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Calcium in PDB 3g81: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha Methyl Mannoside

Protein crystallography data

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha Methyl Mannoside, PDB code: 3g81 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) 26.29 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.384, 107.980, 55.668, 90.00, 92.20, 90.00
R / Rfree (%) 17.8 / 20

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 Alpha Methyl Mannoside (pdb code 3g81). 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 Alpha Methyl Mannoside, PDB code: 3g81:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 3g81

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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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:13.2
occ:1.00
 OD1 A:ASP342 2.2 16.3 1.0
OD1 A:ASN341 2.2 16.9 1.0
O3 A:MMA500 2.4 18.6 1.0
OE1 A:GLU321 2.4 17.2 1.0
OD1 A:ASN323 2.5 17.1 1.0
OE1 A:GLU329 2.5 17.6 1.0
O A:ASP342 2.7 15.6 1.0
O4 A:MMA500 2.7 20.3 1.0
CG A:ASP342 3.3 16.5 1.0
CG A:ASN341 3.3 15.8 1.0
CD A:GLU321 3.3 18.4 1.0
C3 A:MMA500 3.3 23.1 1.0
C4 A:MMA500 3.4 21.9 1.0
CG A:ASN323 3.4 21.0 1.0
CD A:GLU329 3.5 17.4 1.0
OE2 A:GLU321 3.6 19.1 1.0
C A:ASP342 3.6 16.0 1.0
N A:ASP342 3.7 14.7 1.0
ND2 A:ASN341 3.8 18.4 1.0
OE2 A:GLU329 3.8 17.5 1.0
ND2 A:ASN323 3.9 21.0 1.0
CA A:ASP342 4.0 14.7 1.0
OD2 A:ASP342 4.0 16.2 1.0
N A:ASN323 4.1 19.0 1.0
CB A:ASP342 4.2 14.2 1.0
C A:ASN341 4.5 16.9 1.0
CG A:GLU321 4.6 17.9 1.0
CB A:ASN323 4.6 18.5 1.0
CB A:ASN341 4.6 16.6 1.0
N A:ASP324 4.7 16.6 1.0
N A:ASP325 4.7 17.4 1.0
C2 A:MMA500 4.7 27.3 1.0
CB A:ASP325 4.8 20.3 1.0
CA A:ASN323 4.8 19.0 1.0
CG A:GLU329 4.8 17.6 1.0
N A:ARG343 4.8 15.1 1.0
CA A:ASN341 4.8 15.9 1.0
C5 A:MMA500 4.9 26.1 1.0
CB A:GLU329 5.0 17.1 1.0

Calcium binding site 2 out of 9 in 3g81

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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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:13.5
occ:1.00
 OD1 A:ASP330 2.3 17.1 1.0
OE1 A:GLU301 2.4 16.9 1.0
O A:HOH538 2.4 16.2 1.0
OD1 A:ASP324 2.4 17.1 1.0
OE2 A:GLU301 2.5 17.6 1.0
OD2 A:ASP297 2.5 18.3 1.0
O A:GLU329 2.5 16.8 1.0
OD1 A:ASP297 2.7 16.7 1.0
CD A:GLU301 2.7 19.0 1.0
CG A:ASP297 2.9 17.9 1.0
CG A:ASP324 3.3 19.2 1.0
CG A:ASP330 3.4 18.9 1.0
C A:GLU329 3.4 16.5 1.0
CA A:ASP330 3.7 15.1 1.0
CA A:CA403 3.8 30.6 1.0
O A:HOH476 3.8 21.0 1.0
N A:ASP330 4.0 16.6 1.0
CB A:ASP324 4.0 16.4 1.0
CB A:ASP330 4.0 16.8 1.0
OD2 A:ASP324 4.1 19.3 1.0
CG A:GLU301 4.2 21.1 1.0
OD2 A:ASP330 4.3 20.0 1.0
N A:GLU329 4.3 18.3 1.0
CA A:GLU329 4.4 17.4 1.0
CZ A:PHE304 4.4 17.4 1.0
CB A:ASP297 4.5 19.0 1.0
O A:HOH505 4.5 22.1 1.0
CA A:ASP324 4.6 15.8 1.0
N A:GLY302 4.6 20.9 1.0
O A:ASP297 4.7 21.2 1.0
OD2 A:ASP342 4.8 16.2 1.0
O A:HOH42 4.9 19.9 1.0
CA A:GLU301 4.9 21.0 1.0
CB A:GLU301 5.0 21.8 1.0
O A:HOH56 5.0 23.2 1.0
CE1 A:PHE304 5.0 16.8 1.0

Calcium binding site 3 out of 9 in 3g81

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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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:30.6
occ:1.00
 O A:HOH476 2.3 21.0 1.0
O A:HOH505 2.3 22.1 1.0
OD2 A:ASP330 2.4 20.0 1.0
OE1 A:GLU301 2.5 16.9 1.0
OD1 A:ASP330 2.5 17.1 1.0
CG A:ASP330 2.8 18.9 1.0
CD A:GLU301 3.7 19.0 1.0
O A:HOH547 3.7 31.7 1.0
CA A:CA402 3.8 13.5 1.0
OD1 A:ASP324 4.1 17.1 1.0
CB A:ASP330 4.3 16.8 1.0
O A:HOH592 4.4 33.1 1.0
O A:GLY327 4.4 22.4 1.0
CB A:GLU301 4.4 21.8 1.0
CG A:GLU301 4.5 21.1 1.0
O A:ASP297 4.5 21.2 1.0
OE2 A:GLU301 4.5 17.6 1.0
OD2 A:ASP324 4.6 19.3 1.0
OD1 A:ASP297 4.7 16.7 1.0
CG A:ASP324 4.8 19.2 1.0
CA A:SER328 4.9 21.3 1.0
CA A:GLU301 5.0 21.0 1.0

Calcium binding site 4 out of 9 in 3g81

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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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:12.5
occ:1.00
 OD1 B:ASP342 2.2 14.7 1.0
OD1 B:ASN341 2.3 16.0 1.0
OE1 B:GLU329 2.3 16.3 1.0
OD1 B:ASN323 2.4 14.3 1.0
O3 B:MMA500 2.5 16.4 1.0
O B:ASP342 2.5 14.5 1.0
OE1 B:GLU321 2.6 15.0 1.0
O4 B:MMA500 2.6 17.4 1.0
CG B:ASP342 3.3 14.2 1.0
CG B:ASN341 3.3 16.5 1.0
C4 B:MMA500 3.3 21.2 1.0
CD B:GLU329 3.4 17.6 1.0
CG B:ASN323 3.4 16.1 1.0
C3 B:MMA500 3.4 19.2 1.0
CD B:GLU321 3.4 15.3 1.0
C B:ASP342 3.6 14.4 1.0
OE2 B:GLU321 3.7 16.4 1.0
N B:ASP342 3.7 15.3 1.0
OE2 B:GLU329 3.7 16.2 1.0
ND2 B:ASN341 3.7 15.4 1.0
ND2 B:ASN323 4.0 16.8 1.0
CA B:ASP342 4.0 14.5 1.0
OD2 B:ASP342 4.0 16.0 1.0
N B:ASN323 4.1 14.5 1.0
CB B:ASP342 4.2 13.6 1.0
C B:ASN341 4.5 14.6 1.0
CB B:ASN323 4.5 16.1 1.0
CB B:ASP325 4.6 20.3 1.0
CB B:ASN341 4.7 14.7 1.0
CG B:GLU329 4.7 16.5 1.0
CG B:GLU321 4.7 14.7 1.0
N B:ASP325 4.7 18.2 1.0
N B:ARG343 4.7 14.8 1.0
CA B:ASN323 4.7 14.9 1.0
C2 B:MMA500 4.7 23.8 1.0
N B:ASP324 4.7 16.1 1.0
CA B:ASN341 4.9 13.9 1.0
C5 B:MMA500 4.9 27.0 1.0
CB B:GLU329 4.9 18.9 1.0
C B:ASN323 4.9 16.5 1.0
O2 B:MMA500 5.0 26.8 1.0

Calcium binding site 5 out of 9 in 3g81

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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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:17.5
occ:1.00
 O B:HOH536 2.2 18.6 1.0
OD1 B:ASP330 2.2 21.3 1.0
OD2 B:ASP297 2.3 23.9 1.0
O B:GLU329 2.4 16.4 1.0
OD1 B:ASP324 2.7 21.4 1.0
OE1 B:GLU301 2.7 25.1 1.0
OD1 B:ASP297 2.7 21.4 1.0
OE2 B:GLU301 2.7 24.9 1.0
CG B:ASP297 2.8 22.6 1.0
CD B:GLU301 3.0 27.6 1.0
C B:GLU329 3.4 17.5 1.0
CG B:ASP324 3.4 23.1 1.0
CG B:ASP330 3.4 24.9 1.0
CA B:ASP330 3.7 17.8 1.0
O B:HOH464 3.7 29.1 1.0
CA B:CA403 3.9 44.7 1.0
N B:ASP330 4.0 18.2 1.0
CB B:ASP324 4.0 19.2 1.0
CB B:ASP330 4.1 19.6 1.0
OD2 B:ASP324 4.1 22.8 1.0
O B:HOH373 4.3 29.4 1.0
CB B:ASP297 4.3 20.6 1.0
N B:GLU329 4.4 19.8 1.0
OD2 B:ASP330 4.4 23.7 1.0
CA B:GLU329 4.4 17.9 1.0
CZ B:PHE304 4.5 18.1 1.0
CG B:GLU301 4.5 28.9 1.0
CA B:ASP324 4.6 17.5 1.0
O B:HOH443 4.7 29.6 1.0
OD2 B:ASP342 4.7 16.0 1.0
N B:GLY302 4.8 27.2 1.0
O B:ASP297 4.9 25.6 1.0
CE1 B:PHE304 5.0 18.0 1.0
C B:ASP330 5.0 17.0 1.0
CA B:GLU301 5.0 28.3 1.0

Calcium binding site 6 out of 9 in 3g81

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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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:44.7
occ:1.00
 O B:HOH464 2.3 29.1 1.0
O B:HOH443 2.4 29.6 1.0
O B:HOH542 2.5 41.1 1.0
OE1 B:GLU301 2.6 25.1 1.0
OD2 B:ASP330 2.6 23.7 1.0
OD1 B:ASP330 2.7 21.3 1.0
O B:HOH558 2.8 43.5 1.0
CG B:ASP330 2.9 24.9 1.0
CD B:GLU301 3.8 27.6 1.0
CA B:CA402 3.9 17.5 1.0
O B:HOH412 3.9 34.5 1.0
OD1 B:ASP324 4.3 21.4 1.0
CB B:ASP330 4.4 19.6 1.0
O B:GLY327 4.5 26.0 1.0
O B:ASP297 4.5 25.6 1.0
CB B:GLU301 4.5 30.0 1.0
O B:HOH531 4.6 39.9 1.0
CG B:GLU301 4.6 28.9 1.0
OE2 B:GLU301 4.7 24.9 1.0
OD2 B:ASP297 4.7 23.9 1.0
OD1 B:ASP297 4.7 21.4 1.0
OD2 B:ASP324 4.7 22.8 1.0
CA B:GLU301 4.9 28.3 1.0
CG B:ASP324 4.9 23.1 1.0
CG B:ASP297 5.0 22.6 1.0

Calcium binding site 7 out of 9 in 3g81

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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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:14.0
occ:1.00
 OD1 C:ASP342 2.1 17.1 1.0
OE1 C:GLU329 2.3 17.6 1.0
OD1 C:ASN341 2.3 17.7 1.0
OD1 C:ASN323 2.4 17.8 1.0
O3 C:MMA500 2.4 18.6 1.0
OE1 C:GLU321 2.5 17.5 1.0
O C:ASP342 2.6 16.7 1.0
O4 C:MMA500 2.7 21.3 1.0
CG C:ASP342 3.3 15.9 1.0
CG C:ASN341 3.3 18.3 1.0
CD C:GLU329 3.3 20.1 1.0
C3 C:MMA500 3.3 22.4 1.0
CD C:GLU321 3.4 17.3 1.0
CG C:ASN323 3.4 19.0 1.0
C4 C:MMA500 3.4 24.8 1.0
C C:ASP342 3.6 16.7 1.0
OE2 C:GLU321 3.7 18.4 1.0
N C:ASP342 3.7 15.3 1.0
OE2 C:GLU329 3.8 20.4 1.0
ND2 C:ASN341 3.8 18.9 1.0
ND2 C:ASN323 4.0 20.4 1.0
CA C:ASP342 4.0 16.1 1.0
OD2 C:ASP342 4.0 16.5 1.0
N C:ASN323 4.1 16.7 1.0
CB C:ASP342 4.2 15.6 1.0
C C:ASN341 4.5 17.5 1.0
CB C:ASN323 4.6 18.2 1.0
CB C:ASN341 4.6 15.6 1.0
CG C:GLU329 4.6 18.9 1.0
CG C:GLU321 4.6 16.4 1.0
C2 C:MMA500 4.7 26.9 1.0
CB C:ASP325 4.7 22.3 1.0
CA C:ASN323 4.7 16.8 1.0
N C:ASP325 4.8 18.9 1.0
N C:ARG343 4.8 17.9 1.0
N C:ASP324 4.8 17.6 1.0
CB C:GLU329 4.8 17.9 1.0
CA C:ASN341 4.9 15.4 1.0
C5 C:MMA500 4.9 30.0 1.0
O2 C:MMA500 5.0 31.0 1.0
C C:ASN323 5.0 19.6 1.0

Calcium binding site 8 out of 9 in 3g81

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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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:20.6
occ:1.00
 O C:HOH507 2.1 20.4 1.0
OD2 C:ASP297 2.4 27.1 1.0
OD1 C:ASP330 2.5 23.4 1.0
OE2 C:GLU301 2.5 24.9 1.0
O C:GLU329 2.5 21.3 1.0
OE1 C:GLU301 2.6 27.5 1.0
OD1 C:ASP297 2.6 23.5 1.0
OD1 C:ASP324 2.7 21.6 1.0
CG C:ASP297 2.9 26.8 1.0
CD C:GLU301 2.9 28.1 1.0
CG C:ASP324 3.4 25.7 1.0
C C:GLU329 3.4 19.2 1.0
CG C:ASP330 3.6 27.6 1.0
CA C:ASP330 3.8 21.7 1.0
O C:HOH527 3.8 29.9 1.0
CA C:CA403 3.9 43.9 1.0
O C:HOH545 3.9 35.6 1.0
N C:ASP330 4.0 19.8 1.0
CB C:ASP324 4.1 22.1 1.0
OD2 C:ASP324 4.1 21.2 1.0
CB C:ASP330 4.2 22.9 1.0
CZ C:PHE304 4.3 23.0 1.0
CB C:ASP297 4.4 26.6 1.0
CG C:GLU301 4.4 30.1 1.0
N C:GLU329 4.4 21.7 1.0
CA C:GLU329 4.5 20.2 1.0
OD2 C:ASP330 4.6 28.6 1.0
CA C:ASP324 4.6 20.0 1.0
OD2 C:ASP342 4.6 16.5 1.0
N C:GLY302 4.7 29.3 1.0
CE1 C:PHE304 4.7 21.0 1.0
O C:ASP297 4.9 31.5 1.0
O C:HOH416 4.9 32.2 1.0
CA C:GLU301 4.9 32.4 1.0
C C:ASP330 5.0 20.6 1.0

Calcium binding site 9 out of 9 in 3g81

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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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:43.9
occ:1.00
 O C:HOH416 2.2 32.2 1.0
OE1 C:GLU301 2.3 27.5 1.0
O C:HOH527 2.5 29.9 1.0
OD1 C:ASP330 2.6 23.4 1.0
OD2 C:ASP330 2.7 28.6 1.0
O C:HOH569 2.8 39.5 1.0
O C:HOH544 2.8 46.0 1.0
CG C:ASP330 2.9 27.6 1.0
CD C:GLU301 3.6 28.1 1.0
CA C:CA402 3.9 20.6 1.0
CB C:GLU301 4.1 34.3 1.0
O C:HOH392 4.2 36.9 1.0
O C:ASP297 4.2 31.5 1.0
CB C:ASP330 4.3 22.9 1.0
CG C:GLU301 4.3 30.1 1.0
O C:HOH555 4.4 42.1 1.0
OE2 C:GLU301 4.5 24.9 1.0
OD1 C:ASP324 4.5 21.6 1.0
OD1 C:ASP297 4.5 23.5 1.0
CA C:GLU301 4.6 32.4 1.0
OD2 C:ASP297 4.7 27.1 1.0
O C:GLY327 4.8 27.2 1.0
OD2 C:ASP324 4.8 21.2 1.0
CG C:ASP297 4.8 26.8 1.0
O C:HOH378 4.9 32.8 1.0

Reference:

E.Crouch, K.Hartshorn, T.Horlacher, B.Mcdonald, K.Smith, T.Cafarella, B.Seaton, P.H.Seeberger, J.Head. Recognition of Mannosylated Ligands and Influenza A Virus By Human Surfactant Protein D: Contributions of An Extended Site and Residue 343. Biochemistry V. 48 3335 2009.
ISSN: ISSN 0006-2960
PubMed: 19249874
DOI: 10.1021/BI8022703
Page generated: Sat Dec 12 04:12:36 2020

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