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

Go back to Calcium Binding Sites List in 4e52
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

Go back to Calcium Binding Sites List in 4e52
Calcium binding site 2 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 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

Go back to Calcium Binding Sites List in 4e52
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

Go back to Calcium Binding Sites List in 4e52
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

Go back to Calcium Binding Sites List in 4e52
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

Go back to Calcium Binding Sites List in 4e52
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

Go back to Calcium Binding Sites List in 4e52
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

Go back to Calcium Binding Sites List in 4e52
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

Go back to Calcium Binding Sites List in 4e52
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 Dec 12 04:44:35 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy