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

Protein crystallography data

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Maltotriose, PDB code: 2ggu 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) 50.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.730, 108.930, 55.840, 90.00, 91.12, 90.00
R / Rfree (%) 22.1 / 24.8

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

Calcium binding site 1 out of 9 in 2ggu

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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 Maltotriose


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

b:17.9
occ:1.00
 OD1 A:ASP342 2.3 15.0 1.0
OD1 A:ASN341 2.4 16.6 1.0
OD1 A:ASN323 2.4 15.7 1.0
OE1 A:GLU329 2.4 16.3 1.0
OE1 A:GLU321 2.5 18.2 1.0
O A:ASP342 2.6 14.9 1.0
O3C A:MLR3505 2.6 22.4 1.0
O4C A:MLR3505 2.6 19.6 1.0
CG A:ASP342 3.3 16.4 1.0
CG A:ASN341 3.4 16.9 1.0
C3C A:MLR3505 3.4 21.5 1.0
CG A:ASN323 3.4 18.5 1.0
CD A:GLU329 3.4 14.9 1.0
CD A:GLU321 3.4 18.6 1.0
C4C A:MLR3505 3.4 22.0 1.0
C A:ASP342 3.6 15.7 1.0
N A:ASP342 3.7 14.0 1.0
OE2 A:GLU329 3.8 14.5 1.0
ND2 A:ASN341 3.8 14.1 1.0
OE2 A:GLU321 3.8 18.0 1.0
ND2 A:ASN323 3.9 19.6 1.0
OD2 A:ASP342 4.0 18.2 1.0
CA A:ASP342 4.1 13.8 1.0
N A:ASN323 4.2 18.3 1.0
CB A:ASP342 4.3 15.0 1.0
C A:ASN341 4.5 14.9 1.0
CB A:ASP325 4.5 20.9 1.0
N A:ASP325 4.6 18.4 1.0
CG A:GLU321 4.6 17.5 1.0
CB A:ASN323 4.6 17.7 1.0
N A:ASP324 4.7 17.0 1.0
CB A:ASN341 4.7 15.2 1.0
CG A:GLU329 4.7 17.1 1.0
N A:ARG343 4.8 14.0 1.0
CA A:ASN323 4.8 17.9 1.0
CA A:ASN341 4.8 14.7 1.0
C2C A:MLR3505 4.9 23.5 1.0
C5C A:MLR3505 4.9 23.4 1.0
CB A:GLU329 4.9 17.8 1.0

Calcium binding site 2 out of 9 in 2ggu

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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 Maltotriose


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

b:15.2
occ:1.00
 O A:HOH3600 2.2 17.0 1.0
OD2 A:ASP297 2.3 19.7 1.0
OD1 A:ASP324 2.4 17.9 1.0
O A:GLU329 2.4 17.9 1.0
OD1 A:ASP330 2.4 17.5 1.0
OE2 A:GLU301 2.5 16.9 1.0
OE1 A:GLU301 2.5 17.2 1.0
OD1 A:ASP297 2.6 14.6 1.0
CG A:ASP297 2.8 17.3 1.0
CD A:GLU301 2.8 16.3 1.0
C A:GLU329 3.3 17.2 1.0
CG A:ASP324 3.3 20.0 1.0
CG A:ASP330 3.5 18.2 1.0
CA A:ASP330 3.8 17.5 1.0
CA A:CA403 3.8 27.6 1.0
N A:ASP330 3.9 17.2 1.0
CB A:ASP324 4.0 17.2 1.0
O A:HOH3525 4.1 25.3 1.0
CB A:ASP330 4.2 17.4 1.0
OD2 A:ASP324 4.2 16.8 1.0
N A:GLU329 4.3 19.4 1.0
CG A:GLU301 4.3 21.2 1.0
CB A:ASP297 4.3 19.4 1.0
CA A:GLU329 4.4 19.9 1.0
CZ A:PHE304 4.4 18.5 1.0
OD2 A:ASP330 4.4 18.5 1.0
CA A:ASP324 4.6 17.3 1.0
N A:GLY302 4.6 21.7 1.0
OD2 A:ASP342 4.6 18.2 1.0
O A:HOH3602 4.8 25.4 1.0
O A:ASP297 4.8 23.7 1.0
O A:HOH3519 4.8 22.0 1.0
CA A:GLU301 4.9 23.3 1.0
O A:HOH3591 4.9 22.4 1.0
CE1 A:PHE304 4.9 13.4 1.0
CB A:GLU329 4.9 17.8 1.0

Calcium binding site 3 out of 9 in 2ggu

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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 Maltotriose


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

b:27.6
occ:1.00
 O A:HOH3601 2.1 40.6 1.0
OE1 A:GLU301 2.3 17.2 1.0
O A:HOH3602 2.4 25.4 1.0
O A:HOH3525 2.5 25.3 1.0
OD2 A:ASP330 2.5 18.5 1.0
O A:HOH3598 2.5 34.5 1.0
OD1 A:ASP330 2.6 17.5 1.0
CG A:ASP330 2.9 18.2 1.0
CD A:GLU301 3.5 16.3 1.0
CA A:CA402 3.8 15.2 1.0
OD1 A:ASP324 4.2 17.9 1.0
CG A:GLU301 4.3 21.2 1.0
CB A:GLU301 4.3 22.0 1.0
CB A:ASP330 4.4 17.4 1.0
OE2 A:GLU301 4.4 16.9 1.0
O A:ASP297 4.5 23.7 1.0
OD1 A:ASP297 4.7 14.6 1.0
O A:GLY327 4.7 24.1 1.0
CA A:GLU301 4.7 23.3 1.0
OD2 A:ASP324 4.8 16.8 1.0
OD2 A:ASP297 4.8 19.7 1.0
CG A:ASP324 4.9 20.0 1.0
O A:HOH3571 4.9 27.2 1.0
CG A:ASP297 5.0 17.3 1.0

Calcium binding site 4 out of 9 in 2ggu

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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 Maltotriose


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

b:15.3
occ:1.00
 OD1 B:ASP342 2.2 17.0 1.0
OE1 B:GLU329 2.4 19.2 1.0
OD1 B:ASN341 2.4 17.2 1.0
OD1 B:ASN323 2.5 15.9 1.0
OE1 B:GLU321 2.5 16.3 1.0
O3C B:MLR3505 2.5 19.7 1.0
O4C B:MLR3505 2.5 20.2 1.0
O B:ASP342 2.6 13.4 1.0
C3C B:MLR3505 3.3 22.0 1.0
CG B:ASP342 3.3 13.1 1.0
C4C B:MLR3505 3.4 21.4 1.0
CG B:ASN341 3.4 16.2 1.0
CD B:GLU329 3.4 18.6 1.0
CD B:GLU321 3.4 14.5 1.0
CG B:ASN323 3.4 17.5 1.0
C B:ASP342 3.6 14.9 1.0
N B:ASP342 3.7 14.8 1.0
OE2 B:GLU321 3.7 14.8 1.0
ND2 B:ASN341 3.8 16.8 1.0
OE2 B:GLU329 3.8 16.2 1.0
ND2 B:ASN323 3.9 16.5 1.0
OD2 B:ASP342 4.1 16.2 1.0
CA B:ASP342 4.1 14.0 1.0
N B:ASN323 4.2 16.3 1.0
CB B:ASP342 4.3 14.7 1.0
C B:ASN341 4.5 15.7 1.0
CB B:ASN323 4.6 17.4 1.0
CB B:ASP325 4.6 23.6 1.0
CB B:ASN341 4.6 16.2 1.0
N B:ASP324 4.6 16.4 1.0
CG B:GLU321 4.7 14.7 1.0
N B:ASP325 4.7 19.6 1.0
CG B:GLU329 4.7 17.9 1.0
C2C B:MLR3505 4.8 22.4 1.0
C5C B:MLR3505 4.8 23.6 1.0
CA B:ASN323 4.8 16.1 1.0
CA B:ASN341 4.8 16.6 1.0
N B:ARG343 4.8 15.7 1.0
CB B:GLU329 4.9 20.7 1.0
C B:ASN323 4.9 17.0 1.0

Calcium binding site 5 out of 9 in 2ggu

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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 Maltotriose


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

b:22.2
occ:1.00
 O B:HOH3597 2.4 17.8 1.0
OD1 B:ASP330 2.4 18.0 1.0
OD2 B:ASP297 2.4 25.9 1.0
OE1 B:GLU301 2.5 22.5 1.0
OE2 B:GLU301 2.5 22.3 1.0
O B:GLU329 2.5 18.6 1.0
OD1 B:ASP324 2.6 19.3 1.0
OD1 B:ASP297 2.7 21.1 1.0
CD B:GLU301 2.8 24.7 1.0
CG B:ASP297 2.9 24.0 1.0
C B:GLU329 3.4 19.9 1.0
CG B:ASP324 3.4 20.3 1.0
CG B:ASP330 3.5 22.0 1.0
CA B:ASP330 3.7 19.2 1.0
O B:HOH3602 3.8 30.1 1.0
N B:ASP330 4.0 18.0 1.0
CB B:ASP324 4.0 18.0 1.0
CA B:CA403 4.0 41.0 1.0
CB B:ASP330 4.1 19.9 1.0
OD2 B:ASP324 4.3 19.9 1.0
CG B:GLU301 4.3 24.9 1.0
CB B:ASP297 4.5 22.8 1.0
N B:GLU329 4.5 21.5 1.0
CZ B:PHE304 4.5 16.9 1.0
CA B:GLU329 4.5 20.7 1.0
OD2 B:ASP330 4.5 21.0 1.0
CA B:ASP324 4.6 18.6 1.0
OD2 B:ASP342 4.6 16.2 1.0
N B:GLY302 4.7 27.3 1.0
O B:ASP297 4.7 23.7 1.0
CA B:GLU301 4.8 28.3 1.0
O B:HOH3604 4.9 25.9 1.0
C B:ASP330 4.9 19.9 1.0
CE1 B:PHE304 5.0 16.6 1.0
CB B:GLU301 5.0 27.8 1.0

Calcium binding site 6 out of 9 in 2ggu

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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 Maltotriose


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

b:41.0
occ:1.00
 O B:HOH3604 2.3 25.9 1.0
O B:HOH3602 2.4 30.1 1.0
O B:HOH3601 2.4 35.8 1.0
O B:HOH3603 2.5 33.6 1.0
OD2 B:ASP330 2.5 21.0 1.0
OE1 B:GLU301 2.6 22.5 1.0
OD1 B:ASP330 2.7 18.0 1.0
CG B:ASP330 2.9 22.0 1.0
CD B:GLU301 3.8 24.7 1.0
CA B:CA402 4.0 22.2 1.0
O B:ASP297 4.4 23.7 1.0
CB B:GLU301 4.4 27.8 1.0
CB B:ASP330 4.4 19.9 1.0
OD1 B:ASP324 4.4 19.3 1.0
CG B:GLU301 4.5 24.9 1.0
OE2 B:GLU301 4.7 22.3 1.0
CA B:GLU301 4.8 28.3 1.0
OD2 B:ASP297 4.9 25.9 1.0
O B:HOH3533 4.9 35.8 1.0
O B:GLY327 5.0 24.2 1.0
OD1 B:ASP297 5.0 21.1 1.0
OD2 B:ASP324 5.0 19.9 1.0

Calcium binding site 7 out of 9 in 2ggu

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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 Maltotriose


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

b:18.8
occ:1.00
 OD1 C:ASP342 2.2 16.4 1.0
OD1 C:ASN341 2.4 18.7 1.0
OE1 C:GLU329 2.4 18.2 1.0
OD1 C:ASN323 2.4 17.3 1.0
O3C C:MLR3505 2.5 24.7 1.0
O C:ASP342 2.6 19.1 1.0
OE1 C:GLU321 2.6 18.7 1.0
O4C C:MLR3505 2.7 22.8 1.0
CG C:ASP342 3.3 15.9 1.0
C3C C:MLR3505 3.3 25.8 1.0
CG C:ASN341 3.4 19.0 1.0
CD C:GLU321 3.4 18.4 1.0
C4C C:MLR3505 3.4 26.6 1.0
CD C:GLU329 3.5 20.7 1.0
CG C:ASN323 3.5 18.1 1.0
C C:ASP342 3.6 19.1 1.0
N C:ASP342 3.7 20.5 1.0
OE2 C:GLU321 3.7 17.7 1.0
ND2 C:ASN341 3.9 18.7 1.0
OE2 C:GLU329 3.9 18.4 1.0
ND2 C:ASN323 4.0 19.2 1.0
OD2 C:ASP342 4.1 15.7 1.0
CA C:ASP342 4.1 18.1 1.0
N C:ASN323 4.1 20.2 1.0
CB C:ASP342 4.3 18.3 1.0
C C:ASN341 4.5 19.5 1.0
N C:ASP324 4.6 20.0 1.0
CG C:GLU321 4.6 18.4 1.0
CB C:ASN323 4.6 18.5 1.0
CB C:ASN341 4.7 17.7 1.0
CB C:ASP325 4.7 28.8 1.0
N C:ASP325 4.7 22.0 1.0
CG C:GLU329 4.7 18.9 1.0
CA C:ASN323 4.8 19.8 1.0
C2C C:MLR3505 4.8 26.2 1.0
N C:ARG343 4.8 20.0 1.0
CA C:ASN341 4.8 19.3 1.0
CB C:GLU329 4.8 20.3 1.0
C5C C:MLR3505 4.9 28.3 1.0
C C:ASN323 4.9 21.1 1.0
CB C:GLU321 5.0 18.2 1.0

Calcium binding site 8 out of 9 in 2ggu

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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 Maltotriose


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

b:26.5
occ:1.00
 O C:HOH3583 2.4 23.5 1.0
OD1 C:ASP330 2.4 24.4 1.0
O C:GLU329 2.4 17.8 1.0
OE1 C:GLU301 2.5 28.5 1.0
OD1 C:ASP324 2.6 20.5 1.0
OE2 C:GLU301 2.6 25.2 1.0
OD2 C:ASP297 2.6 33.1 1.0
OD1 C:ASP297 2.8 31.0 1.0
CD C:GLU301 2.9 26.6 1.0
CG C:ASP297 3.1 33.9 1.0
C C:GLU329 3.3 21.2 1.0
CG C:ASP324 3.3 22.8 1.0
CG C:ASP330 3.5 23.0 1.0
CA C:ASP330 3.7 21.9 1.0
O C:HOH3577 3.7 39.7 1.0
N C:ASP330 3.8 20.8 1.0
CA C:CA403 3.9 39.3 1.0
CB C:ASP324 3.9 21.4 1.0
CB C:ASP330 4.1 22.1 1.0
OD2 C:ASP324 4.1 20.4 1.0
N C:GLU329 4.3 22.3 1.0
CA C:GLU329 4.4 21.9 1.0
O C:HOH3574 4.4 40.4 1.0
CZ C:PHE304 4.4 27.6 1.0
CG C:GLU301 4.4 31.0 1.0
OD2 C:ASP342 4.5 15.7 1.0
CA C:ASP324 4.5 20.9 1.0
OD2 C:ASP330 4.5 25.2 1.0
CB C:ASP297 4.6 34.7 1.0
N C:GLY302 4.8 35.8 1.0
O C:ASP297 4.9 36.9 1.0
CE1 C:PHE304 4.9 27.8 1.0
CB C:GLU329 4.9 20.3 1.0
C C:ASP330 4.9 21.3 1.0
CA C:GLU301 5.0 35.5 1.0

Calcium binding site 9 out of 9 in 2ggu

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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 Maltotriose


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

b:39.3
occ:1.00
 OE1 C:GLU301 2.2 28.5 1.0
O C:HOH3581 2.3 32.9 1.0
O C:HOH3577 2.4 39.7 1.0
O C:HOH3575 2.6 37.4 1.0
OD1 C:ASP330 2.6 24.4 1.0
OD2 C:ASP330 2.8 25.2 1.0
CG C:ASP330 3.0 23.0 1.0
CD C:GLU301 3.4 26.6 1.0
CB C:GLU301 3.9 33.6 1.0
CA C:CA402 3.9 26.5 1.0
CG C:GLU301 4.0 31.0 1.0
O C:ASP297 4.2 36.9 1.0
CA C:GLU301 4.3 35.5 1.0
OE2 C:GLU301 4.4 25.2 1.0
CB C:ASP330 4.5 22.1 1.0
OD1 C:ASP324 4.5 20.5 1.0
OD2 C:ASP297 4.7 33.1 1.0
OD1 C:ASP297 4.7 31.0 1.0
N C:GLU301 4.8 37.0 1.0
O C:HOH3564 4.8 46.5 1.0
OD2 C:ASP324 4.9 20.4 1.0
CG C:ASP297 4.9 33.9 1.0
O C:GLY327 5.0 27.6 1.0

Reference:

E.Crouch, B.Mcdonald, K.Smith, T.Cafarella, B.Seaton, J.Head. Contributions of Phenylalanine 335 to Ligand Recognition By Human Surfactant Protein D: Ring Interactions with Sp-D Ligands J.Biol.Chem. V. 281 18008 2006.
ISSN: ISSN 0021-9258
PubMed: 16636058
DOI: 10.1074/JBC.M601749200
Page generated: Fri Jul 12 10:45:59 2024

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