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Calcium in PDB 2ork: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Inositol-1-Phosphate

Protein crystallography data

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Inositol-1-Phosphate, PDB code: 2ork 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) 38.66 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.403, 108.010, 55.701, 90.00, 91.83, 90.00
R / Rfree (%) 18.6 / 22.6

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

Calcium binding site 1 out of 9 in 2ork

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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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:15.0
occ:1.00
 OD1 A:ASN341 2.4 12.2 1.0
OD1 A:ASP342 2.4 13.4 1.0
OE1 A:GLU329 2.5 15.5 1.0
OD1 A:ASN323 2.5 14.8 1.0
O A:HOH610 2.6 22.7 1.0
OE1 A:GLU321 2.6 15.6 1.0
O A:ASP342 2.7 12.4 1.0
O A:HOH609 2.7 22.6 1.0
CG A:ASN341 3.4 13.3 1.0
CD A:GLU321 3.4 16.7 1.0
CG A:ASP342 3.5 13.7 1.0
CG A:ASN323 3.5 18.5 1.0
CD A:GLU329 3.5 12.0 1.0
C A:ASP342 3.7 12.8 1.0
OE2 A:GLU321 3.7 18.5 1.0
OE2 A:GLU329 3.8 11.5 1.0
N A:ASP342 3.8 12.7 1.0
ND2 A:ASN341 3.8 13.4 1.0
ND2 A:ASN323 3.9 21.3 1.0
CA A:ASP342 4.1 13.3 1.0
N A:ASN323 4.2 16.7 1.0
OD2 A:ASP342 4.2 14.1 1.0
CB A:ASP342 4.4 13.5 1.0
CB A:ASP325 4.4 18.0 1.0
C A:ASN341 4.6 13.3 1.0
CG A:GLU321 4.7 15.8 1.0
CB A:ASN323 4.7 16.3 1.0
CB A:ASN341 4.7 13.1 1.0
N A:ASP325 4.7 16.3 1.0
N A:ASP324 4.8 15.0 1.0
CG A:GLU329 4.8 14.9 1.0
N A:ARG343 4.8 12.9 1.0
CA A:ASN323 4.8 16.7 1.0
CA A:ASN341 4.9 13.5 1.0
CB A:GLU329 4.9 14.2 1.0

Calcium binding site 2 out of 9 in 2ork

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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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:13.9
occ:1.00
 OD1 A:ASP330 2.3 12.9 1.0
OD1 A:ASP324 2.4 12.3 1.0
OE2 A:GLU301 2.5 14.3 1.0
O A:GLU329 2.5 12.1 1.0
OD2 A:ASP297 2.5 14.9 1.0
OE1 A:GLU301 2.5 11.4 1.0
O A:HOH588 2.6 13.8 1.0
OD1 A:ASP297 2.6 13.0 1.0
CD A:GLU301 2.8 12.4 1.0
CG A:ASP297 2.9 15.4 1.0
CG A:ASP324 3.3 14.8 1.0
C A:GLU329 3.4 13.5 1.0
CG A:ASP330 3.4 12.3 1.0
CA A:ASP330 3.8 13.0 1.0
CA A:CA403 3.8 23.6 1.0
CB A:ASP324 3.9 15.5 1.0
N A:ASP330 4.0 12.5 1.0
CB A:ASP330 4.1 12.2 1.0
OD2 A:ASP324 4.2 12.2 1.0
N A:GLU329 4.2 17.1 1.0
CG A:GLU301 4.4 15.6 1.0
CA A:GLU329 4.4 14.9 1.0
OD2 A:ASP330 4.4 14.1 1.0
O A:HOH590 4.4 22.8 1.0
CZ A:PHE304 4.5 16.9 1.0
CB A:ASP297 4.5 16.0 1.0
CA A:ASP324 4.5 15.4 1.0
OD2 A:ASP342 4.6 14.1 1.0
N A:GLY302 4.7 17.7 1.0
O A:HOH587 4.7 15.7 1.0
O A:ASP297 4.8 17.4 1.0
O A:HOH436 4.9 19.6 1.0
CE1 A:PHE304 4.9 16.3 1.0
O A:HOH414 5.0 21.7 1.0
CB A:GLU329 5.0 14.2 1.0

Calcium binding site 3 out of 9 in 2ork

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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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:23.6
occ:1.00
 O A:HOH604 2.1 35.3 1.0
OE1 A:GLU301 2.3 11.4 1.0
OD2 A:ASP330 2.4 14.1 1.0
OD1 A:ASP330 2.4 12.9 1.0
O A:HOH590 2.5 22.8 1.0
O A:HOH605 2.5 22.9 1.0
O A:HOH587 2.6 15.7 1.0
CG A:ASP330 2.8 12.3 1.0
CD A:GLU301 3.5 12.4 1.0
O A:HOH589 3.7 31.4 1.0
CA A:CA402 3.8 13.9 1.0
OD1 A:ASP324 4.0 12.3 1.0
CB A:ASP330 4.3 12.2 1.0
CG A:GLU301 4.3 15.6 1.0
OE2 A:GLU301 4.4 14.3 1.0
O A:HOH477 4.5 32.0 1.0
CB A:GLU301 4.5 17.3 1.0
OD2 A:ASP324 4.6 12.2 1.0
O A:ASP297 4.7 17.4 1.0
CG A:ASP324 4.7 14.8 1.0
O A:GLY327 4.7 25.3 1.0
OD1 A:ASP297 4.8 13.0 1.0
O A:HOH472 4.9 24.7 1.0

Calcium binding site 4 out of 9 in 2ork

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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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:14.7
occ:1.00
 OD1 B:ASP342 2.2 12.6 1.0
OD1 B:ASN341 2.3 15.7 1.0
OD1 B:ASN323 2.5 16.7 1.0
OE1 B:GLU329 2.5 14.7 1.0
OE1 B:GLU321 2.5 13.0 1.0
O B:ASP342 2.6 13.3 1.0
O4 B:IPD995 2.6 16.9 1.0
O5 B:IPD995 2.7 21.2 1.0
CG B:ASP342 3.3 12.5 1.0
CD B:GLU321 3.3 14.1 1.0
CG B:ASN341 3.4 15.3 1.0
CG B:ASN323 3.4 16.8 1.0
CD B:GLU329 3.4 15.0 1.0
C5 B:IPD995 3.5 24.0 1.0
C4 B:IPD995 3.5 24.8 1.0
C B:ASP342 3.6 13.9 1.0
OE2 B:GLU321 3.6 14.2 1.0
N B:ASP342 3.7 13.7 1.0
OE2 B:GLU329 3.7 16.5 1.0
ND2 B:ASN341 3.8 16.7 1.0
ND2 B:ASN323 3.9 16.9 1.0
CA B:ASP342 4.0 13.1 1.0
OD2 B:ASP342 4.0 16.4 1.0
N B:ASN323 4.2 15.5 1.0
CB B:ASP342 4.2 13.3 1.0
C B:ASN341 4.5 13.6 1.0
CB B:ASN323 4.6 15.3 1.0
CG B:GLU321 4.6 14.9 1.0
CB B:ASP325 4.6 21.0 1.0
CB B:ASN341 4.6 13.9 1.0
N B:ASP324 4.7 17.1 1.0
CG B:GLU329 4.7 15.4 1.0
N B:ASP325 4.7 19.3 1.0
N B:ARG343 4.8 13.5 1.0
CA B:ASN323 4.8 16.1 1.0
CA B:ASN341 4.8 13.4 1.0
CB B:GLU329 4.9 16.0 1.0
C3 B:IPD995 4.9 29.9 1.0
C6 B:IPD995 5.0 28.0 1.0
C B:ASN323 5.0 16.9 1.0
CB B:GLU321 5.0 14.9 1.0

Calcium binding site 5 out of 9 in 2ork

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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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:19.7
occ:1.00
 O B:HOH1137 2.4 18.5 1.0
O B:GLU329 2.4 15.2 1.0
OD1 B:ASP330 2.4 14.2 1.0
OE1 B:GLU301 2.5 21.1 1.0
OD1 B:ASP324 2.6 15.7 1.0
OD2 B:ASP297 2.6 23.4 1.0
OE2 B:GLU301 2.6 20.8 1.0
OD1 B:ASP297 2.6 18.0 1.0
CD B:GLU301 2.9 22.5 1.0
CG B:ASP297 3.0 21.1 1.0
CG B:ASP324 3.3 20.1 1.0
C B:GLU329 3.4 15.7 1.0
CG B:ASP330 3.6 17.9 1.0
O B:HOH1136 3.8 16.7 1.0
CA B:ASP330 3.8 14.8 1.0
CB B:ASP324 3.9 16.9 1.0
CA B:CA403 4.0 36.4 1.0
N B:ASP330 4.0 14.8 1.0
OD2 B:ASP324 4.1 16.4 1.0
CB B:ASP330 4.3 15.1 1.0
N B:GLU329 4.4 17.9 1.0
CG B:GLU301 4.4 25.2 1.0
CA B:GLU329 4.4 16.8 1.0
CB B:ASP297 4.5 20.5 1.0
CZ B:PHE304 4.5 18.3 1.0
CA B:ASP324 4.5 18.2 1.0
OD2 B:ASP342 4.6 16.4 1.0
OD2 B:ASP330 4.6 18.5 1.0
N B:GLY302 4.8 27.8 1.0
O B:HOH1139 4.8 22.6 1.0
O B:ASP297 4.9 21.8 1.0
O B:HOH1141 4.9 30.1 1.0
CE1 B:PHE304 5.0 18.5 1.0
CA B:GLU301 5.0 27.5 1.0

Calcium binding site 6 out of 9 in 2ork

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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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:36.4
occ:1.00
 O B:HOH1139 2.2 22.6 1.0
O B:HOH1136 2.2 16.7 1.0
O B:HOH1143 2.5 33.5 1.0
OE1 B:GLU301 2.5 21.1 1.0
OD1 B:ASP330 2.5 14.2 1.0
O B:HOH1030 2.5 29.5 1.0
OD2 B:ASP330 2.6 18.5 1.0
CG B:ASP330 2.9 17.9 1.0
CD B:GLU301 3.7 22.5 1.0
CA B:CA402 4.0 19.7 1.0
O B:ASP297 4.3 21.8 1.0
O B:HOH1111 4.3 42.3 1.0
OD1 B:ASP324 4.4 15.7 1.0
CB B:GLU301 4.4 27.1 1.0
CB B:ASP330 4.4 15.1 1.0
CG B:GLU301 4.5 25.2 1.0
OE2 B:GLU301 4.7 20.8 1.0
OD1 B:ASP297 4.7 18.0 1.0
CA B:GLU301 4.8 27.5 1.0
O B:GLY327 4.8 20.0 1.0
OD2 B:ASP324 4.8 16.4 1.0
O B:HOH1032 4.9 22.3 1.0
OD2 B:ASP297 5.0 23.4 1.0

Calcium binding site 7 out of 9 in 2ork

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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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:14.3
occ:1.00
 OD1 C:ASP342 2.2 12.8 1.0
OE1 C:GLU329 2.3 13.5 1.0
OD1 C:ASN341 2.4 14.1 1.0
OD1 C:ASN323 2.5 15.1 1.0
O4 C:IPD995 2.6 19.1 1.0
O C:ASP342 2.6 13.6 1.0
O5 C:IPD995 2.6 21.9 1.0
OE1 C:GLU321 2.7 14.7 1.0
CG C:ASP342 3.3 13.5 1.0
CD C:GLU329 3.4 14.1 1.0
CG C:ASN341 3.4 15.4 1.0
C5 C:IPD995 3.4 24.0 1.0
CG C:ASN323 3.5 15.7 1.0
C4 C:IPD995 3.5 22.4 1.0
CD C:GLU321 3.5 14.2 1.0
C C:ASP342 3.6 14.5 1.0
OE2 C:GLU329 3.7 15.1 1.0
N C:ASP342 3.7 14.5 1.0
OE2 C:GLU321 3.8 14.9 1.0
ND2 C:ASN341 3.9 15.9 1.0
ND2 C:ASN323 4.0 19.8 1.0
CA C:ASP342 4.0 13.8 1.0
OD2 C:ASP342 4.1 12.7 1.0
N C:ASN323 4.2 14.3 1.0
CB C:ASP342 4.3 13.7 1.0
C C:ASN341 4.6 14.2 1.0
CG C:GLU329 4.6 15.5 1.0
CB C:ASN323 4.7 15.3 1.0
CB C:ASP325 4.7 18.8 1.0
CG C:GLU321 4.7 14.2 1.0
N C:ASP325 4.7 16.6 1.0
CB C:ASN341 4.7 13.3 1.0
N C:ASP324 4.8 15.4 1.0
N C:ARG343 4.8 15.6 1.0
CB C:GLU329 4.8 16.7 1.0
CA C:ASN323 4.8 14.6 1.0
C3 C:IPD995 4.8 25.2 1.0
CA C:ASN341 4.9 14.1 1.0
C6 C:IPD995 4.9 25.4 1.0

Calcium binding site 8 out of 9 in 2ork

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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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:19.2
occ:1.00
 O C:HOH1126 2.4 12.7 1.0
O C:GLU329 2.4 16.8 1.0
OD1 C:ASP330 2.5 16.1 1.0
OE1 C:GLU301 2.5 17.4 1.0
OE2 C:GLU301 2.5 19.1 1.0
OD2 C:ASP297 2.6 18.7 1.0
OD1 C:ASP324 2.6 14.3 1.0
OD1 C:ASP297 2.7 16.0 1.0
CD C:GLU301 2.9 19.1 1.0
CG C:ASP297 3.0 19.7 1.0
CG C:ASP324 3.4 16.4 1.0
C C:GLU329 3.4 16.9 1.0
CG C:ASP330 3.6 18.4 1.0
O C:HOH1127 3.7 19.5 1.0
CA C:ASP330 3.8 16.5 1.0
CB C:ASP324 3.9 14.8 1.0
CA C:CA403 3.9 28.9 1.0
N C:ASP330 4.0 16.1 1.0
OD2 C:ASP324 4.2 15.0 1.0
CB C:ASP330 4.3 16.0 1.0
CG C:GLU301 4.4 22.1 1.0
CA C:ASP324 4.4 15.6 1.0
N C:GLU329 4.4 18.6 1.0
CA C:GLU329 4.5 17.2 1.0
CZ C:PHE304 4.5 17.9 1.0
OD2 C:ASP342 4.5 12.7 1.0
CB C:ASP297 4.5 19.9 1.0
OD2 C:ASP330 4.6 19.3 1.0
N C:GLY302 4.7 22.8 1.0
O C:ASP297 4.8 22.3 1.0
O C:HOH1130 4.8 19.3 1.0
O C:HOH1000 4.8 15.3 1.0
CE1 C:PHE304 4.9 15.8 1.0
CA C:GLU301 5.0 23.7 1.0

Calcium binding site 9 out of 9 in 2ork

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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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:28.9
occ:1.00
 O C:HOH1130 2.2 19.3 1.0
O C:HOH1127 2.2 19.5 1.0
OE1 C:GLU301 2.3 17.4 1.0
O C:HOH1088 2.5 32.7 1.0
O C:HOH1129 2.5 23.2 1.0
OD1 C:ASP330 2.6 16.1 1.0
OD2 C:ASP330 2.6 19.3 1.0
CG C:ASP330 2.9 18.4 1.0
CD C:GLU301 3.5 19.1 1.0
CA C:CA402 3.9 19.2 1.0
O C:HOH1025 4.1 22.6 1.0
CB C:GLU301 4.1 22.8 1.0
CG C:GLU301 4.2 22.1 1.0
O C:ASP297 4.3 22.3 1.0
OD1 C:ASP324 4.3 14.3 1.0
CB C:ASP330 4.4 16.0 1.0
OE2 C:GLU301 4.5 19.1 1.0
OD1 C:ASP297 4.7 16.0 1.0
CA C:GLU301 4.7 23.7 1.0
O C:HOH1143 4.8 42.4 1.0
OD2 C:ASP324 4.8 15.0 1.0
CG C:ASP324 4.9 16.4 1.0
O C:HOH1060 5.0 26.2 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 14:41:33 2024

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