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Calcium in PDB 2ric: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose

Protein crystallography data

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose, PDB code: 2ric was solved by H.Wang, J.Head, P.Kosma, S.Sheikh, B.Mcdonald, K.Smith, T.Cafarella, B.Seaton, E.Crouch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.404, 107.531, 55.698, 90.00, 90.28, 90.00
R / Rfree (%) 20.5 / 23

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose (pdb code 2ric). 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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose, PDB code: 2ric:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2ric

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Calcium binding site 1 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose


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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:28.8
occ:1.00
 OE1 A:GLU329 2.5 25.9 1.0
OD1 A:ASN341 2.5 31.1 1.0
OD1 A:ASP342 2.6 30.8 1.0
OD1 A:ASN323 2.6 30.6 1.0
O A:ASP342 2.7 28.6 1.0
OE1 A:GLU321 2.7 32.3 1.0
O6 A:GMH356 2.7 44.9 1.0
O7 A:GMH356 3.0 46.5 1.0
CG A:ASP342 3.4 30.8 1.0
CG A:ASN341 3.5 31.3 1.0
CD A:GLU329 3.5 29.5 1.0
CG A:ASN323 3.5 33.1 1.0
CD A:GLU321 3.6 32.2 1.0
C7 A:GMH356 3.6 47.5 1.0
C6 A:GMH356 3.7 48.8 1.0
C A:ASP342 3.8 29.5 1.0
OE2 A:GLU329 3.8 29.3 1.0
ND2 A:ASN341 3.8 29.1 1.0
OE2 A:GLU321 3.8 28.8 1.0
N A:ASP342 3.9 28.2 1.0
ND2 A:ASN323 3.9 32.2 1.0
OD2 A:ASP342 4.0 29.7 1.0
CA A:ASP342 4.2 28.3 1.0
N A:ASN323 4.2 31.1 1.0
CB A:ASP342 4.4 29.2 1.0
CB A:ASP325 4.6 32.7 1.0
C A:ASN341 4.6 29.9 1.0
N A:ASP325 4.6 30.8 1.0
N A:ASP324 4.7 29.7 1.0
CB A:ASN323 4.8 31.5 1.0
CG A:GLU329 4.8 30.0 1.0
CB A:ASN341 4.8 30.6 1.0
CG A:GLU321 4.8 31.4 1.0
CA A:ASN323 4.9 31.8 1.0
O5 A:GMH356 4.9 51.6 1.0
CB A:GLU329 4.9 31.4 1.0
N A:ARG343 4.9 30.0 1.0
CA A:ASN341 4.9 30.3 1.0
C5 A:GMH356 4.9 50.7 1.0

Calcium binding site 2 out of 9 in 2ric

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Calcium binding site 2 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose


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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:33.8
occ:1.00
 O A:HOH408 2.6 26.6 1.0
O A:GLU329 2.6 30.8 1.0
OD1 A:ASP330 2.6 33.2 1.0
OD2 A:ASP297 2.6 37.8 1.0
OD1 A:ASP324 2.7 29.8 1.0
OE1 A:GLU301 2.7 32.4 1.0
OD1 A:ASP297 2.8 35.4 1.0
OE2 A:GLU301 2.8 32.9 1.0
CG A:ASP297 3.1 36.5 1.0
CD A:GLU301 3.1 34.0 1.0
C A:GLU329 3.3 31.0 1.0
CG A:ASP324 3.4 33.4 1.0
CG A:ASP330 3.7 33.3 1.0
CA A:ASP330 3.7 30.9 1.0
N A:ASP330 3.9 31.8 1.0
CB A:ASP324 4.0 30.8 1.0
CA A:CA403 4.1 46.9 1.0
N A:GLU329 4.2 33.5 1.0
OD2 A:ASP324 4.2 30.4 1.0
CB A:ASP330 4.3 30.9 1.0
CA A:GLU329 4.3 32.3 1.0
O A:HOH529 4.4 50.4 1.0
CZ A:PHE304 4.5 31.7 1.0
OD2 A:ASP342 4.6 29.7 1.0
CA A:ASP324 4.6 29.6 1.0
CB A:ASP297 4.6 35.7 1.0
CG A:GLU301 4.6 34.0 1.0
O A:HOH479 4.6 37.0 1.0
OD2 A:ASP330 4.7 31.3 1.0
N A:GLY302 4.7 36.8 1.0
O A:ASP297 4.9 36.1 1.0
CB A:GLU329 4.9 31.4 1.0
C A:ASP330 4.9 29.9 1.0
O A:HOH454 4.9 38.5 1.0

Calcium binding site 3 out of 9 in 2ric

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Calcium binding site 3 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose


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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:46.9
occ:1.00
 OD1 A:ASP330 2.7 33.2 1.0
O A:HOH409 2.7 31.4 1.0
OD2 A:ASP330 2.7 31.3 1.0
OE1 A:GLU301 2.7 32.4 1.0
O A:HOH529 2.8 50.4 1.0
O A:HOH527 2.9 59.5 1.0
CG A:ASP330 3.1 33.3 1.0
CD A:GLU301 3.9 34.0 1.0
CA A:CA402 4.1 33.8 1.0
OD1 A:ASP324 4.5 29.8 1.0
CB A:GLU301 4.5 36.2 1.0
CB A:ASP330 4.6 30.9 1.0
CG A:GLU301 4.6 34.0 1.0
O A:ASP297 4.6 36.1 1.0
O A:GLY327 4.8 37.7 1.0
OD2 A:ASP324 4.8 30.4 1.0
CA A:SER328 4.9 39.3 1.0
OE2 A:GLU301 4.9 32.9 1.0
CA A:GLU301 4.9 37.0 1.0

Calcium binding site 4 out of 9 in 2ric

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Calcium binding site 4 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose


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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:24.1
occ:1.00
 OD1 B:ASP342 2.5 21.3 1.0
OE1 B:GLU329 2.5 21.7 1.0
OD1 B:ASN341 2.5 23.8 1.0
OD1 B:ASN323 2.5 21.0 1.0
OE1 B:GLU321 2.6 22.6 1.0
O6 B:GMH356 2.6 23.8 1.0
O B:ASP342 2.7 21.2 1.0
O7 B:GMH356 2.8 25.6 1.0
CG B:ASP342 3.4 23.4 1.0
C7 B:GMH356 3.5 24.6 1.0
CD B:GLU321 3.5 26.9 1.0
CD B:GLU329 3.5 24.2 1.0
CG B:ASN323 3.5 24.4 1.0
CG B:ASN341 3.5 25.3 1.0
C6 B:GMH356 3.5 26.8 1.0
C B:ASP342 3.7 22.4 1.0
N B:ASP342 3.7 23.1 1.0
OE2 B:GLU321 3.8 26.6 1.0
OE2 B:GLU329 3.8 24.2 1.0
ND2 B:ASN341 3.9 23.9 1.0
ND2 B:ASN323 4.0 23.4 1.0
CA B:ASP342 4.1 22.8 1.0
OD2 B:ASP342 4.1 22.9 1.0
N B:ASN323 4.2 25.4 1.0
CB B:ASP342 4.3 21.2 1.0
C B:ASN341 4.5 23.6 1.0
CB B:ASP325 4.6 26.1 1.0
CB B:ASN323 4.6 24.4 1.0
CG B:GLU321 4.7 25.8 1.0
N B:ASP325 4.7 26.3 1.0
N B:ASP324 4.7 23.7 1.0
CB B:ASN341 4.8 23.6 1.0
CG B:GLU329 4.8 23.8 1.0
C5 B:GMH356 4.8 27.1 1.0
N B:ARG343 4.8 22.9 1.0
CA B:ASN323 4.8 25.3 1.0
CA B:ASN341 4.9 23.8 1.0
CB B:GLU329 4.9 25.4 1.0
O5 B:GMH356 4.9 28.9 1.0

Calcium binding site 5 out of 9 in 2ric

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Calcium binding site 5 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose


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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:25.1
occ:1.00
 O B:GLU329 2.5 23.8 1.0
OE1 B:GLU301 2.5 25.0 1.0
O B:HOH405 2.5 24.2 1.0
OD1 B:ASP330 2.6 29.4 1.0
OD2 B:ASP297 2.6 28.4 1.0
OD1 B:ASP324 2.6 25.3 1.0
OD1 B:ASP297 2.8 26.2 1.0
OE2 B:GLU301 2.8 27.0 1.0
CD B:GLU301 3.0 28.6 1.0
CG B:ASP297 3.1 29.0 1.0
CG B:ASP324 3.4 27.8 1.0
C B:GLU329 3.4 26.0 1.0
CG B:ASP330 3.7 31.4 1.0
CA B:ASP330 3.8 25.5 1.0
CA B:CA403 3.9 30.1 1.0
CB B:ASP324 3.9 24.3 1.0
O B:HOH404 3.9 30.1 1.0
N B:ASP330 3.9 26.3 1.0
OD2 B:ASP324 4.2 25.4 1.0
CB B:ASP330 4.3 26.9 1.0
O B:HOH496 4.4 33.8 1.0
N B:GLU329 4.4 27.1 1.0
CA B:ASP324 4.5 24.8 1.0
CA B:GLU329 4.5 25.7 1.0
OD2 B:ASP342 4.5 22.9 1.0
CG B:GLU301 4.5 27.7 1.0
CZ B:PHE304 4.5 24.2 1.0
CB B:ASP297 4.6 27.2 1.0
OD2 B:ASP330 4.6 29.8 1.0
N B:GLY302 4.7 29.0 1.0
O B:ASP297 4.8 30.2 1.0
C B:ASP330 5.0 25.5 1.0
CE1 B:PHE304 5.0 23.7 1.0
O B:HOH443 5.0 35.0 1.0

Calcium binding site 6 out of 9 in 2ric

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Calcium binding site 6 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose


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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:30.1
occ:1.00
 OE1 B:GLU301 2.5 25.0 1.0
O B:HOH410 2.5 26.1 1.0
O B:HOH404 2.6 30.1 1.0
OD1 B:ASP330 2.6 29.4 1.0
OD2 B:ASP330 2.7 29.8 1.0
O B:HOH494 2.7 30.2 1.0
O B:HOH535 2.7 33.1 1.0
CG B:ASP330 3.0 31.4 1.0
CD B:GLU301 3.7 28.6 1.0
CA B:CA402 3.9 25.1 1.0
O B:HOH430 4.2 28.6 1.0
CB B:GLU301 4.2 29.9 1.0
OD1 B:ASP324 4.3 25.3 1.0
CG B:GLU301 4.3 27.7 1.0
O B:ASP297 4.3 30.2 1.0
CB B:ASP330 4.5 26.9 1.0
CA B:GLU301 4.6 29.7 1.0
OE2 B:GLU301 4.6 27.0 1.0
O B:HOH488 4.7 38.6 1.0
OD1 B:ASP297 4.8 26.2 1.0
OD2 B:ASP297 4.9 28.4 1.0
OD2 B:ASP324 4.9 25.4 1.0
O B:GLY327 4.9 27.2 1.0
CG B:ASP324 5.0 27.8 1.0

Calcium binding site 7 out of 9 in 2ric

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Calcium binding site 7 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose


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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:27.2
occ:1.00
 OD1 C:ASP342 2.5 24.5 1.0
OD1 C:ASN341 2.5 25.4 1.0
OE1 C:GLU329 2.6 24.3 1.0
OD1 C:ASN323 2.6 25.4 1.0
O6 C:GMH356 2.6 27.9 1.0
O C:ASP342 2.6 25.4 1.0
OE1 C:GLU321 2.7 23.8 1.0
O7 C:GMH356 2.9 31.9 1.0
CG C:ASP342 3.4 24.3 1.0
CD C:GLU321 3.4 26.2 1.0
CG C:ASN341 3.4 24.4 1.0
CD C:GLU329 3.5 23.4 1.0
C7 C:GMH356 3.5 31.2 1.0
CG C:ASN323 3.5 28.5 1.0
C6 C:GMH356 3.5 31.0 1.0
C C:ASP342 3.7 27.3 1.0
OE2 C:GLU321 3.7 27.8 1.0
N C:ASP342 3.7 25.2 1.0
OE2 C:GLU329 3.8 24.8 1.0
ND2 C:ASN341 3.8 25.4 1.0
ND2 C:ASN323 4.0 26.8 1.0
OD2 C:ASP342 4.1 23.6 1.0
CA C:ASP342 4.1 26.3 1.0
N C:ASN323 4.2 26.9 1.0
CB C:ASP342 4.3 23.2 1.0
C C:ASN341 4.5 25.1 1.0
CG C:GLU321 4.6 25.4 1.0
CB C:ASN323 4.6 26.4 1.0
CB C:ASP325 4.6 27.1 1.0
N C:ASP325 4.7 26.8 1.0
CB C:ASN341 4.7 25.3 1.0
N C:ASP324 4.8 24.9 1.0
CG C:GLU329 4.8 24.2 1.0
C5 C:GMH356 4.8 33.2 1.0
N C:ARG343 4.8 26.9 1.0
CA C:ASN323 4.8 26.4 1.0
CA C:ASN341 4.8 25.4 1.0
CB C:GLU329 5.0 23.3 1.0
O5 C:GMH356 5.0 33.7 1.0

Calcium binding site 8 out of 9 in 2ric

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Calcium binding site 8 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose


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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:27.3
occ:1.00
 O C:GLU329 2.6 25.4 1.0
O C:HOH405 2.6 26.1 1.0
OD2 C:ASP297 2.6 27.9 1.0
OD1 C:ASP330 2.6 28.3 1.0
OD1 C:ASP324 2.6 25.9 1.0
OE1 C:GLU301 2.6 27.6 1.0
OE2 C:GLU301 2.8 27.0 1.0
OD1 C:ASP297 2.8 27.9 1.0
CG C:ASP297 3.0 29.7 1.0
CD C:GLU301 3.1 30.3 1.0
CG C:ASP324 3.4 27.9 1.0
C C:GLU329 3.4 25.7 1.0
CG C:ASP330 3.7 28.3 1.0
CA C:ASP330 3.8 25.3 1.0
CB C:ASP324 3.9 26.3 1.0
CA C:CA403 3.9 31.8 1.0
O C:HOH406 4.0 36.2 1.0
N C:ASP330 4.0 26.1 1.0
OD2 C:ASP324 4.2 25.9 1.0
CB C:ASP330 4.3 23.9 1.0
CZ C:PHE304 4.4 27.5 1.0
CA C:ASP324 4.4 26.7 1.0
N C:GLU329 4.4 26.5 1.0
OD2 C:ASP342 4.5 23.6 1.0
CA C:GLU329 4.5 26.8 1.0
CB C:ASP297 4.5 28.1 1.0
CG C:GLU301 4.6 30.6 1.0
O C:HOH493 4.6 39.3 1.0
OD2 C:ASP330 4.7 24.6 1.0
N C:GLY302 4.7 32.5 1.0
O C:ASP297 4.9 29.6 1.0
CE1 C:PHE304 4.9 26.8 1.0
O C:HOH423 4.9 29.7 1.0

Calcium binding site 9 out of 9 in 2ric

Go back to Calcium Binding Sites List in 2ric
Calcium binding site 9 out of 9 in the Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose


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 the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptopyranosyl-(1-3)-L-Glycero-D-Manno-Heptopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:31.8
occ:1.00
 OE1 C:GLU301 2.5 27.6 1.0
O C:HOH487 2.6 28.4 1.0
OD1 C:ASP330 2.6 28.3 1.0
OD2 C:ASP330 2.6 24.6 1.0
O C:HOH409 2.6 29.3 1.0
O C:HOH406 2.7 36.2 1.0
O C:HOH547 2.8 51.1 1.0
CG C:ASP330 3.0 28.3 1.0
CD C:GLU301 3.7 30.3 1.0
CA C:CA402 3.9 27.3 1.0
O C:HOH455 4.1 33.2 1.0
O C:ASP297 4.3 29.6 1.0
CB C:GLU301 4.3 33.1 1.0
OD1 C:ASP324 4.4 25.9 1.0
CG C:GLU301 4.4 30.6 1.0
CB C:ASP330 4.4 23.9 1.0
O C:HOH544 4.5 43.3 1.0
O C:HOH450 4.6 41.8 1.0
OE2 C:GLU301 4.6 27.0 1.0
OD1 C:ASP297 4.7 27.9 1.0
CA C:GLU301 4.7 33.9 1.0
O C:HOH434 4.9 29.9 1.0
OD2 C:ASP297 4.9 27.9 1.0
OD2 C:ASP324 4.9 25.9 1.0

Reference:

H.Wang, J.Head, P.Kosma, H.Brade, S.Muller-Loennies, S.Sheikh, B.Mcdonald, K.Smith, T.Cafarella, B.Seaton, E.Crouch. Recognition of Heptoses and the Inner Core of Bacterial Lipopolysaccharides By Surfactant Protein D. Biochemistry V. 47 710 2008.
ISSN: ISSN 0006-2960
PubMed: 18092821
DOI: 10.1021/BI7020553
Page generated: Tue Jul 8 08:15:04 2025

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