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Calcium in PDB 2rid: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside

Protein crystallography data

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside, PDB code: 2rid was solved by H.Wang, J.Head, P.Kosma, S.Sheikh, B.Mcdonald, K.Smith, T.Cafarella, B.Seaton, E.Crouch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.603, 108.615, 55.628, 90.00, 90.91, 90.00
R / Rfree (%) 20.5 / 23.2

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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside (pdb code 2rid). 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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside, PDB code: 2rid:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2rid

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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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside


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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:21.6
occ:1.00
 OD1 A:ASN341 2.5 21.5 1.0
OD1 A:ASP342 2.5 22.3 1.0
OE1 A:GLU329 2.5 18.6 1.0
OD1 A:ASN323 2.6 24.1 1.0
OE1 A:GLU321 2.6 22.2 1.0
O A:ASP342 2.7 20.1 1.0
O3 A:291501 2.7 27.8 1.0
O4 A:291501 2.8 27.8 1.0
CG A:ASP342 3.4 22.1 1.0
CD A:GLU321 3.5 24.7 1.0
C3 A:291501 3.5 32.1 1.0
CG A:ASN341 3.5 23.9 1.0
CG A:ASN323 3.5 26.6 1.0
CD A:GLU329 3.5 19.6 1.0
C4 A:291501 3.7 33.7 1.0
C A:ASP342 3.7 21.8 1.0
N A:ASP342 3.8 22.0 1.0
OE2 A:GLU321 3.8 21.8 1.0
OE2 A:GLU329 3.9 20.6 1.0
ND2 A:ASN341 3.9 22.9 1.0
ND2 A:ASN323 3.9 24.1 1.0
OD2 A:ASP342 4.0 20.6 1.0
CA A:ASP342 4.2 20.9 1.0
N A:ASN323 4.2 24.7 1.0
CB A:ASP342 4.4 20.0 1.0
C A:ASN341 4.6 23.4 1.0
CB A:ASP325 4.6 27.9 1.0
N A:ASP325 4.6 25.1 1.0
N A:ASP324 4.7 23.6 1.0
CG A:GLU321 4.7 24.2 1.0
CB A:ASN323 4.7 24.3 1.0
CB A:ASN341 4.8 23.0 1.0
CG A:GLU329 4.8 21.4 1.0
CA A:ASN323 4.8 24.4 1.0
N A:ARG343 4.9 21.2 1.0
CA A:ASN341 4.9 22.6 1.0
CB A:GLU329 4.9 23.0 1.0
C2 A:291501 4.9 35.5 1.0

Calcium binding site 2 out of 9 in 2rid

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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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside


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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:22.6
occ:1.00
 OE1 A:GLU301 2.6 21.4 1.0
OD1 A:ASP324 2.6 24.0 1.0
O A:GLU329 2.6 22.2 1.0
OD2 A:ASP297 2.6 32.5 1.0
OD1 A:ASP330 2.6 21.8 1.0
OE2 A:GLU301 2.7 22.4 1.0
O A:HOH503 2.7 22.9 1.0
OD1 A:ASP297 2.8 27.4 1.0
CD A:GLU301 3.0 26.1 1.0
CG A:ASP297 3.1 29.1 1.0
CG A:ASP324 3.4 25.7 1.0
C A:GLU329 3.4 24.1 1.0
CG A:ASP330 3.6 24.8 1.0
CA A:ASP330 3.8 23.1 1.0
CA A:CA403 3.9 26.1 1.0
N A:ASP330 3.9 22.6 1.0
CB A:ASP324 4.0 22.9 1.0
OD2 A:ASP324 4.1 22.4 1.0
CB A:ASP330 4.2 21.9 1.0
N A:GLU329 4.3 24.0 1.0
CZ A:PHE304 4.4 25.6 1.0
O A:HOH622 4.4 33.5 1.0
CA A:GLU329 4.5 23.8 1.0
CG A:GLU301 4.5 26.3 1.0
CA A:ASP324 4.5 24.1 1.0
OD2 A:ASP330 4.5 23.0 1.0
CB A:ASP297 4.6 28.4 1.0
OD2 A:ASP342 4.6 20.6 1.0
N A:GLY302 4.7 27.5 1.0
O A:HOH585 4.8 26.5 1.0
O A:ASP297 4.8 31.2 1.0
O A:HOH544 4.9 26.9 1.0

Calcium binding site 3 out of 9 in 2rid

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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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside


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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:26.1
occ:1.00
 OE1 A:GLU301 2.5 21.4 1.0
O A:HOH584 2.6 25.8 1.0
OD2 A:ASP330 2.6 23.0 1.0
O A:HOH622 2.7 33.5 1.0
OD1 A:ASP330 2.7 21.8 1.0
O A:HOH646 2.7 35.1 1.0
CG A:ASP330 3.0 24.8 1.0
O A:HOH647 3.3 77.2 1.0
CD A:GLU301 3.7 26.1 1.0
CA A:CA402 3.9 22.6 1.0
OD1 A:ASP324 4.3 24.0 1.0
CB A:GLU301 4.4 26.7 1.0
CG A:GLU301 4.4 26.3 1.0
CB A:ASP330 4.5 21.9 1.0
OE2 A:GLU301 4.6 22.4 1.0
O A:ASP297 4.6 31.2 1.0
OD2 A:ASP324 4.7 22.4 1.0
OD1 A:ASP297 4.8 27.4 1.0
O A:GLY327 4.8 27.8 1.0
O A:HOH525 4.8 31.0 1.0
CA A:GLU301 4.9 28.4 1.0
CG A:ASP324 4.9 25.7 1.0

Calcium binding site 4 out of 9 in 2rid

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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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside


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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:19.4
occ:1.00
 OD1 B:ASP342 2.5 19.9 1.0
OE1 B:GLU329 2.5 20.0 1.0
OD1 B:ASN341 2.6 22.0 1.0
OD1 B:ASN323 2.6 18.1 1.0
OE1 B:GLU321 2.6 16.8 1.0
O B:ASP342 2.6 15.7 1.0
O3 B:291502 2.7 22.0 1.0
O4 B:291502 2.8 24.9 1.0
CG B:ASP342 3.4 20.8 1.0
CD B:GLU321 3.5 18.4 1.0
CD B:GLU329 3.5 21.6 1.0
CG B:ASN341 3.5 21.6 1.0
CG B:ASN323 3.5 20.5 1.0
C4 B:291502 3.6 29.0 1.0
C3 B:291502 3.6 29.6 1.0
C B:ASP342 3.6 19.6 1.0
N B:ASP342 3.7 19.4 1.0
OE2 B:GLU329 3.8 19.6 1.0
OE2 B:GLU321 3.8 18.9 1.0
ND2 B:ASN341 3.8 21.8 1.0
OD2 B:ASP342 4.0 20.8 1.0
ND2 B:ASN323 4.0 19.0 1.0
CA B:ASP342 4.1 18.7 1.0
N B:ASN323 4.2 22.2 1.0
CB B:ASP342 4.3 19.8 1.0
C B:ASN341 4.5 19.6 1.0
CB B:ASP325 4.6 24.9 1.0
CB B:ASN323 4.6 20.7 1.0
N B:ASP325 4.7 23.9 1.0
CG B:GLU321 4.7 19.3 1.0
N B:ASP324 4.7 20.9 1.0
CB B:ASN341 4.7 19.7 1.0
N B:ARG343 4.7 18.8 1.0
CG B:GLU329 4.7 19.5 1.0
CA B:ASN341 4.8 19.5 1.0
CA B:ASN323 4.8 21.0 1.0
CB B:GLU329 4.9 22.3 1.0
C2 B:291502 4.9 31.5 1.0

Calcium binding site 5 out of 9 in 2rid

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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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside


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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:24.9
occ:1.00
 O B:GLU329 2.5 20.8 1.0
OD1 B:ASP330 2.6 23.3 1.0
OE1 B:GLU301 2.6 21.0 1.0
O B:HOH584 2.6 26.5 1.0
OD1 B:ASP324 2.7 21.6 1.0
OD2 B:ASP297 2.7 25.7 1.0
OD1 B:ASP297 2.7 23.0 1.0
OE2 B:GLU301 2.8 23.1 1.0
CD B:GLU301 3.0 24.8 1.0
CG B:ASP297 3.1 25.0 1.0
C B:GLU329 3.4 21.9 1.0
CG B:ASP324 3.4 24.5 1.0
CG B:ASP330 3.6 26.1 1.0
CA B:ASP330 3.8 22.5 1.0
CA B:CA403 3.9 27.3 1.0
N B:ASP330 3.9 20.9 1.0
CB B:ASP324 4.0 21.8 1.0
O B:HOH504 4.0 32.1 1.0
OD2 B:ASP324 4.3 23.3 1.0
CB B:ASP330 4.3 21.9 1.0
N B:GLU329 4.4 23.6 1.0
CZ B:PHE304 4.5 24.3 1.0
O B:HOH590 4.5 36.6 1.0
CA B:GLU329 4.5 22.1 1.0
OD2 B:ASP342 4.5 20.8 1.0
CA B:ASP324 4.5 22.8 1.0
CG B:GLU301 4.5 26.0 1.0
OD2 B:ASP330 4.6 24.3 1.0
CB B:ASP297 4.6 25.1 1.0
N B:GLY302 4.8 30.9 1.0
CE1 B:PHE304 4.9 22.5 1.0
O B:ASP297 4.9 28.7 1.0
O B:HOH547 4.9 32.3 1.0
C B:ASP330 5.0 21.2 1.0

Calcium binding site 6 out of 9 in 2rid

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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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside


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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:27.3
occ:1.00
 OE1 B:GLU301 2.5 21.0 1.0
O B:HOH585 2.6 22.8 1.0
O B:HOH513 2.6 26.6 1.0
OD2 B:ASP330 2.6 24.3 1.0
OD1 B:ASP330 2.7 23.3 1.0
O B:HOH516 2.8 36.0 1.0
O B:HOH504 2.8 32.1 1.0
CG B:ASP330 3.0 26.1 1.0
CD B:GLU301 3.7 24.8 1.0
CA B:CA402 3.9 24.9 1.0
O B:HOH527 4.2 28.7 1.0
CB B:GLU301 4.2 28.1 1.0
O B:ASP297 4.3 28.7 1.0
OD1 B:ASP324 4.4 21.6 1.0
CG B:GLU301 4.4 26.0 1.0
CB B:ASP330 4.5 21.9 1.0
O B:HOH604 4.6 40.3 1.0
CA B:GLU301 4.6 30.3 1.0
OE2 B:GLU301 4.6 23.1 1.0
O B:HOH571 4.7 36.5 1.0
OD1 B:ASP297 4.7 23.0 1.0
OD2 B:ASP324 4.9 23.3 1.0
OD2 B:ASP297 4.9 25.7 1.0
O B:HOH522 4.9 29.3 1.0

Calcium binding site 7 out of 9 in 2rid

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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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside


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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:20.7
occ:1.00
 OD1 C:ASP342 2.5 19.5 1.0
OD1 C:ASN341 2.5 22.6 1.0
OE1 C:GLU329 2.5 21.6 1.0
OD1 C:ASN323 2.6 18.6 1.0
O C:ASP342 2.6 22.2 1.0
OE1 C:GLU321 2.7 22.4 1.0
O3 C:291503 2.7 25.4 1.0
O4 C:291503 2.8 25.0 1.0
CG C:ASP342 3.4 20.2 1.0
CD C:GLU329 3.4 23.3 1.0
CD C:GLU321 3.4 21.4 1.0
CG C:ASN341 3.5 22.6 1.0
C4 C:291503 3.5 30.5 1.0
CG C:ASN323 3.6 21.3 1.0
C3 C:291503 3.6 28.1 1.0
C C:ASP342 3.7 22.7 1.0
OE2 C:GLU321 3.7 21.4 1.0
OE2 C:GLU329 3.7 20.9 1.0
N C:ASP342 3.7 20.8 1.0
ND2 C:ASN341 3.9 22.2 1.0
OD2 C:ASP342 4.0 16.7 1.0
ND2 C:ASN323 4.1 21.4 1.0
CA C:ASP342 4.1 20.9 1.0
N C:ASN323 4.2 21.6 1.0
CB C:ASP342 4.3 18.2 1.0
C C:ASN341 4.5 21.7 1.0
CB C:ASP325 4.6 25.8 1.0
CG C:GLU321 4.6 20.9 1.0
CB C:ASN323 4.7 21.4 1.0
N C:ASP325 4.7 23.1 1.0
CG C:GLU329 4.7 21.2 1.0
CB C:ASN341 4.7 21.1 1.0
N C:ASP324 4.7 21.1 1.0
CA C:ASN323 4.8 21.5 1.0
N C:ARG343 4.8 22.1 1.0
CA C:ASN341 4.8 20.9 1.0
CB C:GLU329 4.9 23.2 1.0
C2 C:291503 4.9 31.9 1.0
C C:ASN323 5.0 22.4 1.0
O2 C:291503 5.0 29.4 1.0

Calcium binding site 8 out of 9 in 2rid

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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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside


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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:26.3
occ:1.00
 O C:HOH509 2.6 22.1 1.0
O C:GLU329 2.6 20.2 1.0
OE1 C:GLU301 2.6 26.7 1.0
OD2 C:ASP297 2.7 25.8 1.0
OD1 C:ASP330 2.7 22.6 1.0
OD1 C:ASP324 2.7 22.5 1.0
OE2 C:GLU301 2.7 24.1 1.0
OD1 C:ASP297 2.8 25.1 1.0
CD C:GLU301 3.0 28.1 1.0
CG C:ASP297 3.1 27.2 1.0
CG C:ASP324 3.3 24.1 1.0
C C:GLU329 3.4 22.4 1.0
CG C:ASP330 3.8 25.8 1.0
CB C:ASP324 3.8 22.4 1.0
CA C:ASP330 3.9 23.5 1.0
O C:HOH510 3.9 30.3 1.0
CA C:CA403 4.0 29.6 1.0
N C:ASP330 4.0 22.6 1.0
OD2 C:ASP324 4.2 23.5 1.0
N C:GLU329 4.4 23.8 1.0
CB C:ASP330 4.4 23.7 1.0
CZ C:PHE304 4.4 25.0 1.0
CA C:ASP324 4.4 22.4 1.0
CA C:GLU329 4.5 22.1 1.0
OD2 C:ASP342 4.5 16.7 1.0
CG C:GLU301 4.5 28.5 1.0
CB C:ASP297 4.6 27.0 1.0
O C:HOH585 4.6 31.4 1.0
OD2 C:ASP330 4.7 26.2 1.0
N C:GLY302 4.8 29.8 1.0
O C:HOH536 4.8 25.6 1.0
O C:ASP297 4.9 28.4 1.0
CE1 C:PHE304 4.9 23.0 1.0

Calcium binding site 9 out of 9 in 2rid

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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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside


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 Allyl 7-O- Carbamoyl-L-Glycero-D-Manno-Heptopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:29.6
occ:1.00
 OE1 C:GLU301 2.5 26.7 1.0
OD2 C:ASP330 2.7 26.2 1.0
O C:HOH513 2.7 31.1 1.0
OD1 C:ASP330 2.7 22.6 1.0
O C:HOH510 2.8 30.3 1.0
O C:HOH507 2.8 32.0 1.0
O C:HOH621 2.9 44.8 1.0
CG C:ASP330 3.0 25.8 1.0
CD C:GLU301 3.7 28.1 1.0
CA C:CA402 4.0 26.3 1.0
O C:HOH605 4.0 50.2 1.0
CB C:GLU301 4.3 30.6 1.0
O C:HOH558 4.3 33.9 1.0
O C:ASP297 4.3 28.4 1.0
CG C:GLU301 4.4 28.5 1.0
OD1 C:ASP324 4.5 22.5 1.0
CB C:ASP330 4.5 23.7 1.0
O C:HOH599 4.7 40.3 1.0
OE2 C:GLU301 4.7 24.1 1.0
CA C:GLU301 4.7 31.2 1.0
OD1 C:ASP297 4.8 25.1 1.0
O C:HOH525 4.9 27.5 1.0
OD2 C:ASP324 5.0 23.5 1.0

Reference:

H.Wang, J.Head, P.Kosma, H.Brade, S.Muller-Loennies, S.Sheikh, B.Mcdonald, K.Smith, T.Cafarella, B.Seaton, E.Crouch. Recognition of Heptoses and the Inner Core of Bacterial Lipopolysaccharides By Surfactant Protein D. Biochemistry V. 47 710 2008.
ISSN: ISSN 0006-2960
PubMed: 18092821
DOI: 10.1021/BI7020553
Page generated: Tue Jul 8 08:16:27 2025

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