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Calcium in PDB 3ikr: Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D

Protein crystallography data

The structure of Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D, PDB code: 3ikr 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) 39.79 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.520, 108.450, 55.820, 90.00, 91.25, 90.00
R / Rfree (%) 19.3 / 21.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D (pdb code 3ikr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D, PDB code: 3ikr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3ikr

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Calcium binding site 1 out of 10 in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric 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 Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:14.5
occ:1.00
 OD1 A:ASP342 2.3 14.9 1.0
OD1 A:ASN341 2.4 15.4 1.0
OE1 A:GLU329 2.4 15.2 1.0
OD1 A:ASN323 2.5 16.2 1.0
O3 A:MAN405 2.5 23.6 1.0
O4 A:MAN405 2.6 17.4 1.0
O A:ASP342 2.6 14.8 1.0
OE1 A:GLU321 2.6 18.7 1.0
C4 A:MAN405 3.3 26.9 1.0
CG A:ASP342 3.3 15.5 1.0
C3 A:MAN405 3.3 28.1 1.0
CG A:ASN323 3.4 18.8 1.0
CG A:ASN341 3.4 15.7 1.0
CD A:GLU329 3.4 13.1 1.0
CD A:GLU321 3.5 19.2 1.0
C A:ASP342 3.7 15.3 1.0
OE2 A:GLU329 3.7 14.9 1.0
ND2 A:ASN323 3.7 21.3 1.0
N A:ASP342 3.8 14.0 1.0
ND2 A:ASN341 3.8 16.7 1.0
OE2 A:GLU321 3.8 20.8 1.0
OD2 A:ASP342 4.0 13.7 1.0
CA A:ASP342 4.1 13.6 1.0
N A:ASN323 4.2 16.2 1.0
CB A:ASP342 4.3 13.2 1.0
C A:ASN341 4.6 15.7 1.0
CB A:ASP325 4.6 20.3 1.0
CB A:ASN323 4.6 16.7 1.0
N A:ASP325 4.7 17.0 1.0
N A:ASP324 4.7 15.1 1.0
CB A:ASN341 4.7 15.2 1.0
CG A:GLU321 4.7 19.6 1.0
C2 A:MAN405 4.7 30.5 1.0
C5 A:MAN405 4.7 29.3 1.0
CG A:GLU329 4.7 14.9 1.0
CA A:ASN323 4.8 15.7 1.0
N A:ARG343 4.8 14.6 1.0
CA A:ASN341 4.9 14.6 1.0
O2 A:MAN405 4.9 33.4 1.0
CB A:GLU329 5.0 14.9 1.0

Calcium binding site 2 out of 10 in 3ikr

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Calcium binding site 2 out of 10 in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric 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 Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:13.3
occ:1.00
 O A:HOH66 2.4 13.7 1.0
OD1 A:ASP330 2.4 16.5 1.0
OE2 A:GLU301 2.5 14.2 1.0
OD1 A:ASP324 2.5 16.2 1.0
O A:GLU329 2.5 13.6 1.0
OD2 A:ASP297 2.5 15.6 1.0
OE1 A:GLU301 2.5 15.8 1.0
OD1 A:ASP297 2.7 14.8 1.0
CD A:GLU301 2.8 15.4 1.0
CG A:ASP297 2.9 14.4 1.0
CG A:ASP324 3.3 17.4 1.0
C A:GLU329 3.3 14.0 1.0
CG A:ASP330 3.5 17.1 1.0
CA A:ASP330 3.8 13.5 1.0
CA A:CA403 3.9 15.8 1.0
N A:ASP330 3.9 13.6 1.0
CB A:ASP324 4.0 15.0 1.0
OD2 A:ASP324 4.1 16.1 1.0
CB A:ASP330 4.2 13.4 1.0
N A:GLU329 4.3 16.8 1.0
CG A:GLU301 4.3 17.0 1.0
O A:HOH108 4.3 21.8 1.0
CZ A:PHE304 4.4 14.6 1.0
CA A:GLU329 4.4 14.1 1.0
OD2 A:ASP330 4.5 16.4 1.0
CB A:ASP297 4.5 15.6 1.0
CA A:ASP324 4.5 14.2 1.0
N A:GLY302 4.6 17.0 1.0
OD2 A:ASP342 4.6 13.7 1.0
O A:HOH363 4.7 19.4 1.0
O A:ASP297 4.9 16.2 1.0
O A:HOH68 4.9 21.8 1.0
CE1 A:PHE304 4.9 14.7 1.0
CB A:GLU329 4.9 14.9 1.0
O A:HOH53 4.9 17.1 1.0
CA A:GLU301 5.0 16.7 1.0

Calcium binding site 3 out of 10 in 3ikr

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Calcium binding site 3 out of 10 in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric 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 Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:15.8
occ:1.00
 O A:HOH428 2.3 29.6 1.0
OE1 A:GLU301 2.3 15.8 1.0
O A:HOH108 2.4 21.8 1.0
O A:HOH100 2.4 22.3 1.0
OD2 A:ASP330 2.4 16.4 1.0
O A:HOH53 2.5 17.1 1.0
OD1 A:ASP330 2.6 16.5 1.0
CG A:ASP330 2.9 17.1 1.0
CD A:GLU301 3.5 15.4 1.0
CA A:CA402 3.9 13.3 1.0
CG A:GLU301 4.3 17.0 1.0
OD1 A:ASP324 4.3 16.2 1.0
CB A:GLU301 4.3 16.6 1.0
CB A:ASP330 4.4 13.4 1.0
OE2 A:GLU301 4.4 14.2 1.0
O A:ASP297 4.5 16.2 1.0
OD2 A:ASP324 4.7 16.1 1.0
O A:HOH516 4.7 38.4 1.0
O A:GLY327 4.8 20.9 1.0
OD1 A:ASP297 4.8 14.8 1.0
CA A:GLU301 4.8 16.7 1.0
CG A:ASP324 4.9 17.4 1.0
O A:HOH32 4.9 22.1 1.0
OD2 A:ASP297 5.0 15.6 1.0

Calcium binding site 4 out of 10 in 3ikr

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Calcium binding site 4 out of 10 in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric 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 Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:19.1
occ:1.00
 OE1 A:GLU232 2.2 19.8 1.0
OE1 B:GLU232 2.2 20.3 1.0
OE1 C:GLU232 2.2 16.6 1.0
O B:HOH67 2.3 19.3 1.0
O B:HOH36 2.4 18.5 1.0
O C:HOH25 2.4 19.1 1.0
CD A:GLU232 3.2 18.6 1.0
CD B:GLU232 3.2 20.3 1.0
CD C:GLU232 3.3 18.0 1.0
OE2 A:GLU232 3.8 19.1 1.0
OE2 B:GLU232 3.8 19.9 1.0
OE2 C:GLU232 3.8 16.4 1.0
CA A:GLU232 4.2 13.4 1.0
CA B:GLU232 4.2 15.6 1.0
NZ C:LYS246 4.3 15.2 1.0
CA C:GLU232 4.3 12.8 1.0
CB A:GLU232 4.3 14.7 1.0
CG A:GLU232 4.3 17.5 1.0
NZ B:LYS246 4.4 15.7 1.0
O B:GLU232 4.4 16.1 1.0
CG B:GLU232 4.4 18.1 1.0
CG C:GLU232 4.4 13.7 1.0
CB B:GLU232 4.4 15.9 1.0
CB C:GLU232 4.4 13.1 1.0
O A:GLU232 4.4 14.4 1.0
O C:GLU232 4.5 14.8 1.0
NZ A:LYS246 4.5 14.2 1.0
O C:HOH51 4.8 28.6 1.0
C B:GLU232 4.8 15.6 1.0
C A:GLU232 4.8 13.7 1.0
C C:GLU232 4.9 13.3 1.0
O B:HOH430 4.9 23.2 1.0

Calcium binding site 5 out of 10 in 3ikr

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Calcium binding site 5 out of 10 in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric 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 Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:11.5
occ:1.00
 OD1 B:ASP342 2.3 12.4 1.0
OD1 B:ASN341 2.4 12.4 1.0
OD1 B:ASN323 2.4 12.9 1.0
OE1 B:GLU329 2.5 12.5 1.0
OE1 B:GLU321 2.5 14.6 1.0
O4 B:MAN405 2.6 15.0 1.0
O B:ASP342 2.6 11.7 1.0
O3 B:MAN405 2.6 15.2 1.0
CG B:ASP342 3.3 12.7 1.0
C4 B:MAN405 3.4 22.2 1.0
C3 B:MAN405 3.4 20.4 1.0
CG B:ASN341 3.4 11.5 1.0
CG B:ASN323 3.4 12.7 1.0
CD B:GLU321 3.4 14.5 1.0
CD B:GLU329 3.4 12.3 1.0
C B:ASP342 3.6 11.6 1.0
N B:ASP342 3.7 11.2 1.0
OE2 B:GLU321 3.8 15.5 1.0
OE2 B:GLU329 3.8 13.9 1.0
ND2 B:ASN341 3.8 13.0 1.0
ND2 B:ASN323 3.9 14.9 1.0
OD2 B:ASP342 4.0 12.8 1.0
CA B:ASP342 4.1 11.9 1.0
N B:ASN323 4.2 12.3 1.0
CB B:ASP342 4.3 10.8 1.0
C B:ASN341 4.5 12.6 1.0
CB B:ASN323 4.6 14.0 1.0
CG B:GLU321 4.6 13.5 1.0
CB B:ASN341 4.7 12.7 1.0
CB B:ASP325 4.7 17.0 1.0
N B:ASP324 4.7 13.3 1.0
N B:ASP325 4.7 14.4 1.0
CG B:GLU329 4.7 14.3 1.0
N B:ARG343 4.8 11.6 1.0
C2 B:MAN405 4.8 25.3 1.0
C5 B:MAN405 4.8 26.5 1.0
CA B:ASN323 4.8 12.5 1.0
CA B:ASN341 4.8 12.2 1.0
CB B:GLU329 4.9 14.6 1.0

Calcium binding site 6 out of 10 in 3ikr

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Calcium binding site 6 out of 10 in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric 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 Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:13.3
occ:1.00
 O B:HOH14 2.3 14.8 1.0
OD1 B:ASP330 2.4 14.9 1.0
OE1 B:GLU301 2.5 15.6 1.0
O B:GLU329 2.5 13.6 1.0
OE2 B:GLU301 2.5 16.2 1.0
OD2 B:ASP297 2.5 17.9 1.0
OD1 B:ASP324 2.6 15.8 1.0
OD1 B:ASP297 2.7 15.7 1.0
CD B:GLU301 2.8 17.3 1.0
CG B:ASP297 3.0 15.8 1.0
CG B:ASP324 3.4 16.6 1.0
C B:GLU329 3.4 13.1 1.0
CG B:ASP330 3.5 16.7 1.0
CA B:ASP330 3.8 12.9 1.0
CA B:CA403 3.9 17.8 1.0
O B:HOH15 3.9 17.4 1.0
CB B:ASP324 3.9 15.0 1.0
N B:ASP330 4.0 12.8 1.0
CB B:ASP330 4.2 14.0 1.0
OD2 B:ASP324 4.3 16.2 1.0
CG B:GLU301 4.3 17.8 1.0
O B:HOH77 4.4 24.6 1.0
N B:GLU329 4.5 15.1 1.0
CB B:ASP297 4.5 15.6 1.0
OD2 B:ASP330 4.5 16.7 1.0
CA B:GLU329 4.5 14.2 1.0
CA B:ASP324 4.5 14.3 1.0
CZ B:PHE304 4.5 15.7 1.0
OD2 B:ASP342 4.6 12.8 1.0
N B:GLY302 4.7 20.5 1.0
O B:ASP297 4.8 17.9 1.0
CA B:GLU301 4.9 19.9 1.0
O B:HOH84 4.9 24.8 1.0
CE1 B:PHE304 5.0 15.6 1.0
O B:HOH364 5.0 20.1 1.0
CB B:GLU301 5.0 20.8 1.0

Calcium binding site 7 out of 10 in 3ikr

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Calcium binding site 7 out of 10 in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric 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 Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:17.8
occ:1.00
 O B:HOH364 2.3 20.1 1.0
O B:HOH15 2.3 17.4 1.0
OE1 B:GLU301 2.4 15.6 1.0
O B:HOH143 2.4 24.1 1.0
O B:HOH26 2.4 18.7 1.0
OD2 B:ASP330 2.5 16.7 1.0
OD1 B:ASP330 2.5 14.9 1.0
CG B:ASP330 2.8 16.7 1.0
CD B:GLU301 3.6 17.3 1.0
CA B:CA402 3.9 13.3 1.0
CB B:GLU301 4.2 20.8 1.0
O B:HOH45 4.2 21.2 1.0
CG B:GLU301 4.3 17.8 1.0
OD1 B:ASP324 4.3 15.8 1.0
O B:ASP297 4.3 17.9 1.0
CB B:ASP330 4.4 14.0 1.0
OE2 B:GLU301 4.5 16.2 1.0
O B:HOH368 4.7 37.1 1.0
CA B:GLU301 4.7 19.9 1.0
OD1 B:ASP297 4.7 15.7 1.0
O B:HOH389 4.8 37.3 1.0
O B:HOH384 4.8 33.5 1.0
OD2 B:ASP297 4.9 17.9 1.0
O B:HOH44 4.9 20.0 1.0
OD2 B:ASP324 5.0 16.2 1.0
CG B:ASP297 5.0 15.8 1.0
O B:GLY327 5.0 19.0 1.0

Calcium binding site 8 out of 10 in 3ikr

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Calcium binding site 8 out of 10 in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric 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 Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:13.5
occ:1.00
 OD1 C:ASP342 2.3 12.5 1.0
OD1 C:ASN341 2.4 13.5 1.0
OD1 C:ASN323 2.4 14.7 1.0
OE1 C:GLU329 2.5 15.3 1.0
OE1 C:GLU321 2.5 15.9 1.0
O4 C:MAN405 2.5 16.9 1.0
O C:ASP342 2.6 15.1 1.0
O3 C:MAN405 2.7 16.3 1.0
CG C:ASP342 3.3 13.5 1.0
CD C:GLU321 3.4 14.4 1.0
C4 C:MAN405 3.4 23.6 1.0
C3 C:MAN405 3.4 22.1 1.0
CG C:ASN341 3.4 14.2 1.0
CG C:ASN323 3.4 15.0 1.0
CD C:GLU329 3.5 15.9 1.0
C C:ASP342 3.6 14.7 1.0
N C:ASP342 3.7 13.6 1.0
OE2 C:GLU321 3.7 17.8 1.0
OE2 C:GLU329 3.8 16.4 1.0
ND2 C:ASN341 3.8 16.0 1.0
ND2 C:ASN323 4.0 18.6 1.0
OD2 C:ASP342 4.0 13.8 1.0
CA C:ASP342 4.1 14.1 1.0
N C:ASN323 4.1 14.0 1.0
CB C:ASP342 4.3 13.5 1.0
C C:ASN341 4.5 14.7 1.0
CG C:GLU321 4.6 14.5 1.0
CB C:ASN323 4.6 14.8 1.0
CB C:ASN341 4.7 13.6 1.0
CB C:ASP325 4.7 20.4 1.0
N C:ASP325 4.7 17.2 1.0
CG C:GLU329 4.8 14.8 1.0
N C:ASP324 4.8 14.8 1.0
CA C:ASN323 4.8 14.3 1.0
C5 C:MAN405 4.8 27.5 1.0
N C:ARG343 4.8 14.1 1.0
C2 C:MAN405 4.8 26.1 1.0
CA C:ASN341 4.9 14.7 1.0
CB C:GLU329 4.9 15.3 1.0
C C:ASN323 5.0 15.6 1.0

Calcium binding site 9 out of 10 in 3ikr

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Calcium binding site 9 out of 10 in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric 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 Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:15.7
occ:1.00
 OD1 C:ASP330 2.4 16.2 1.0
O C:GLU329 2.4 14.8 1.0
O C:HOH22 2.4 14.1 1.0
OE1 C:GLU301 2.5 18.5 1.0
OE2 C:GLU301 2.5 16.7 1.0
OD2 C:ASP297 2.5 19.9 1.0
OD1 C:ASP324 2.6 17.6 1.0
OD1 C:ASP297 2.7 16.8 1.0
CD C:GLU301 2.8 18.5 1.0
CG C:ASP297 3.0 18.6 1.0
C C:GLU329 3.4 14.7 1.0
CG C:ASP324 3.4 17.6 1.0
CG C:ASP330 3.5 20.0 1.0
CA C:ASP330 3.8 16.0 1.0
O C:HOH17 3.9 19.9 1.0
CA C:CA403 3.9 19.3 1.0
CB C:ASP324 3.9 16.2 1.0
N C:ASP330 4.0 16.0 1.0
CB C:ASP330 4.2 17.1 1.0
OD2 C:ASP324 4.3 16.2 1.0
CG C:GLU301 4.3 18.1 1.0
CA C:ASP324 4.4 16.2 1.0
N C:GLU329 4.4 17.8 1.0
CA C:GLU329 4.5 15.2 1.0
CZ C:PHE304 4.5 16.0 1.0
CB C:ASP297 4.5 17.0 1.0
OD2 C:ASP330 4.5 19.9 1.0
OD2 C:ASP342 4.6 13.8 1.0
N C:GLY302 4.7 20.0 1.0
O C:ASP297 4.8 20.7 1.0
O C:HOH125 4.9 23.1 1.0
CE1 C:PHE304 4.9 15.3 1.0
CA C:GLU301 4.9 20.7 1.0
C C:ASP330 5.0 15.1 1.0
CB C:GLU329 5.0 15.3 1.0

Calcium binding site 10 out of 10 in 3ikr

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Calcium binding site 10 out of 10 in the Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric 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 10 of Crystal Structure of Alpha 1-4 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:19.3
occ:1.00
 OE1 C:GLU301 2.3 18.5 1.0
O C:HOH121 2.4 20.1 1.0
O C:HOH17 2.4 19.9 1.0
O C:HOH61 2.5 21.0 1.0
OD2 C:ASP330 2.5 19.9 1.0
OD1 C:ASP330 2.5 16.2 1.0
O C:HOH112 2.5 27.3 1.0
CG C:ASP330 2.8 20.0 1.0
CD C:GLU301 3.5 18.5 1.0
CA C:CA402 3.9 15.7 1.0
CB C:GLU301 4.1 20.4 1.0
CG C:GLU301 4.2 18.1 1.0
O C:HOH177 4.2 27.2 1.0
OD1 C:ASP324 4.3 17.6 1.0
CB C:ASP330 4.4 17.1 1.0
O C:ASP297 4.4 20.7 1.0
OE2 C:GLU301 4.4 16.7 1.0
CA C:GLU301 4.7 20.7 1.0
OD1 C:ASP297 4.7 16.8 1.0
O C:HOH412 4.8 34.1 1.0
OD2 C:ASP297 4.9 19.9 1.0
OD2 C:ASP324 4.9 16.2 1.0
O C:GLY327 5.0 20.8 1.0
CG C:ASP324 5.0 17.6 1.0
O C:HOH82 5.0 25.0 1.0

Reference:

A.K.Shrive, C.Martin, I.Burns, J.M.Paterson, J.D.Martin, J.P.Townsend, P.Waters, H.W.Clark, U.Kishore, K.B.M.Reid, T.J.Greenhough. Structural Characterisation of Ligand-Binding Determinants in Human Lung Surfactant Protein D: Influence of ASP325 J.Mol.Biol. V. 394 776 2009.
ISSN: ISSN 0022-2836
PubMed: 19799916
DOI: 10.1016/J.JMB.2009.09.057
Page generated: Sat Jul 13 11:36:08 2024

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