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Calcium in PDB 1pwb: High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose

Protein crystallography data

The structure of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose, PDB code: 1pwb was solved by A.K.Shrive, H.A.Tharia, P.Strong, U.Kishore, I.Burns, P.J.Rizkallah, K.B.Reid, T.J.Greenhough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.10 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.480, 108.300, 55.780, 90.00, 91.43, 90.00
R / Rfree (%) 20.5 / 22.8

Calcium Binding Sites:

The binding sites of Calcium atom in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose (pdb code 1pwb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose, PDB code: 1pwb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1pwb

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Calcium binding site 1 out of 9 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:13.6
occ:1.00
 OD1 A:ASP342 2.4 11.6 1.0
OD1 A:ASN341 2.4 12.1 1.0
OE1 A:GLU329 2.5 13.2 1.0
OE1 A:GLU321 2.5 14.1 1.0
O3 A:GLC405 2.5 13.8 1.0
OD1 A:ASN323 2.5 15.1 1.0
O4 A:GLC405 2.6 12.8 1.0
O A:ASP342 2.7 11.6 1.0
C4 A:GLC405 3.3 16.2 1.0
CD A:GLU321 3.3 14.7 1.0
C3 A:GLC405 3.3 15.9 1.0
CG A:ASP342 3.4 12.2 1.0
CG A:ASN341 3.4 11.7 1.0
CG A:ASN323 3.5 16.5 1.0
CD A:GLU329 3.5 13.4 1.0
OE2 A:GLU321 3.6 15.7 1.0
C A:ASP342 3.7 11.3 1.0
N A:ASP342 3.8 11.4 1.0
OE2 A:GLU329 3.8 13.7 1.0
ND2 A:ASN341 3.9 12.4 1.0
ND2 A:ASN323 3.9 18.4 1.0
OD2 A:ASP342 4.1 11.2 1.0
N A:ASN323 4.2 14.6 1.0
CA A:ASP342 4.2 11.6 1.0
CB A:ASP342 4.4 10.7 1.0
C A:ASN341 4.6 12.2 1.0
CG A:GLU321 4.6 13.9 1.0
CB A:ASP325 4.6 15.3 1.0
CB A:ASN323 4.7 14.7 1.0
CB A:ASN341 4.7 11.2 1.0
N A:ASP325 4.7 13.7 1.0
C2 A:GLC405 4.7 17.4 1.0
N A:ASP324 4.7 12.5 1.0
C5 A:GLC405 4.8 17.5 1.0
CG A:GLU329 4.8 13.7 1.0
CA A:ASN323 4.8 14.1 1.0
CA A:ASN341 4.9 11.8 1.0
N A:ARG343 4.9 11.7 1.0
CB A:GLU329 5.0 12.3 1.0
CB A:GLU321 5.0 14.7 1.0

Calcium binding site 2 out of 9 in 1pwb

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Calcium binding site 2 out of 9 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:13.3
occ:1.00
 OD1 A:ASP330 2.4 13.4 1.0
O A:GLU329 2.4 11.4 1.0
OD1 A:ASP324 2.5 13.3 1.0
OE1 A:GLU301 2.5 13.1 1.0
O A:HOH411 2.5 12.2 1.0
OE2 A:GLU301 2.5 13.9 1.0
OD2 A:ASP297 2.5 12.9 1.0
OD1 A:ASP297 2.7 12.9 1.0
CD A:GLU301 2.8 14.2 1.0
CG A:ASP297 3.0 11.6 1.0
CG A:ASP324 3.3 13.6 1.0
C A:GLU329 3.3 10.8 1.0
CG A:ASP330 3.5 14.5 1.0
CA A:ASP330 3.8 12.0 1.0
CA A:CA403 3.9 15.8 1.0
N A:ASP330 3.9 10.9 1.0
CB A:ASP324 4.0 11.7 1.0
OD2 A:ASP324 4.1 14.9 1.0
CB A:ASP330 4.2 12.7 1.0
N A:GLU329 4.3 13.7 1.0
O A:HOH475 4.3 23.2 1.0
CG A:GLU301 4.3 14.8 1.0
CA A:GLU329 4.4 12.4 1.0
CZ A:PHE304 4.5 11.9 1.0
OD2 A:ASP330 4.5 15.9 1.0
CB A:ASP297 4.5 13.2 1.0
CA A:ASP324 4.5 12.6 1.0
OD2 A:ASP342 4.6 11.2 1.0
N A:GLY302 4.6 16.6 1.0
O A:ASP297 4.8 14.9 1.0
O A:HOH426 4.8 16.3 1.0
O A:HOH414 4.8 16.1 1.0
O A:HOH417 4.9 14.7 1.0
CB A:GLU329 4.9 12.3 1.0
CE1 A:PHE304 5.0 12.7 1.0
CA A:GLU301 5.0 15.7 1.0
C A:ASP330 5.0 11.7 1.0

Calcium binding site 3 out of 9 in 1pwb

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Calcium binding site 3 out of 9 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:15.8
occ:1.00
 O A:HOH417 2.4 14.7 1.0
OE1 A:GLU301 2.4 13.1 1.0
O A:HOH461 2.4 17.7 1.0
O A:HOH564 2.5 48.7 1.0
O A:HOH475 2.5 23.2 1.0
OD2 A:ASP330 2.6 15.9 1.0
OD1 A:ASP330 2.6 13.4 1.0
CG A:ASP330 2.9 14.5 1.0
CD A:GLU301 3.5 14.2 1.0
CA A:CA402 3.9 13.3 1.0
CB A:GLU301 4.2 15.2 1.0
CG A:GLU301 4.3 14.8 1.0
OD1 A:ASP324 4.3 13.3 1.0
O A:ASP297 4.4 14.9 1.0
CB A:ASP330 4.5 12.7 1.0
OE2 A:GLU301 4.5 13.9 1.0
OD1 A:ASP297 4.7 12.9 1.0
CA A:GLU301 4.7 15.7 1.0
OD2 A:ASP324 4.8 14.9 1.0
O A:HOH425 4.9 16.2 1.0
O A:GLY327 4.9 18.0 1.0
CG A:ASP324 5.0 13.6 1.0

Calcium binding site 4 out of 9 in 1pwb

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Calcium binding site 4 out of 9 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:10.8
occ:1.00
 OD1 B:ASP342 2.4 10.8 1.0
OE1 B:GLU329 2.4 11.4 1.0
OD1 B:ASN341 2.5 12.3 1.0
OD1 B:ASN323 2.5 11.7 1.0
O4 B:GLC405 2.5 12.0 1.0
O3 B:GLC405 2.6 13.3 1.0
O B:ASP342 2.6 10.9 1.0
OE1 B:GLU321 2.6 11.6 1.0
C4 B:GLC405 3.3 15.4 1.0
C3 B:GLC405 3.3 16.0 1.0
CG B:ASP342 3.4 11.0 1.0
CD B:GLU329 3.4 10.4 1.0
CG B:ASN341 3.5 11.5 1.0
CD B:GLU321 3.5 10.2 1.0
CG B:ASN323 3.5 12.0 1.0
C B:ASP342 3.6 10.7 1.0
OE2 B:GLU329 3.7 11.2 1.0
N B:ASP342 3.7 10.6 1.0
OE2 B:GLU321 3.8 13.2 1.0
ND2 B:ASN341 3.9 10.8 1.0
ND2 B:ASN323 4.0 12.3 1.0
OD2 B:ASP342 4.1 11.1 1.0
CA B:ASP342 4.1 10.8 1.0
N B:ASN323 4.2 11.3 1.0
CB B:ASP342 4.3 10.2 1.0
C B:ASN341 4.5 11.3 1.0
CB B:ASP325 4.5 16.3 1.0
CB B:ASN323 4.7 12.2 1.0
N B:ASP325 4.7 13.1 1.0
CG B:GLU329 4.7 11.3 1.0
CB B:ASN341 4.7 10.9 1.0
CG B:GLU321 4.7 11.1 1.0
N B:ASP324 4.7 11.6 1.0
C5 B:GLC405 4.7 18.6 1.0
C2 B:GLC405 4.8 19.1 1.0
N B:ARG343 4.8 11.0 1.0
CA B:ASN323 4.8 11.3 1.0
CA B:ASN341 4.8 10.8 1.0
CB B:GLU329 4.9 12.3 1.0
C B:ASN323 5.0 12.0 1.0

Calcium binding site 5 out of 9 in 1pwb

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Calcium binding site 5 out of 9 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:12.8
occ:1.00
 OD1 B:ASP330 2.4 14.3 1.0
O B:HOH409 2.4 13.3 1.0
O B:GLU329 2.5 10.8 1.0
OD2 B:ASP297 2.5 15.8 1.0
OE2 B:GLU301 2.5 14.7 1.0
OE1 B:GLU301 2.5 14.9 1.0
OD1 B:ASP324 2.5 15.1 1.0
OD1 B:ASP297 2.7 14.8 1.0
CD B:GLU301 2.8 14.4 1.0
CG B:ASP297 3.0 14.5 1.0
C B:GLU329 3.4 11.8 1.0
CG B:ASP324 3.4 15.3 1.0
CG B:ASP330 3.6 14.8 1.0
CA B:ASP330 3.8 12.0 1.0
CA B:CA403 3.9 18.1 1.0
O B:HOH417 3.9 16.0 1.0
N B:ASP330 4.0 12.2 1.0
CB B:ASP324 4.0 12.8 1.0
OD2 B:ASP324 4.2 16.6 1.0
CB B:ASP330 4.2 13.1 1.0
CG B:GLU301 4.3 15.2 1.0
O B:HOH465 4.4 27.1 1.0
N B:GLU329 4.5 13.9 1.0
CB B:ASP297 4.5 13.6 1.0
CA B:GLU329 4.5 12.5 1.0
OD2 B:ASP330 4.5 15.8 1.0
CZ B:PHE304 4.5 12.8 1.0
CA B:ASP324 4.6 12.6 1.0
OD2 B:ASP342 4.6 11.1 1.0
N B:GLY302 4.7 18.1 1.0
O B:ASP297 4.8 16.4 1.0
O B:HOH461 4.9 23.9 1.0
O B:HOH420 4.9 16.9 1.0
CA B:GLU301 5.0 18.9 1.0
CE1 B:PHE304 5.0 11.8 1.0
C B:ASP330 5.0 11.5 1.0

Calcium binding site 6 out of 9 in 1pwb

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Calcium binding site 6 out of 9 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:18.1
occ:1.00
 O B:HOH420 2.2 16.9 1.0
O B:HOH429 2.3 19.2 1.0
OE1 B:GLU301 2.4 14.9 1.0
O B:HOH417 2.4 16.0 1.0
O B:HOH501 2.4 23.1 1.0
OD1 B:ASP330 2.5 14.3 1.0
OD2 B:ASP330 2.5 15.8 1.0
CG B:ASP330 2.9 14.8 1.0
CD B:GLU301 3.6 14.4 1.0
CA B:CA402 3.9 12.8 1.0
CB B:GLU301 4.2 17.6 1.0
O B:HOH466 4.2 22.0 1.0
O B:ASP297 4.3 16.4 1.0
CG B:GLU301 4.3 15.2 1.0
OD1 B:ASP324 4.3 15.1 1.0
CB B:ASP330 4.4 13.1 1.0
O B:HOH580 4.4 35.6 1.0
OE2 B:GLU301 4.5 14.7 1.0
O B:HOH487 4.6 25.3 1.0
OD1 B:ASP297 4.7 14.8 1.0
CA B:GLU301 4.7 18.9 1.0
O B:HOH578 4.8 38.7 1.0
OD2 B:ASP297 4.8 15.8 1.0
OD2 B:ASP324 4.9 16.6 1.0
CG B:ASP297 5.0 14.5 1.0

Calcium binding site 7 out of 9 in 1pwb

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Calcium binding site 7 out of 9 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:13.0
occ:1.00
 OD1 C:ASP342 2.3 10.8 1.0
OD1 C:ASN341 2.4 12.0 1.0
OE1 C:GLU329 2.4 12.6 1.0
OD1 C:ASN323 2.5 11.2 1.0
O3 C:GLC405 2.5 13.0 1.0
OE1 C:GLU321 2.6 12.0 1.0
O C:ASP342 2.6 10.9 1.0
O4 C:GLC405 2.7 14.6 1.0
CG C:ASP342 3.3 10.2 1.0
C3 C:GLC405 3.4 18.1 1.0
C4 C:GLC405 3.4 18.9 1.0
CG C:ASN341 3.4 12.2 1.0
CD C:GLU329 3.4 13.2 1.0
CD C:GLU321 3.4 12.2 1.0
CG C:ASN323 3.5 12.6 1.0
C C:ASP342 3.7 11.6 1.0
OE2 C:GLU321 3.7 13.8 1.0
N C:ASP342 3.7 11.2 1.0
OE2 C:GLU329 3.8 13.6 1.0
ND2 C:ASN341 3.8 12.1 1.0
ND2 C:ASN323 4.0 13.6 1.0
OD2 C:ASP342 4.1 10.4 1.0
CA C:ASP342 4.1 11.4 1.0
N C:ASN323 4.2 11.1 1.0
CB C:ASP342 4.3 10.8 1.0
C C:ASN341 4.5 11.5 1.0
CB C:ASP325 4.6 17.0 1.0
CB C:ASN323 4.7 11.3 1.0
CG C:GLU321 4.7 10.8 1.0
N C:ASP325 4.7 12.3 1.0
CB C:ASN341 4.7 11.1 1.0
CG C:GLU329 4.7 11.9 1.0
N C:ASP324 4.8 11.6 1.0
C2 C:GLC405 4.8 19.6 1.0
CA C:ASN323 4.8 11.1 1.0
C5 C:GLC405 4.8 21.7 1.0
N C:ARG343 4.8 12.6 1.0
CA C:ASN341 4.9 11.4 1.0
CB C:GLU329 4.9 11.7 1.0
C C:ASN323 5.0 12.1 1.0

Calcium binding site 8 out of 9 in 1pwb

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Calcium binding site 8 out of 9 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:15.0
occ:1.00
 O C:GLU329 2.4 12.6 1.0
O C:HOH406 2.4 12.1 1.0
OD1 C:ASP330 2.4 14.4 1.0
OD1 C:ASP324 2.5 13.4 1.0
OD2 C:ASP297 2.5 14.7 1.0
OE2 C:GLU301 2.6 15.3 1.0
OE1 C:GLU301 2.6 16.0 1.0
OD1 C:ASP297 2.7 13.4 1.0
CD C:GLU301 2.9 17.2 1.0
CG C:ASP297 3.0 14.3 1.0
CG C:ASP324 3.3 13.4 1.0
C C:GLU329 3.3 13.4 1.0
CG C:ASP330 3.6 16.8 1.0
CA C:ASP330 3.8 13.5 1.0
O C:HOH417 3.9 16.1 1.0
CA C:CA403 3.9 17.8 1.0
CB C:ASP324 3.9 12.4 1.0
N C:ASP330 3.9 12.6 1.0
OD2 C:ASP324 4.2 13.3 1.0
CB C:ASP330 4.3 14.4 1.0
CG C:GLU301 4.4 17.1 1.0
N C:GLU329 4.4 15.2 1.0
CA C:ASP324 4.4 11.5 1.0
CA C:GLU329 4.4 13.2 1.0
CZ C:PHE304 4.5 15.2 1.0
OD2 C:ASP330 4.5 17.2 1.0
CB C:ASP297 4.5 14.8 1.0
OD2 C:ASP342 4.6 10.4 1.0
N C:GLY302 4.7 18.9 1.0
O C:ASP297 4.8 17.5 1.0
CE1 C:PHE304 4.9 14.1 1.0
O C:HOH433 4.9 20.4 1.0
O C:HOH441 4.9 16.8 1.0
CB C:GLU329 5.0 11.7 1.0
CA C:GLU301 5.0 19.5 1.0
C C:ASP330 5.0 12.3 1.0
O C:HOH409 5.0 15.0 1.0

Calcium binding site 9 out of 9 in 1pwb

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Calcium binding site 9 out of 9 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:17.8
occ:1.00
 OE1 C:GLU301 2.3 16.0 1.0
O C:HOH417 2.3 16.1 1.0
O C:HOH418 2.4 18.6 1.0
O C:HOH441 2.4 16.8 1.0
OD2 C:ASP330 2.5 17.2 1.0
OD1 C:ASP330 2.5 14.4 1.0
O C:HOH489 2.6 23.3 1.0
CG C:ASP330 2.9 16.8 1.0
CD C:GLU301 3.5 17.2 1.0
CA C:CA402 3.9 15.0 1.0
CB C:GLU301 4.1 18.8 1.0
CG C:GLU301 4.2 17.1 1.0
O C:HOH446 4.2 19.8 1.0
OD1 C:ASP324 4.2 13.4 1.0
O C:ASP297 4.4 17.5 1.0
CB C:ASP330 4.4 14.4 1.0
OE2 C:GLU301 4.4 15.3 1.0
CA C:GLU301 4.6 19.5 1.0
O C:HOH520 4.7 30.9 1.0
OD1 C:ASP297 4.7 13.4 1.0
OD2 C:ASP324 4.9 13.3 1.0
O C:HOH422 4.9 19.2 1.0
OD2 C:ASP297 4.9 14.7 1.0
CG C:ASP324 4.9 13.4 1.0

Reference:

A.K.Shrive, H.A.Tharia, P.Strong, U.Kishore, I.Burns, P.J.Rizkallah, K.B.Reid, T.J.Greenhough. High-Resolution Structural Insights Into Ligand Binding and Immune Cell Recognition By Human Lung Surfactant Protein D J.Mol.Biol. V. 331 509 2003.
ISSN: ISSN 0022-2836
PubMed: 12888356
DOI: 10.1016/S0022-2836(03)00761-7
Page generated: Thu Jul 11 13:54:14 2024

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