ASP330 4.2 16.1 1.0
O A:HOH517 4.3 23.5 1.0
CG A:GLU301 4.3 17.9 1.0
N A:GLU329 4.3 18.6 1.0
CZ A:PHE304 4.4 19.7 1.0
OD2 A:ASP330 4.4 18.9 1.0
CB A:ASP297 4.4 18.9 1.0
CA A:GLU329 4.4 17.9 1.0
CA A:ASP324 4.5 17.8 1.0
N A:GLY302 4.6 21.9 1.0
OD2 A:ASP342 4.7 16.6 1.0
O A:HOH509 4.7 21.7 1.0
O A:ASP297 4.8 20.0 1.0
O A:HOH513 4.9 24.0 1.0
CB A:GLU329 4.9 16.9 1.0
O A:HOH503 4.9 19.6 1.0
CE1 A:PHE304 4.9 19.3 1.0
C A:ASP330 5.0 16.5 1.0
CA A:GLU301 5.0 20.1 1.0

Calcium binding site 3 out of 9 in 4e52

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Calcium binding site 3 out of 9 in the Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D


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 Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:19.5
occ:1.00
 OE1 A:GLU301 2.4 15.6 1.0
O A:HOH545 2.4 23.4 1.0
O A:HOH503 2.4 19.6 1.0
O A:HOH517 2.4 23.5 1.0
OD2 A:ASP330 2.4 18.9 1.0
OD1 A:ASP330 2.6 17.8 1.0
CG A:ASP330 2.8 20.0 1.0
CD A:GLU301 3.5 17.2 1.0
CA A:CA402 3.9 17.1 1.0
OD1 A:ASP324 4.2 16.1 1.0
CG A:GLU301 4.3 17.9 1.0
CB A:GLU301 4.3 20.0 1.0
CB A:ASP330 4.4 16.1 1.0
OE2 A:GLU301 4.4 15.8 1.0
O A:ASP297 4.4 20.0 1.0
OD2 A:ASP324 4.7 18.1 1.0
OD1 A:ASP297 4.7 18.8 1.0
O A:GLY327 4.7 21.5 1.0
CA A:GLU301 4.8 20.1 1.0
CG A:ASP324 4.9 19.6 1.0
OD2 A:ASP297 4.9 19.6 1.0
O A:HOH526 4.9 23.0 1.0
O A:HOH629 5.0 39.3 1.0

Calcium binding site 4 out of 9 in 4e52

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Calcium binding site 4 out of 9 in the Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D


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 Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:15.9
occ:1.00
 OD1 B:ASP342 2.3 14.8 1.0
OD1 B:ASN341 2.4 15.6 1.0
O6 B:GMH404 2.4 18.4 1.0
OD1 B:ASN323 2.4 16.1 1.0
OE1 B:GLU329 2.4 15.6 1.0
O B:ASP342 2.6 16.1 1.0
OE1 B:GLU321 2.6 16.0 1.0
O7 B:GMH404 2.6 18.0 1.0
CG B:ASP342 3.3 15.2 1.0
C7 B:GMH404 3.3 19.6 1.0
C6 B:GMH404 3.3 21.6 1.0
CG B:ASN341 3.4 16.4 1.0
CD B:GLU321 3.4 16.4 1.0
CD B:GLU329 3.4 17.8 1.0
CG B:ASN323 3.4 16.6 1.0
C B:ASP342 3.6 15.2 1.0
OE2 B:GLU321 3.7 17.0 1.0
N B:ASP342 3.7 15.7 1.0
OE2 B:GLU329 3.8 18.4 1.0
ND2 B:ASN341 3.8 16.5 1.0
ND2 B:ASN323 4.0 16.2 1.0
OD2 B:ASP342 4.0 15.2 1.0
CA B:ASP342 4.1 16.7 1.0
N B:ASN323 4.1 15.3 1.0
CB B:ASP342 4.3 15.8 1.0
C B:ASN341 4.5 15.9 1.0
CB B:ASN323 4.6 15.3 1.0
CB B:ASP325 4.6 19.9 1.0
N B:ASP324 4.7 15.2 1.0
CB B:ASN341 4.7 15.6 1.0
CG B:GLU321 4.7 16.6 1.0
N B:ASP325 4.7 18.7 1.0
C5 B:GMH404 4.7 25.6 1.0
CG B:GLU329 4.7 17.0 1.0
N B:ARG343 4.8 16.5 1.0
CA B:ASN323 4.8 15.2 1.0
CA B:ASN341 4.8 15.2 1.0
O5 B:GMH404 4.9 27.1 1.0
CB B:GLU329 4.9 19.3 1.0
C B:ASN323 5.0 16.4 1.0

Calcium binding site 5 out of 9 in 4e52

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Calcium binding site 5 out of 9 in the Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D


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 Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:17.6
occ:1.00
 O B:HOH502 2.3 17.0 1.0
OD1 B:ASP330 2.4 19.5 1.0
O B:GLU329 2.4 17.1 1.0
OD2 B:ASP297 2.5 21.0 1.0
OE2 B:GLU301 2.5 20.2 1.0
OE1 B:GLU301 2.5 20.7 1.0
OD1 B:ASP324 2.6 19.3 1.0
OD1 B:ASP297 2.6 18.2 1.0
CD B:GLU301 2.9 22.4 1.0
CG B:ASP297 2.9 19.7 1.0
C B:GLU329 3.4 17.9 1.0
CG B:ASP324 3.4 21.4 1.0
CG B:ASP330 3.5 22.1 1.0
CA B:ASP330 3.7 17.1 1.0
O B:HOH501 3.9 25.0 1.0
CA B:CA403 3.9 24.9 1.0
N B:ASP330 4.0 17.5 1.0
CB B:ASP324 4.0 18.4 1.0
CB B:ASP330 4.2 18.1 1.0
OD2 B:ASP324 4.2 19.5 1.0
O B:HOH586 4.3 31.3 1.0
CG B:GLU301 4.4 22.4 1.0
CB B:ASP297 4.4 19.4 1.0
OD2 B:ASP330 4.5 21.9 1.0
N B:GLU329 4.5 19.9 1.0
CZ B:PHE304 4.5 19.9 1.0
CA B:GLU329 4.5 19.0 1.0
OD2 B:ASP342 4.6 15.2 1.0
CA B:ASP324 4.6 18.3 1.0
N B:GLY302 4.8 22.6 1.0
O B:ASP297 4.9 21.1 1.0
CE1 B:PHE304 4.9 20.5 1.0
CA B:GLU301 5.0 24.1 1.0
O B:HOH575 5.0 28.4 1.0
C B:ASP330 5.0 16.9 1.0
O B:HOH509 5.0 22.7 1.0

Calcium binding site 6 out of 9 in 4e52

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Calcium binding site 6 out of 9 in the Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D


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 Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:24.9
occ:1.00
 O B:HOH509 2.3 22.7 1.0
O B:HOH501 2.4 25.0 1.0
OE1 B:GLU301 2.4 20.7 1.0
O B:HOH596 2.4 28.0 1.0
O B:HOH554 2.4 30.0 1.0
OD2 B:ASP330 2.5 21.9 1.0
OD1 B:ASP330 2.6 19.5 1.0
CG B:ASP330 2.9 22.1 1.0
CD B:GLU301 3.6 22.4 1.0
CA B:CA402 3.9 17.6 1.0
CB B:GLU301 4.2 24.0 1.0
O B:HOH549 4.3 28.2 1.0
CG B:GLU301 4.3 22.4 1.0
O B:ASP297 4.4 21.1 1.0
CB B:ASP330 4.4 18.1 1.0
OD1 B:ASP324 4.4 19.3 1.0
O B:HOH611 4.5 42.8 1.0
OE2 B:GLU301 4.5 20.2 1.0
OD1 B:ASP297 4.6 18.2 1.0
CA B:GLU301 4.7 24.1 1.0
O B:HOH692 4.7 39.1 1.0
OD2 B:ASP297 4.8 21.0 1.0
OD2 B:ASP324 4.9 19.5 1.0
CG B:ASP297 5.0 19.7 1.0
O B:HOH532 5.0 24.2 1.0
O B:GLY327 5.0 24.1 1.0

Calcium binding site 7 out of 9 in 4e52

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Calcium binding site 7 out of 9 in the Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D


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 Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:16.4
occ:1.00
 OD1 C:ASP342 2.2 15.7 1.0
OE1 C:GLU329 2.3 16.8 1.0
OD1 C:ASN323 2.4 15.7 1.0
OD1 C:ASN341 2.4 16.6 1.0
O6 C:GMH404 2.4 21.4 1.0
O7 C:GMH404 2.5 20.7 1.0
OE1 C:GLU321 2.5 16.7 1.0
O C:ASP342 2.6 16.4 1.0
C7 C:GMH404 3.3 23.5 1.0
CG C:ASP342 3.3 16.1 1.0
C6 C:GMH404 3.3 24.7 1.0
CD C:GLU329 3.4 17.1 1.0
CG C:ASN341 3.4 18.4 1.0
CD C:GLU321 3.4 16.6 1.0
CG C:ASN323 3.4 18.2 1.0
C C:ASP342 3.6 17.9 1.0
N C:ASP342 3.7 16.7 1.0
OE2 C:GLU321 3.7 19.0 1.0
ND2 C:ASN341 3.8 18.2 1.0
OE2 C:GLU329 3.8 17.7 1.0
OD2 C:ASP342 4.0 16.0 1.0
ND2 C:ASN323 4.0 20.4 1.0
CA C:ASP342 4.1 16.6 1.0
N C:ASN323 4.2 16.2 1.0
CB C:ASP342 4.3 15.4 1.0
C C:ASN341 4.5 18.2 1.0
CB C:ASN323 4.6 16.5 1.0
CG C:GLU321 4.6 16.5 1.0
CG C:GLU329 4.6 16.5 1.0
CB C:ASN341 4.7 16.6 1.0
C5 C:GMH404 4.7 27.6 1.0
CB C:ASP325 4.7 20.7 1.0
N C:ASP324 4.7 16.6 1.0
N C:ASP325 4.7 17.1 1.0
CA C:ASN323 4.8 16.7 1.0
N C:ARG343 4.8 19.0 1.0
CB C:GLU329 4.8 18.5 1.0
CA C:ASN341 4.9 17.4 1.0
O5 C:GMH404 4.9 30.1 1.0
C C:ASN323 5.0 16.8 1.0

Calcium binding site 8 out of 9 in 4e52

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Calcium binding site 8 out of 9 in the Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D


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 Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:19.0
occ:1.00
 O C:HOH504 2.3 15.2 1.0
OD1 C:ASP330 2.4 20.9 1.0
OE2 C:GLU301 2.4 19.4 1.0
OD2 C:ASP297 2.4 23.4 1.0
O C:GLU329 2.5 18.5 1.0
OE1 C:GLU301 2.5 21.4 1.0
OD1 C:ASP324 2.6 19.1 1.0
OD1 C:ASP297 2.7 19.9 1.0
CD C:GLU301 2.8 22.0 1.0
CG C:ASP297 2.9 22.1 1.0
C C:GLU329 3.4 18.5 1.0
CG C:ASP324 3.4 21.0 1.0
CG C:ASP330 3.6 21.6 1.0
CA C:ASP330 3.8 18.6 1.0
O C:HOH501 3.9 22.4 1.0
CA C:CA403 3.9 23.4 1.0
CB C:ASP324 3.9 17.5 1.0
N C:ASP330 4.0 19.2 1.0
CB C:ASP330 4.2 19.3 1.0
OD2 C:ASP324 4.3 17.9 1.0
CG C:GLU301 4.3 23.4 1.0
CB C:ASP297 4.5 21.6 1.0
N C:GLU329 4.5 20.6 1.0
CA C:ASP324 4.5 17.3 1.0
CZ C:PHE304 4.5 19.6 1.0
CA C:GLU329 4.5 19.3 1.0
OD2 C:ASP330 4.5 20.9 1.0
OD2 C:ASP342 4.6 16.0 1.0
N C:GLY302 4.7 25.2 1.0
O C:HOH510 4.8 18.8 1.0
O C:HOH579 4.8 25.6 1.0
O C:ASP297 4.9 24.2 1.0
CA C:GLU301 4.9 25.9 1.0
CE1 C:PHE304 4.9 18.0 1.0
C C:ASP330 5.0 18.3 1.0

Calcium binding site 9 out of 9 in 4e52

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Calcium binding site 9 out of 9 in the Crystal Structure of Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D


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 Haemophilus Eagan 4A Polysaccharide Bound Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:23.4
occ:1.00
 OE1 C:GLU301 2.3 21.4 1.0
O C:HOH524 2.4 23.3 1.0
O C:HOH507 2.4 24.5 1.0
O C:HOH501 2.4 22.4 1.0
OD2 C:ASP330 2.5 20.9 1.0
O C:HOH508 2.5 29.4 1.0
OD1 C:ASP330 2.5 20.9 1.0
CG C:ASP330 2.8 21.6 1.0
CD C:GLU301 3.5 22.0 1.0
CA C:CA402 3.9 19.0 1.0
O C:HOH530 4.2 26.3 1.0
CB C:GLU301 4.2 24.6 1.0
CG C:GLU301 4.2 23.4 1.0
OD1 C:ASP324 4.3 19.1 1.0
CB C:ASP330 4.3 19.3 1.0
O C:ASP297 4.4 24.2 1.0
OE2 C:GLU301 4.4 19.4 1.0
O C:HOH641 4.6 39.6 1.0
O C:HOH617 4.6 43.3 1.0
CA C:GLU301 4.7 25.9 1.0
OD1 C:ASP297 4.8 19.9 1.0
OD2 C:ASP297 4.8 23.4 1.0
O C:HOH542 4.9 31.1 1.0
OD2 C:ASP324 5.0 17.9 1.0

Reference:

H.W.Clark, R.M.Mackay, M.E.Deadman, D.W.Hood, J.Madsen, E.R.Moxon, J.P.Townsend, K.B.Reid, A.Ahmed, A.J.Shaw, T.J.Greenhough, A.K.Shrive. Crystal Structure of A Complex of Surfactant Protein D (Sp-D) and Haemophilus Influenzae Lipopolysaccharide Reveals Shielding of Core Structures in Sp-D-Resistant Strains. Infect.Immun. V. 84 1585 2016.
ISSN: ISSN 0019-9567
PubMed: 26953329
DOI: 10.1128/IAI.01239-15
Page generated: Sat Jul 13 23:45:40 2024

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