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Calcium in PDB 2os9: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Myoinositol

Protein crystallography data

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Myoinositol, PDB code: 2os9 was solved by J.F.Head, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.87 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.564, 108.692, 55.774, 90.00, 91.49, 90.00
R / Rfree (%) 19.5 / 22.3

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 Myoinositol (pdb code 2os9). 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 Myoinositol, PDB code: 2os9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2os9

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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 Myoinositol


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 Myoinositol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:20.8
occ:1.00
 OD1 A:ASP342 2.3 19.4 1.0
OD1 A:ASN341 2.4 21.6 1.0
OE1 A:GLU329 2.5 19.1 1.0
OD1 A:ASN323 2.5 21.4 1.0
OE1 A:GLU321 2.5 23.0 1.0
O1 A:INS631 2.5 31.1 1.0
O A:ASP342 2.6 18.4 1.0
O6 A:INS631 2.7 26.8 1.0
CD A:GLU321 3.4 24.2 1.0
CG A:ASN323 3.4 23.8 1.0
CG A:ASP342 3.4 20.6 1.0
CG A:ASN341 3.4 21.1 1.0
C1 A:INS631 3.5 34.4 1.0
C6 A:INS631 3.5 32.8 1.0
CD A:GLU329 3.5 19.3 1.0
C A:ASP342 3.6 19.0 1.0
OE2 A:GLU321 3.7 25.8 1.0
N A:ASP342 3.8 19.1 1.0
ND2 A:ASN323 3.8 22.1 1.0
ND2 A:ASN341 3.9 24.2 1.0
OE2 A:GLU329 3.9 20.3 1.0
CA A:ASP342 4.1 19.0 1.0
OD2 A:ASP342 4.2 18.7 1.0
N A:ASN323 4.3 22.6 1.0
CB A:ASP342 4.3 18.7 1.0
CB A:ASP325 4.5 24.8 1.0
C A:ASN341 4.6 20.6 1.0
CG A:GLU321 4.6 23.3 1.0
N A:ASP325 4.7 23.0 1.0
CB A:ASN323 4.7 22.0 1.0
CB A:ASN341 4.7 20.8 1.0
CG A:GLU329 4.8 20.3 1.0
N A:ASP324 4.8 21.3 1.0
N A:ARG343 4.8 18.5 1.0
CA A:ASN323 4.9 22.2 1.0
CB A:GLU329 4.9 20.5 1.0
C2 A:INS631 4.9 36.6 1.0
CA A:ASN341 4.9 20.7 1.0
C5 A:INS631 4.9 34.4 1.0

Calcium binding site 2 out of 9 in 2os9

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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 Myoinositol


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 Myoinositol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:19.7
occ:1.00
 OD1 A:ASP330 2.4 19.2 1.0
OD1 A:ASP324 2.4 20.7 1.0
O A:GLU329 2.5 18.9 1.0
O A:HOH651 2.5 21.0 1.0
OD2 A:ASP297 2.5 20.9 1.0
OE1 A:GLU301 2.5 19.6 1.0
OE2 A:GLU301 2.5 20.1 1.0
OD1 A:ASP297 2.7 20.9 1.0
CD A:GLU301 2.8 20.1 1.0
CG A:ASP297 3.0 19.7 1.0
CG A:ASP324 3.3 21.2 1.0
C A:GLU329 3.3 20.1 1.0
CG A:ASP330 3.5 20.2 1.0
CA A:ASP330 3.8 19.5 1.0
CA A:CA403 3.9 23.0 1.0
CB A:ASP324 3.9 21.1 1.0
N A:ASP330 3.9 19.5 1.0
OD2 A:ASP324 4.1 20.3 1.0
O A:HOH666 4.2 28.4 1.0
CB A:ASP330 4.2 19.6 1.0
N A:GLU329 4.3 22.1 1.0
CG A:GLU301 4.3 21.2 1.0
CZ A:PHE304 4.4 21.5 1.0
CA A:GLU329 4.4 20.8 1.0
OD2 A:ASP330 4.4 20.7 1.0
CB A:ASP297 4.5 20.8 1.0
CA A:ASP324 4.5 21.3 1.0
OD2 A:ASP342 4.6 18.7 1.0
N A:GLY302 4.6 22.9 1.0
O A:HOH650 4.8 21.1 1.0
O A:HOH647 4.8 25.8 1.0
CE1 A:PHE304 4.9 21.2 1.0
O A:ASP297 4.9 22.3 1.0
O A:HOH637 4.9 21.1 1.0
CB A:GLU329 4.9 20.5 1.0
CA A:GLU301 5.0 23.4 1.0

Calcium binding site 3 out of 9 in 2os9

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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 Myoinositol


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 Myoinositol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:23.0
occ:1.00
 O A:HOH666 2.3 28.4 1.0
OE1 A:GLU301 2.3 19.6 1.0
O A:HOH688 2.4 26.9 1.0
O A:HOH637 2.4 21.1 1.0
OD2 A:ASP330 2.4 20.7 1.0
O A:HOH788 2.5 48.5 1.0
OD1 A:ASP330 2.5 19.2 1.0
CG A:ASP330 2.8 20.2 1.0
CD A:GLU301 3.5 20.1 1.0
CA A:CA402 3.9 19.7 1.0
OD1 A:ASP324 4.2 20.7 1.0
CG A:GLU301 4.2 21.2 1.0
CB A:GLU301 4.3 22.5 1.0
CB A:ASP330 4.4 19.6 1.0
OE2 A:GLU301 4.4 20.1 1.0
O A:ASP297 4.5 22.3 1.0
OD1 A:ASP297 4.7 20.9 1.0
OD2 A:ASP324 4.7 20.3 1.0
O A:GLY327 4.7 25.5 1.0
CA A:GLU301 4.8 23.4 1.0
CG A:ASP324 4.9 21.2 1.0
O A:HOH648 4.9 24.1 1.0

Calcium binding site 4 out of 9 in 2os9

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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 Myoinositol


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 Myoinositol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:17.5
occ:1.00
 OD1 B:ASP342 2.3 16.2 1.0
OE1 B:GLU329 2.4 19.1 1.0
OD1 B:ASN323 2.4 17.2 1.0
OD1 B:ASN341 2.4 18.3 1.0
OE1 B:GLU321 2.5 16.0 1.0
O B:ASP342 2.5 16.5 1.0
O6 B:INS632 2.6 22.9 0.5
O6 B:INS632 2.6 15.2 0.5
O1 B:INS632 2.6 20.2 0.5
O1 B:INS632 2.7 18.5 0.5
CG B:ASP342 3.4 17.7 1.0
CD B:GLU329 3.4 17.8 1.0
CD B:GLU321 3.4 15.7 1.0
CG B:ASN323 3.4 19.2 1.0
CG B:ASN341 3.4 18.4 1.0
C6 B:INS632 3.5 22.3 0.5
C6 B:INS632 3.5 16.9 0.5
C1 B:INS632 3.5 22.0 0.5
C B:ASP342 3.5 18.0 1.0
C1 B:INS632 3.5 18.2 0.5
OE2 B:GLU321 3.7 19.2 1.0
OE2 B:GLU329 3.7 18.4 1.0
N B:ASP342 3.8 17.7 1.0
ND2 B:ASN341 3.9 19.1 1.0
ND2 B:ASN323 4.0 20.0 1.0
CA B:ASP342 4.0 17.9 1.0
OD2 B:ASP342 4.1 18.7 1.0
N B:ASN323 4.2 18.3 1.0
CB B:ASP342 4.3 18.3 1.0
CB B:ASP325 4.5 21.2 1.0
C B:ASN341 4.5 17.6 1.0
CB B:ASN323 4.6 18.2 1.0
CG B:GLU321 4.6 17.8 1.0
N B:ASP325 4.6 20.2 1.0
CG B:GLU329 4.7 19.1 1.0
N B:ARG343 4.7 18.1 1.0
CB B:ASN341 4.7 17.4 1.0
N B:ASP324 4.7 18.9 1.0
CA B:ASN323 4.8 18.6 1.0
CB B:GLU329 4.9 19.5 1.0
CA B:ASN341 4.9 17.2 1.0
C5 B:INS632 4.9 19.0 0.5
C5 B:INS632 4.9 23.6 0.5
C2 B:INS632 4.9 24.1 0.5
C2 B:INS632 4.9 20.5 0.5

Calcium binding site 5 out of 9 in 2os9

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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 Myoinositol


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 Myoinositol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:21.2
occ:1.00
 OD1 B:ASP330 2.4 21.2 1.0
OD2 B:ASP297 2.4 25.4 1.0
O B:GLU329 2.5 18.5 1.0
OE2 B:GLU301 2.5 22.9 1.0
OE1 B:GLU301 2.5 23.9 1.0
O B:HOH643 2.6 20.4 1.0
OD1 B:ASP324 2.6 20.4 1.0
OD1 B:ASP297 2.7 21.3 1.0
CD B:GLU301 2.9 25.5 1.0
CG B:ASP297 2.9 23.3 1.0
C B:GLU329 3.4 19.5 1.0
CG B:ASP324 3.4 22.0 1.0
CG B:ASP330 3.5 22.7 1.0
CA B:ASP330 3.8 19.7 1.0
CA B:CA403 3.9 25.8 1.0
O B:HOH655 3.9 23.7 1.0
N B:ASP330 4.0 19.3 1.0
CB B:ASP324 4.0 20.2 1.0
CB B:ASP330 4.2 20.2 1.0
OD2 B:ASP324 4.2 21.6 1.0
CG B:GLU301 4.4 27.5 1.0
OD2 B:ASP330 4.4 22.3 1.0
O B:HOH802 4.4 36.4 1.0
CB B:ASP297 4.4 23.1 1.0
CA B:GLU329 4.5 19.8 1.0
N B:GLU329 4.5 20.6 1.0
CA B:ASP324 4.5 19.9 1.0
CZ B:PHE304 4.5 25.2 1.0
OD2 B:ASP342 4.6 18.7 1.0
N B:GLY302 4.8 28.8 1.0
O B:ASP297 4.8 24.6 1.0
CE1 B:PHE304 5.0 24.5 1.0
O B:HOH703 5.0 34.4 1.0
CA B:GLU301 5.0 29.4 1.0
C B:ASP330 5.0 19.2 1.0

Calcium binding site 6 out of 9 in 2os9

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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 Myoinositol


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 Myoinositol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:25.8
occ:1.00
 OE1 B:GLU301 2.3 23.9 1.0
O B:HOH648 2.4 25.4 1.0
O B:HOH674 2.4 23.9 1.0
OD2 B:ASP330 2.5 22.3 1.0
O B:HOH655 2.5 23.7 1.0
O B:HOH697 2.5 33.8 1.0
OD1 B:ASP330 2.6 21.2 1.0
CG B:ASP330 2.8 22.7 1.0
CD B:GLU301 3.6 25.5 1.0
CA B:CA402 3.9 21.2 1.0
O B:HOH696 4.1 28.0 1.0
O B:ASP297 4.2 24.6 1.0
CB B:GLU301 4.2 29.4 1.0
CG B:GLU301 4.3 27.5 1.0
OD1 B:ASP324 4.3 20.4 1.0
CB B:ASP330 4.4 20.2 1.0
OE2 B:GLU301 4.5 22.9 1.0
O B:HOH754 4.6 41.8 1.0
OD1 B:ASP297 4.6 21.3 1.0
CA B:GLU301 4.7 29.4 1.0
O B:HOH719 4.7 39.8 1.0
O B:HOH786 4.8 47.8 1.0
OD2 B:ASP297 4.8 25.4 1.0
O B:HOH645 4.9 23.4 1.0
OD2 B:ASP324 4.9 21.6 1.0
O B:GLY327 4.9 24.1 1.0
CG B:ASP297 5.0 23.3 1.0
CG B:ASP324 5.0 22.0 1.0

Calcium binding site 7 out of 9 in 2os9

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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 Myoinositol


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 Myoinositol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:17.7
occ:1.00
 OE1 C:GLU329 2.3 17.4 1.0
OD1 C:ASP342 2.3 14.7 1.0
OD1 C:ASN341 2.4 17.5 1.0
OD1 C:ASN323 2.4 17.0 1.0
O1 C:INS633 2.5 23.8 0.5
O C:ASP342 2.5 16.5 1.0
O6 C:INS633 2.6 23.7 0.5
O6 C:INS633 2.6 15.2 0.5
OE1 C:GLU321 2.6 17.3 1.0
O1 C:INS633 2.7 13.4 0.5
CD C:GLU329 3.3 16.7 1.0
CG C:ASP342 3.4 14.9 1.0
C1 C:INS633 3.4 25.1 0.5
C6 C:INS633 3.4 25.1 0.5
CG C:ASN341 3.4 17.7 1.0
C6 C:INS633 3.4 17.1 0.5
C1 C:INS633 3.5 17.5 0.5
CD C:GLU321 3.5 16.7 1.0
CG C:ASN323 3.5 18.2 1.0
C C:ASP342 3.5 17.4 1.0
OE2 C:GLU329 3.7 19.3 1.0
N C:ASP342 3.8 16.8 1.0
OE2 C:GLU321 3.8 18.9 1.0
ND2 C:ASN341 3.9 18.7 1.0
CA C:ASP342 4.0 16.9 1.0
ND2 C:ASN323 4.1 19.2 1.0
OD2 C:ASP342 4.1 17.3 1.0
N C:ASN323 4.2 17.1 1.0
CB C:ASP342 4.3 15.9 1.0
CB C:ASP325 4.5 21.0 1.0
C C:ASN341 4.5 18.2 1.0
CG C:GLU329 4.6 16.1 1.0
CB C:ASN323 4.7 17.2 1.0
N C:ARG343 4.7 18.4 1.0
CG C:GLU321 4.7 16.2 1.0
N C:ASP325 4.7 19.6 1.0
CB C:ASN341 4.7 16.9 1.0
C2 C:INS633 4.7 25.8 0.5
N C:ASP324 4.7 17.4 1.0
CA C:ASN323 4.8 17.0 1.0
C5 C:INS633 4.8 26.4 0.5
C5 C:INS633 4.8 18.5 0.5
CB C:GLU329 4.8 18.9 1.0
O2 C:INS633 4.9 27.0 0.5
CA C:ASN341 4.9 17.8 1.0
C2 C:INS633 4.9 20.2 0.5

Calcium binding site 8 out of 9 in 2os9

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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 Myoinositol


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 Myoinositol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:20.2
occ:1.00
 O C:HOH642 2.4 19.7 1.0
O C:GLU329 2.4 19.1 1.0
OE2 C:GLU301 2.5 19.3 1.0
OD1 C:ASP330 2.5 21.8 1.0
OE1 C:GLU301 2.5 21.8 1.0
OD2 C:ASP297 2.5 24.9 1.0
OD1 C:ASP324 2.6 20.4 1.0
OD1 C:ASP297 2.6 22.1 1.0
CD C:GLU301 2.8 22.4 1.0
CG C:ASP297 2.9 23.0 1.0
CG C:ASP324 3.4 20.5 1.0
C C:GLU329 3.4 19.3 1.0
CG C:ASP330 3.6 22.7 1.0
CA C:ASP330 3.8 19.9 1.0
CB C:ASP324 3.9 18.7 1.0
CA C:CA403 3.9 25.9 1.0
O C:HOH644 3.9 21.9 1.0
N C:ASP330 4.0 19.2 1.0
OD2 C:ASP324 4.3 20.1 1.0
CB C:ASP330 4.3 19.8 1.0
CG C:GLU301 4.3 25.8 1.0
CB C:ASP297 4.4 23.8 1.0
CA C:ASP324 4.5 18.4 1.0
CA C:GLU329 4.5 19.6 1.0
N C:GLU329 4.5 21.5 1.0
CZ C:PHE304 4.5 22.6 1.0
OD2 C:ASP342 4.5 17.3 1.0
OD2 C:ASP330 4.5 22.7 1.0
N C:GLY302 4.6 28.0 1.0
O C:HOH717 4.7 31.3 1.0
O C:ASP297 4.9 26.1 1.0
CE1 C:PHE304 4.9 22.3 1.0
O C:HOH652 4.9 22.5 1.0
CA C:GLU301 5.0 28.8 1.0

Calcium binding site 9 out of 9 in 2os9

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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 Myoinositol


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 Myoinositol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:25.9
occ:1.00
 O C:HOH648 2.3 24.5 1.0
OE1 C:GLU301 2.4 21.8 1.0
O C:HOH674 2.4 23.3 1.0
OD2 C:ASP330 2.4 22.7 1.0
O C:HOH644 2.4 21.9 1.0
OD1 C:ASP330 2.5 21.8 1.0
O C:HOH685 2.6 26.6 1.0
CG C:ASP330 2.8 22.7 1.0
CD C:GLU301 3.5 22.4 1.0
CA C:CA402 3.9 20.2 1.0
O C:HOH688 4.1 28.2 1.0
CB C:GLU301 4.2 28.3 1.0
OD1 C:ASP324 4.2 20.4 1.0
CG C:GLU301 4.3 25.8 1.0
O C:ASP297 4.3 26.1 1.0
O C:HOH741 4.3 43.5 1.0
CB C:ASP330 4.3 19.8 1.0
OE2 C:GLU301 4.5 19.3 1.0
OD1 C:ASP297 4.6 22.1 1.0
CA C:GLU301 4.7 28.8 1.0
O C:HOH777 4.7 36.6 1.0
O C:HOH669 4.8 29.8 1.0
OD2 C:ASP324 4.9 20.1 1.0
CG C:ASP324 5.0 20.5 1.0
OD2 C:ASP297 5.0 24.9 1.0
O C:GLY327 5.0 23.9 1.0

Reference:

E.Crouch, B.Mcdonald, K.Smith, M.Roberts, T.Mealy, B.Seaton, J.Head. Critical Role of Arg/LYS343 in the Species-Dependent Recognition of Phosphatidylinositol By Pulmonary Surfactant Protein D. Biochemistry V. 46 5160 2007.
ISSN: ISSN 0006-2960
PubMed: 17417879
DOI: 10.1021/BI700037X
Page generated: Fri Jul 12 14:42:21 2024

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