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Calcium in PDB 2ggx: Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside

Protein crystallography data

The structure of Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside, PDB code: 2ggx was solved by J.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 (°) 55.431, 106.400, 55.080, 90.00, 92.65, 90.00
R / Rfree (%) 21.4 / 23.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside (pdb code 2ggx). 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 Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside, PDB code: 2ggx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2ggx

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Calcium binding site 1 out of 9 in the Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside


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 Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:22.0
occ:1.00
 OD1 A:ASP342 2.2 21.2 1.0
OE1 A:GLU329 2.4 21.1 1.0
OD1 A:ASN323 2.4 24.6 1.0
OE1 A:GLU321 2.4 23.7 1.0
OD1 A:ASN341 2.5 26.0 1.0
O3A A:NPJ700 2.6 31.5 1.0
O A:ASP342 2.6 19.7 1.0
O4A A:NPJ700 2.6 32.2 1.0
CG A:ASP342 3.3 22.8 1.0
CD A:GLU321 3.3 23.8 1.0
CG A:ASN323 3.4 29.9 1.0
C3A A:NPJ700 3.4 33.2 1.0
CD A:GLU329 3.4 20.6 1.0
C4A A:NPJ700 3.5 32.7 1.0
CG A:ASN341 3.5 24.6 1.0
C A:ASP342 3.6 20.8 1.0
OE2 A:GLU321 3.7 24.2 1.0
N A:ASP342 3.7 20.9 1.0
OE2 A:GLU329 3.8 19.9 1.0
ND2 A:ASN323 3.9 28.7 1.0
OD2 A:ASP342 4.0 21.8 1.0
ND2 A:ASN341 4.0 23.3 1.0
CA A:ASP342 4.1 21.2 1.0
N A:ASN323 4.1 26.7 1.0
CB A:ASP342 4.3 20.5 1.0
CG A:GLU321 4.5 23.1 1.0
C A:ASN341 4.5 21.8 1.0
CB A:ASP325 4.6 27.5 1.0
N A:ASP324 4.6 24.6 1.0
CB A:ASN323 4.6 27.1 1.0
N A:ASP325 4.6 25.8 1.0
CG A:GLU329 4.7 21.4 1.0
CB A:ASN341 4.7 22.6 1.0
CA A:ASN323 4.8 26.2 1.0
N A:ARG343 4.8 19.6 1.0
CA A:ASN341 4.9 21.9 1.0
C2A A:NPJ700 4.9 33.6 1.0
C5A A:NPJ700 4.9 33.1 1.0
CB A:GLU329 4.9 23.0 1.0
CB A:GLU321 5.0 24.9 1.0

Calcium binding site 2 out of 9 in 2ggx

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Calcium binding site 2 out of 9 in the Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside


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 Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:21.7
occ:1.00
 O A:HOH777 2.3 25.6 1.0
OD1 A:ASP330 2.4 20.3 1.0
OD2 A:ASP297 2.4 26.1 1.0
O A:GLU329 2.4 19.2 1.0
OD1 A:ASP324 2.5 23.3 1.0
OE2 A:GLU301 2.5 21.9 1.0
OE1 A:GLU301 2.6 22.9 1.0
OD1 A:ASP297 2.7 22.4 1.0
CD A:GLU301 2.9 24.3 1.0
CG A:ASP297 2.9 23.2 1.0
C A:GLU329 3.3 21.2 1.0
CG A:ASP324 3.3 27.0 1.0
CG A:ASP330 3.5 21.9 1.0
CA A:ASP330 3.7 21.9 1.0
CA A:CA403 3.8 30.1 1.0
N A:ASP330 3.9 20.6 1.0
CB A:ASP324 4.0 22.8 1.0
O A:HOH788 4.1 34.5 1.0
OD2 A:ASP324 4.1 25.5 1.0
CB A:ASP330 4.2 19.9 1.0
N A:GLU329 4.2 24.2 1.0
OD2 A:ASP330 4.4 21.1 1.0
CA A:GLU329 4.4 22.5 1.0
CG A:GLU301 4.4 26.6 1.0
CZ A:PHE304 4.4 26.5 1.0
CB A:ASP297 4.4 25.6 1.0
CA A:ASP324 4.5 24.2 1.0
N A:GLY302 4.6 26.8 1.0
OD2 A:ASP342 4.7 21.8 1.0
O A:HOH703 4.7 25.1 1.0
O A:ASP297 4.8 24.8 1.0
CB A:GLU329 4.9 23.0 1.0
O A:HOH778 4.9 25.5 1.0
O A:HOH718 4.9 25.3 1.0
CA A:GLU301 5.0 28.2 1.0
C A:ASP330 5.0 22.5 1.0
CE1 A:PHE304 5.0 25.0 1.0

Calcium binding site 3 out of 9 in 2ggx

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Calcium binding site 3 out of 9 in the Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside


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 Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:30.1
occ:1.00
 O A:HOH788 2.3 34.5 1.0
O A:HOH703 2.4 25.1 1.0
OE1 A:GLU301 2.4 22.9 1.0
O A:HOH784 2.4 44.2 1.0
OD2 A:ASP330 2.5 21.1 1.0
OD1 A:ASP330 2.6 20.3 1.0
CG A:ASP330 2.9 21.9 1.0
CD A:GLU301 3.6 24.3 1.0
CA A:CA402 3.8 21.7 1.0
OD1 A:ASP324 4.2 23.3 1.0
CG A:GLU301 4.4 26.6 1.0
CB A:GLU301 4.4 27.0 1.0
CB A:ASP330 4.4 19.9 1.0
OE2 A:GLU301 4.5 21.9 1.0
O A:ASP297 4.5 24.8 1.0
OD2 A:ASP324 4.7 25.5 1.0
OD1 A:ASP297 4.7 22.4 1.0
O A:GLY327 4.8 26.8 1.0
CG A:ASP324 4.9 27.0 1.0
CA A:GLU301 4.9 28.2 1.0
OD2 A:ASP297 4.9 26.1 1.0
O A:HOH720 5.0 34.9 1.0

Calcium binding site 4 out of 9 in 2ggx

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Calcium binding site 4 out of 9 in the Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside


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 Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:19.1
occ:1.00
 OD1 B:ASP342 2.3 19.7 1.0
OE1 B:GLU329 2.4 21.2 1.0
OD1 B:ASN341 2.4 23.0 1.0
OD1 B:ASN323 2.4 22.6 1.0
OE1 B:GLU321 2.5 16.1 1.0
O3A B:NPJ700 2.5 18.7 1.0
O4A B:NPJ700 2.5 19.6 1.0
O B:ASP342 2.6 18.8 1.0
C3A B:NPJ700 3.3 22.6 1.0
CD B:GLU321 3.3 20.9 1.0
CG B:ASP342 3.3 20.3 1.0
C4A B:NPJ700 3.4 22.8 1.0
CG B:ASN341 3.4 22.4 1.0
CD B:GLU329 3.4 22.8 1.0
CG B:ASN323 3.4 21.6 1.0
OE2 B:GLU321 3.6 19.9 1.0
C B:ASP342 3.7 18.8 1.0
N B:ASP342 3.7 19.4 1.0
OE2 B:GLU329 3.8 19.1 1.0
ND2 B:ASN341 3.8 20.7 1.0
ND2 B:ASN323 4.0 21.8 1.0
OD2 B:ASP342 4.0 19.4 1.0
CA B:ASP342 4.1 19.9 1.0
N B:ASN323 4.2 21.4 1.0
CB B:ASP342 4.3 19.7 1.0
C B:ASN341 4.4 19.8 1.0
CB B:ASP325 4.5 29.9 1.0
CG B:GLU321 4.6 19.8 1.0
CB B:ASN323 4.6 20.6 1.0
CB B:ASN341 4.6 20.9 1.0
CG B:GLU329 4.7 22.7 1.0
N B:ASP325 4.7 26.2 1.0
N B:ASP324 4.7 23.4 1.0
C2A B:NPJ700 4.7 25.2 1.0
CA B:ASN341 4.8 20.1 1.0
C5A B:NPJ700 4.8 24.9 1.0
CA B:ASN323 4.8 22.8 1.0
N B:ARG343 4.8 19.9 1.0
CB B:GLU329 4.9 23.3 1.0
C B:ASN323 5.0 22.1 1.0

Calcium binding site 5 out of 9 in 2ggx

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Calcium binding site 5 out of 9 in the Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside


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 Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:24.2
occ:1.00
 OD2 B:ASP297 2.4 30.4 1.0
OD1 B:ASP330 2.4 25.1 1.0
O B:HOH783 2.4 20.5 1.0
O B:GLU329 2.5 21.8 1.0
OE1 B:GLU301 2.5 28.7 1.0
OD1 B:ASP324 2.6 26.0 1.0
OE2 B:GLU301 2.6 28.9 1.0
OD1 B:ASP297 2.6 25.9 1.0
CG B:ASP297 2.9 28.8 1.0
CD B:GLU301 2.9 31.5 1.0
C B:GLU329 3.4 23.8 1.0
CG B:ASP324 3.4 26.4 1.0
CG B:ASP330 3.5 26.6 1.0
CA B:ASP330 3.7 23.7 1.0
CA B:CA403 3.9 33.2 1.0
CB B:ASP324 3.9 23.5 1.0
N B:ASP330 3.9 22.8 1.0
O B:HOH784 4.0 28.7 1.0
CB B:ASP330 4.2 24.3 1.0
OD2 B:ASP324 4.3 25.4 1.0
CB B:ASP297 4.4 29.1 1.0
CG B:GLU301 4.4 32.7 1.0
N B:GLU329 4.4 25.7 1.0
OD2 B:ASP330 4.4 26.3 1.0
CA B:GLU329 4.5 24.3 1.0
CZ B:PHE304 4.5 23.8 1.0
CA B:ASP324 4.5 24.8 1.0
OD2 B:ASP342 4.6 19.4 1.0
O B:ASP297 4.7 31.2 1.0
N B:GLY302 4.7 33.0 1.0
CA B:GLU301 4.9 35.0 1.0
CE1 B:PHE304 4.9 23.5 1.0
O B:HOH787 4.9 27.1 1.0
C B:ASP330 5.0 21.8 1.0

Calcium binding site 6 out of 9 in 2ggx

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Calcium binding site 6 out of 9 in the Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside


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 Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:33.2
occ:1.00
 O B:HOH787 2.3 27.1 1.0
OE1 B:GLU301 2.4 28.7 1.0
OD2 B:ASP330 2.4 26.3 1.0
O B:HOH784 2.4 28.7 1.0
O B:HOH788 2.4 40.1 1.0
O B:HOH781 2.5 24.2 1.0
OD1 B:ASP330 2.6 25.1 1.0
CG B:ASP330 2.8 26.6 1.0
CD B:GLU301 3.6 31.5 1.0
CA B:CA402 3.9 24.2 1.0
CB B:GLU301 4.2 33.9 1.0
O B:ASP297 4.2 31.2 1.0
CG B:GLU301 4.3 32.7 1.0
OD1 B:ASP324 4.3 26.0 1.0
CB B:ASP330 4.3 24.3 1.0
O B:HOH754 4.5 33.3 1.0
OE2 B:GLU301 4.5 28.9 1.0
O B:HOH768 4.6 48.1 1.0
OD1 B:ASP297 4.7 25.9 1.0
CA B:GLU301 4.7 35.0 1.0
OD2 B:ASP297 4.8 30.4 1.0
CG B:ASP297 4.9 28.8 1.0
O B:HOH725 4.9 30.5 1.0
O B:GLY327 5.0 27.8 1.0

Calcium binding site 7 out of 9 in 2ggx

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Calcium binding site 7 out of 9 in the Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside


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 Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:20.7
occ:1.00
 OD1 C:ASP342 2.3 19.3 1.0
OE1 C:GLU329 2.3 21.5 1.0
OD1 C:ASN341 2.4 22.6 1.0
ND2 C:ASN323 2.5 17.9 1.0
O4A C:NPJ700 2.5 25.7 1.0
O3A C:NPJ700 2.5 23.2 1.0
OE1 C:GLU321 2.6 23.4 1.0
O C:ASP342 2.6 19.6 1.0
C3A C:NPJ700 3.3 27.2 1.0
CG C:ASP342 3.3 20.9 1.0
C4A C:NPJ700 3.4 29.1 1.0
CG C:ASN341 3.4 20.9 1.0
CD C:GLU329 3.4 23.1 1.0
CD C:GLU321 3.4 19.8 1.0
CG C:ASN323 3.5 24.3 1.0
C C:ASP342 3.7 21.0 1.0
N C:ASP342 3.7 19.1 1.0
OE2 C:GLU321 3.8 19.9 1.0
ND2 C:ASN341 3.8 22.4 1.0
OE2 C:GLU329 3.8 24.9 1.0
OD1 C:ASN323 4.0 24.1 1.0
OD2 C:ASP342 4.0 20.6 1.0
CA C:ASP342 4.1 19.8 1.0
N C:ASN323 4.1 22.1 1.0
CB C:ASP342 4.3 19.2 1.0
C C:ASN341 4.5 19.9 1.0
CB C:ASP325 4.6 32.1 1.0
CG C:GLU321 4.6 20.2 1.0
CB C:ASN341 4.6 19.9 1.0
CB C:ASN323 4.7 20.5 1.0
N C:ASP325 4.7 27.1 1.0
CG C:GLU329 4.7 23.2 1.0
N C:ASP324 4.7 23.1 1.0
C5A C:NPJ700 4.8 30.7 1.0
C2A C:NPJ700 4.8 27.1 1.0
CA C:ASN323 4.8 21.9 1.0
N C:ARG343 4.8 21.7 1.0
CA C:ASN341 4.8 19.8 1.0
CB C:GLU329 4.9 23.9 1.0
C C:ASN323 4.9 21.1 1.0

Calcium binding site 8 out of 9 in 2ggx

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Calcium binding site 8 out of 9 in the Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside


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 Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:27.0
occ:1.00
 OD1 C:ASP330 2.3 24.3 1.0
O C:HOH702 2.4 18.8 1.0
O C:GLU329 2.4 25.6 1.0
OD2 C:ASP297 2.5 30.4 1.0
OD1 C:ASP324 2.5 26.0 1.0
OE2 C:GLU301 2.5 27.5 1.0
OE1 C:GLU301 2.6 29.7 1.0
OD1 C:ASP297 2.7 26.6 1.0
CD C:GLU301 2.9 29.0 1.0
CG C:ASP297 2.9 30.5 1.0
CG C:ASP324 3.3 28.1 1.0
C C:GLU329 3.4 25.3 1.0
CG C:ASP330 3.5 26.2 1.0
CA C:ASP330 3.7 24.7 1.0
CB C:ASP324 3.8 24.9 1.0
O C:HOH776 3.9 32.4 1.0
CA C:CA403 3.9 38.4 1.0
N C:ASP330 4.0 24.1 1.0
CB C:ASP330 4.1 24.5 1.0
OD2 C:ASP324 4.2 25.3 1.0
CG C:GLU301 4.4 31.2 1.0
CZ C:PHE304 4.4 28.5 1.0
N C:GLU329 4.4 26.0 1.0
OD2 C:ASP330 4.4 27.1 1.0
CB C:ASP297 4.4 30.6 1.0
CA C:ASP324 4.5 24.0 1.0
CA C:GLU329 4.5 24.9 1.0
OD2 C:ASP342 4.6 20.6 1.0
N C:GLY302 4.7 32.5 1.0
O C:ASP297 4.7 33.0 1.0
CE1 C:PHE304 4.9 27.1 1.0
CA C:GLU301 4.9 34.3 1.0
C C:ASP330 5.0 24.8 1.0

Calcium binding site 9 out of 9 in 2ggx

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Calcium binding site 9 out of 9 in the Crystal Structure of the Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside


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 Trimer Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with P-Nitrophenyl Maltoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:38.4
occ:1.00
 OE1 C:GLU301 2.3 29.7 1.0
O C:HOH776 2.3 32.4 1.0
O C:HOH779 2.4 30.2 1.0
O C:HOH774 2.5 27.3 1.0
OD2 C:ASP330 2.6 27.1 1.0
O C:HOH777 2.6 39.7 1.0
OD1 C:ASP330 2.7 24.3 1.0
CG C:ASP330 2.9 26.2 1.0
CD C:GLU301 3.5 29.0 1.0
CA C:CA402 3.9 27.0 1.0
CB C:GLU301 4.1 32.6 1.0
CG C:GLU301 4.2 31.2 1.0
OD1 C:ASP324 4.3 26.0 1.0
O C:ASP297 4.3 33.0 1.0
CB C:ASP330 4.4 24.5 1.0
OE2 C:GLU301 4.5 27.5 1.0
CA C:GLU301 4.6 34.3 1.0
OD1 C:ASP297 4.7 26.6 1.0
OD2 C:ASP324 4.8 25.3 1.0
OD2 C:ASP297 4.9 30.4 1.0
CG C:ASP324 4.9 28.1 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 10:46:02 2024

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