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Calcium in PDB 2rib: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptose

Protein crystallography data

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with L-Glycero-D- Manno-Heptose, PDB code: 2rib 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 (°) 55.200, 107.441, 55.506, 90.00, 91.51, 90.00
R / Rfree (%) 18.6 / 20.4

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

Calcium binding site 1 out of 9 in 2rib

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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 L-Glycero-D- Manno-Heptose


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 L-Glycero-D- Manno-Heptose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:23.6
occ:1.00
 OD1 A:ASP342 2.5 22.3 1.0
OE1 A:GLU329 2.6 20.3 1.0
OD1 A:ASN341 2.6 23.9 1.0
O6 A:GMH356 2.6 30.0 1.0
O A:ASP342 2.7 21.2 1.0
OD1 A:ASN323 2.7 25.6 1.0
OE1 A:GLU321 2.7 23.3 1.0
O7 A:GMH356 2.9 26.1 1.0
CG A:ASP342 3.4 24.5 1.0
CG A:ASN341 3.5 24.1 1.0
CD A:GLU329 3.5 21.6 1.0
CD A:GLU321 3.5 24.0 1.0
CG A:ASN323 3.5 26.9 1.0
C7 A:GMH356 3.6 29.5 1.0
C6 A:GMH356 3.6 31.6 1.0
C A:ASP342 3.7 23.0 1.0
N A:ASP342 3.8 24.2 1.0
OE2 A:GLU321 3.8 25.4 1.0
OE2 A:GLU329 3.8 22.2 1.0
ND2 A:ASN341 3.9 24.9 1.0
ND2 A:ASN323 3.9 26.8 1.0
OD2 A:ASP342 4.0 21.2 1.0
CA A:ASP342 4.1 23.0 1.0
N A:ASN323 4.2 24.4 1.0
CB A:ASP342 4.3 22.3 1.0
CB A:ASP325 4.5 24.6 1.0
C A:ASN341 4.5 24.8 1.0
N A:ASP325 4.6 23.9 1.0
N A:ASP324 4.7 22.6 1.0
CB A:ASN323 4.7 24.8 1.0
CG A:GLU321 4.7 24.3 1.0
CB A:ASN341 4.8 24.7 1.0
CG A:GLU329 4.8 22.0 1.0
C5 A:GMH356 4.8 34.2 1.0
O5 A:GMH356 4.8 35.7 1.0
CA A:ASN323 4.9 24.3 1.0
N A:ARG343 4.9 23.9 1.0
CA A:ASN341 4.9 24.2 1.0
CB A:GLU329 4.9 23.9 1.0

Calcium binding site 2 out of 9 in 2rib

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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 L-Glycero-D- Manno-Heptose


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 L-Glycero-D- Manno-Heptose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:22.8
occ:1.00
 O A:GLU329 2.6 20.1 1.0
OD1 A:ASP330 2.6 24.0 1.0
OE1 A:GLU301 2.6 21.7 1.0
OD2 A:ASP297 2.7 23.5 1.0
OD1 A:ASP324 2.7 24.3 1.0
O A:HOH528 2.7 25.4 1.0
OE2 A:GLU301 2.7 21.6 1.0
OD1 A:ASP297 2.8 23.1 1.0
CD A:GLU301 3.0 23.3 1.0
CG A:ASP297 3.1 22.8 1.0
C A:GLU329 3.4 22.4 1.0
CG A:ASP324 3.4 25.9 1.0
CG A:ASP330 3.7 25.9 1.0
CA A:ASP330 3.8 22.1 1.0
N A:ASP330 3.9 22.8 1.0
CA A:CA403 3.9 27.8 1.0
CB A:ASP324 4.0 23.2 1.0
OD2 A:ASP324 4.2 25.1 1.0
CB A:ASP330 4.3 21.0 1.0
N A:GLU329 4.3 24.2 1.0
O A:HOH540 4.4 31.4 1.0
CZ A:PHE304 4.4 23.0 1.0
CA A:GLU329 4.4 23.0 1.0
CG A:GLU301 4.5 23.5 1.0
CA A:ASP324 4.6 22.9 1.0
CB A:ASP297 4.6 24.1 1.0
OD2 A:ASP342 4.6 21.2 1.0
OD2 A:ASP330 4.6 24.2 1.0
N A:GLY302 4.6 25.1 1.0
O A:HOH483 4.7 27.6 1.0
O A:ASP297 4.8 25.6 1.0
O A:HOH428 4.9 29.0 1.0
CE1 A:PHE304 4.9 23.7 1.0
C A:ASP330 4.9 21.0 1.0
CA A:GLU301 5.0 26.1 1.0
CB A:GLU329 5.0 23.9 1.0

Calcium binding site 3 out of 9 in 2rib

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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 L-Glycero-D- Manno-Heptose


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 L-Glycero-D- Manno-Heptose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:27.8
occ:1.00
 OE1 A:GLU301 2.5 21.7 1.0
OD1 A:ASP330 2.6 24.0 1.0
O A:HOH547 2.6 33.3 1.0
O A:HOH540 2.6 31.4 1.0
OD2 A:ASP330 2.7 24.2 1.0
O A:HOH407 2.7 27.0 1.0
O A:HOH548 2.9 57.2 1.0
CG A:ASP330 3.0 25.9 1.0
CD A:GLU301 3.7 23.3 1.0
CA A:CA402 3.9 22.8 1.0
OD1 A:ASP324 4.4 24.3 1.0
CB A:GLU301 4.4 25.1 1.0
CG A:GLU301 4.4 23.5 1.0
CB A:ASP330 4.5 21.0 1.0
O A:ASP297 4.5 25.6 1.0
OE2 A:GLU301 4.6 21.6 1.0
OD2 A:ASP324 4.8 25.1 1.0
O A:GLY327 4.8 27.0 1.0
CA A:GLU301 4.8 26.1 1.0
O A:HOH413 4.9 27.4 1.0
OD1 A:ASP297 4.9 23.1 1.0
CA A:SER328 4.9 29.0 1.0
CG A:ASP324 5.0 25.9 1.0

Calcium binding site 4 out of 9 in 2rib

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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 L-Glycero-D- Manno-Heptose


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 L-Glycero-D- Manno-Heptose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:18.6
occ:1.00
 OD1 B:ASP342 2.5 16.7 1.0
OD1 B:ASN341 2.5 18.2 1.0
OE1 B:GLU329 2.5 18.4 1.0
OD1 B:ASN323 2.5 16.8 1.0
OE1 B:GLU321 2.6 17.2 1.0
O B:ASP342 2.6 15.2 1.0
O6 B:GMH356 2.7 18.9 1.0
O7 B:GMH356 2.8 19.3 1.0
CG B:ASP342 3.4 17.4 1.0
CD B:GLU321 3.4 18.8 1.0
CG B:ASN341 3.5 20.2 1.0
CD B:GLU329 3.5 19.8 1.0
CG B:ASN323 3.5 17.5 1.0
C7 B:GMH356 3.5 19.0 1.0
C6 B:GMH356 3.6 21.1 1.0
C B:ASP342 3.6 17.6 1.0
OE2 B:GLU321 3.7 16.9 1.0
N B:ASP342 3.7 17.6 1.0
OE2 B:GLU329 3.8 17.2 1.0
ND2 B:ASN341 3.9 18.9 1.0
OD2 B:ASP342 4.1 18.9 1.0
ND2 B:ASN323 4.1 18.4 1.0
CA B:ASP342 4.1 17.4 1.0
N B:ASN323 4.2 19.2 1.0
CB B:ASP342 4.3 16.8 1.0
C B:ASN341 4.5 18.7 1.0
CB B:ASP325 4.6 21.6 1.0
N B:ASP325 4.6 21.0 1.0
CB B:ASN323 4.6 17.8 1.0
CG B:GLU321 4.6 17.3 1.0
N B:ASP324 4.7 18.6 1.0
CB B:ASN341 4.7 18.7 1.0
CG B:GLU329 4.8 19.1 1.0
N B:ARG343 4.8 18.8 1.0
CA B:ASN323 4.8 18.4 1.0
CA B:ASN341 4.9 19.1 1.0
C5 B:GMH356 4.9 23.9 1.0
CB B:GLU329 4.9 20.4 1.0
O5 B:GMH356 5.0 22.5 1.0
C B:ASN323 5.0 19.4 1.0

Calcium binding site 5 out of 9 in 2rib

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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 L-Glycero-D- Manno-Heptose


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 L-Glycero-D- Manno-Heptose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:21.9
occ:1.00
 O B:HOH544 2.5 20.2 1.0
O B:GLU329 2.6 17.3 1.0
OD1 B:ASP330 2.6 20.4 1.0
OE1 B:GLU301 2.6 22.5 1.0
OD2 B:ASP297 2.6 22.2 1.0
OD1 B:ASP324 2.6 20.2 1.0
OE2 B:GLU301 2.7 22.2 1.0
OD1 B:ASP297 2.8 20.2 1.0
CD B:GLU301 3.0 25.2 1.0
CG B:ASP297 3.1 23.0 1.0
CG B:ASP324 3.4 21.5 1.0
C B:GLU329 3.5 20.6 1.0
CG B:ASP330 3.7 24.2 1.0
CA B:ASP330 3.8 19.6 1.0
CB B:ASP324 3.9 19.0 1.0
CA B:CA403 3.9 27.8 1.0
O B:HOH545 4.0 27.1 1.0
N B:ASP330 4.0 19.5 1.0
OD2 B:ASP324 4.2 20.8 1.0
CB B:ASP330 4.3 19.6 1.0
N B:GLU329 4.5 21.4 1.0
CA B:ASP324 4.5 20.4 1.0
OD2 B:ASP342 4.5 18.9 1.0
CZ B:PHE304 4.5 23.2 1.0
CG B:GLU301 4.5 25.4 1.0
CA B:GLU329 4.5 20.2 1.0
CB B:ASP297 4.6 22.5 1.0
OD2 B:ASP330 4.6 23.1 1.0
O B:ASP297 4.7 27.5 1.0
N B:GLY302 4.8 26.8 1.0
CE1 B:PHE304 4.9 21.4 1.0
CA B:GLU301 5.0 27.7 1.0

Calcium binding site 6 out of 9 in 2rib

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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 L-Glycero-D- Manno-Heptose


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 L-Glycero-D- Manno-Heptose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:27.8
occ:1.00
 OE1 B:GLU301 2.5 22.5 1.0
OD1 B:ASP330 2.6 20.4 1.0
O B:HOH548 2.6 28.7 1.0
O B:HOH545 2.7 27.1 1.0
O B:HOH546 2.7 25.2 1.0
OD2 B:ASP330 2.7 23.1 1.0
O B:HOH564 2.8 35.8 1.0
CG B:ASP330 3.0 24.2 1.0
CD B:GLU301 3.8 25.2 1.0
CA B:CA402 3.9 21.9 1.0
O B:HOH438 4.2 32.5 1.0
O B:ASP297 4.3 27.5 1.0
CB B:GLU301 4.3 27.6 1.0
OD1 B:ASP324 4.4 20.2 1.0
CG B:GLU301 4.5 25.4 1.0
CB B:ASP330 4.5 19.6 1.0
O B:HOH518 4.5 35.3 1.0
OE2 B:GLU301 4.7 22.2 1.0
CA B:GLU301 4.7 27.7 1.0
OD1 B:ASP297 4.8 20.2 1.0
OD2 B:ASP324 4.9 20.8 1.0
O B:HOH440 5.0 29.5 1.0

Calcium binding site 7 out of 9 in 2rib

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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 L-Glycero-D- Manno-Heptose


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 L-Glycero-D- Manno-Heptose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:19.3
occ:1.00
 OE1 C:GLU329 2.5 17.3 1.0
OD1 C:ASP342 2.5 18.5 1.0
OD1 C:ASN323 2.5 17.2 1.0
OD1 C:ASN341 2.5 17.6 1.0
OE1 C:GLU321 2.6 18.8 1.0
O C:ASP342 2.7 16.4 1.0
O6 C:GMH356 2.7 21.0 1.0
O7 C:GMH356 2.8 19.9 1.0
CG C:ASP342 3.4 18.2 1.0
CD C:GLU321 3.4 20.1 1.0
CD C:GLU329 3.4 21.8 1.0
CG C:ASN341 3.5 20.5 1.0
C7 C:GMH356 3.5 21.6 1.0
CG C:ASN323 3.6 21.2 1.0
C6 C:GMH356 3.6 23.0 1.0
C C:ASP342 3.7 19.7 1.0
OE2 C:GLU321 3.7 21.6 1.0
N C:ASP342 3.7 17.8 1.0
OE2 C:GLU329 3.8 20.2 1.0
ND2 C:ASN341 3.8 19.4 1.0
OD2 C:ASP342 4.0 19.2 1.0
CA C:ASP342 4.1 17.4 1.0
ND2 C:ASN323 4.2 20.8 1.0
N C:ASN323 4.2 19.3 1.0
CB C:ASP342 4.3 17.2 1.0
C C:ASN341 4.5 20.1 1.0
CB C:ASP325 4.6 23.5 1.0
CG C:GLU321 4.6 20.8 1.0
N C:ASP325 4.7 20.7 1.0
CB C:ASN323 4.7 19.4 1.0
CG C:GLU329 4.7 19.3 1.0
CB C:ASN341 4.7 19.2 1.0
N C:ASP324 4.7 18.5 1.0
N C:ARG343 4.8 20.1 1.0
CA C:ASN323 4.8 19.8 1.0
C5 C:GMH356 4.9 25.9 1.0
CA C:ASN341 4.9 19.9 1.0
CB C:GLU329 4.9 19.8 1.0
O5 C:GMH356 4.9 27.6 1.0
C C:ASN323 5.0 19.9 1.0

Calcium binding site 8 out of 9 in 2rib

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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 L-Glycero-D- Manno-Heptose


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 L-Glycero-D- Manno-Heptose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:23.3
occ:1.00
 O C:HOH523 2.6 20.7 1.0
O C:GLU329 2.6 19.6 1.0
OD1 C:ASP330 2.6 21.8 1.0
OE1 C:GLU301 2.6 23.6 1.0
OD1 C:ASP324 2.6 20.8 1.0
OD2 C:ASP297 2.7 24.7 1.0
OE2 C:GLU301 2.7 22.7 1.0
OD1 C:ASP297 2.8 22.4 1.0
CD C:GLU301 3.0 25.9 1.0
CG C:ASP297 3.1 26.3 1.0
CG C:ASP324 3.4 23.6 1.0
C C:GLU329 3.4 20.3 1.0
CG C:ASP330 3.7 25.4 1.0
CA C:ASP330 3.8 21.1 1.0
CB C:ASP324 3.9 21.3 1.0
O C:HOH482 3.9 27.7 1.0
N C:ASP330 4.0 20.4 1.0
CA C:CA403 4.0 28.6 1.0
OD2 C:ASP324 4.3 22.3 1.0
CB C:ASP330 4.3 21.6 1.0
CZ C:PHE304 4.4 23.9 1.0
CA C:ASP324 4.4 19.4 1.0
N C:GLU329 4.4 21.7 1.0
CA C:GLU329 4.5 21.1 1.0
CG C:GLU301 4.5 26.9 1.0
OD2 C:ASP342 4.5 19.2 1.0
CB C:ASP297 4.6 24.3 1.0
OD2 C:ASP330 4.6 24.7 1.0
N C:GLY302 4.7 28.4 1.0
O C:HOH487 4.8 32.7 1.0
O C:ASP297 4.8 27.3 1.0
CE1 C:PHE304 4.9 23.6 1.0
O C:HOH415 4.9 23.7 1.0
CA C:GLU301 5.0 28.9 1.0

Calcium binding site 9 out of 9 in 2rib

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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 L-Glycero-D- Manno-Heptose


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 L-Glycero-D- Manno-Heptose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:28.6
occ:1.00
 OE1 C:GLU301 2.5 23.6 1.0
O C:HOH537 2.6 29.5 1.0
OD2 C:ASP330 2.6 24.7 1.0
O C:HOH524 2.7 27.7 1.0
OD1 C:ASP330 2.7 21.8 1.0
O C:HOH482 2.8 27.7 1.0
O C:HOH536 2.8 40.8 1.0
CG C:ASP330 3.0 25.4 1.0
CD C:GLU301 3.7 25.9 1.0
CA C:CA402 4.0 23.3 1.0
O C:HOH441 4.2 29.0 1.0
CB C:GLU301 4.3 28.7 1.0
O C:ASP297 4.3 27.3 1.0
OD1 C:ASP324 4.4 20.8 1.0
CG C:GLU301 4.4 26.9 1.0
CB C:ASP330 4.5 21.6 1.0
OE2 C:GLU301 4.6 22.7 1.0
CA C:GLU301 4.7 28.9 1.0
O C:HOH480 4.7 46.9 1.0
OD1 C:ASP297 4.9 22.4 1.0
O C:HOH450 4.9 28.7 1.0
OD2 C:ASP324 5.0 22.3 1.0
OD2 C:ASP297 5.0 24.7 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: Fri Jul 12 15:57:18 2024

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