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Calcium in PDB 3ikq: Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D

Protein crystallography data

The structure of Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D, PDB code: 3ikq was solved by A.K.Shrive, T.J.Greenhough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.45 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.910, 108.780, 56.080, 90.00, 90.19, 90.00
R / Rfree (%) 20.2 / 23.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D (pdb code 3ikq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D, PDB code: 3ikq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3ikq

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Calcium binding site 1 out of 10 in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D


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 Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:21.5
occ:1.00
OD1 A:ASP342 2.3 20.8 1.0
OE1 A:GLU329 2.3 17.2 1.0
OE1 A:GLU321 2.4 25.2 1.0
OD1 A:ASN341 2.5 19.3 1.0
OD1 A:ASN323 2.6 25.2 1.0
O4 A:MAN405 2.6 30.3 1.0
O A:ASP342 2.7 16.4 1.0
O3 A:MAN405 2.8 28.8 1.0
CG A:ASP342 3.2 19.9 1.0
CD A:GLU321 3.3 26.6 1.0
CD A:GLU329 3.4 17.3 1.0
C4 A:MAN405 3.4 33.8 1.0
CG A:ASN323 3.4 25.7 1.0
CG A:ASN341 3.5 20.1 1.0
C3 A:MAN405 3.6 33.7 1.0
C A:ASP342 3.7 18.9 1.0
OE2 A:GLU321 3.7 27.5 1.0
OE2 A:GLU329 3.7 18.4 1.0
N A:ASP342 3.8 18.4 1.0
OD2 A:ASP342 3.8 20.5 1.0
ND2 A:ASN323 3.8 25.7 1.0
ND2 A:ASN341 3.9 18.2 1.0
CA A:ASP342 4.1 18.6 1.0
N A:ASN323 4.2 22.8 1.0
CB A:ASP342 4.2 19.7 1.0
CG A:GLU321 4.5 24.7 1.0
C A:ASN341 4.6 19.4 1.0
CB A:ASN323 4.7 23.3 1.0
CG A:GLU329 4.7 18.1 1.0
N A:ASP324 4.7 22.2 1.0
CB A:ASP325 4.7 25.1 1.0
CB A:ASN341 4.8 18.8 1.0
N A:ASP325 4.8 22.9 1.0
N A:ARG343 4.8 19.1 1.0
CA A:ASN323 4.8 23.1 1.0
C5 A:MAN405 4.8 34.7 1.0
CB A:GLU329 4.9 20.0 1.0
CA A:ASN341 4.9 18.7 1.0
C2 A:MAN405 5.0 35.2 1.0
CB A:GLU321 5.0 25.8 1.0

Calcium binding site 2 out of 10 in 3ikq

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Calcium binding site 2 out of 10 in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D


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 Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:21.4
occ:1.00
OD1 A:ASP330 2.4 24.2 1.0
OD2 A:ASP297 2.5 25.5 1.0
OD1 A:ASP324 2.5 22.3 1.0
OE2 A:GLU301 2.5 19.5 1.0
OE1 A:GLU301 2.6 21.4 1.0
O A:GLU329 2.6 19.2 1.0
OD1 A:ASP297 2.9 26.7 1.0
CD A:GLU301 2.9 23.5 1.0
CG A:ASP297 3.0 26.2 1.0
CG A:ASP324 3.3 22.9 1.0
C A:GLU329 3.4 20.7 1.0
CG A:ASP330 3.5 23.3 1.0
CA A:ASP330 3.8 21.7 1.0
N A:ASP330 4.0 20.6 1.0
CB A:ASP324 4.0 19.4 1.0
CA A:CA403 4.0 25.0 1.0
O A:HOH64 4.0 26.6 1.0
OD2 A:ASP324 4.1 25.2 1.0
CB A:ASP330 4.2 22.4 1.0
N A:GLU329 4.3 20.9 1.0
CG A:GLU301 4.4 25.2 1.0
CA A:GLU329 4.5 21.0 1.0
OD2 A:ASP330 4.5 22.2 1.0
CA A:ASP324 4.5 21.3 1.0
CB A:ASP297 4.5 26.4 1.0
CZ A:PHE304 4.6 18.7 1.0
N A:GLY302 4.7 28.7 1.0
OD2 A:ASP342 4.8 20.5 1.0
O A:HOH161 4.8 26.5 1.0
O A:HOH45 4.8 18.1 1.0
O A:ASP297 4.8 29.1 1.0
O A:HOH159 5.0 19.7 1.0
CB A:GLU329 5.0 20.0 1.0

Calcium binding site 3 out of 10 in 3ikq

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Calcium binding site 3 out of 10 in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D


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 Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:25.0
occ:1.00
O A:HOH159 2.3 19.7 1.0
OE1 A:GLU301 2.3 21.4 1.0
O A:HOH64 2.5 26.6 1.0
OD2 A:ASP330 2.6 22.2 1.0
OD1 A:ASP330 2.7 24.2 1.0
CG A:ASP330 3.0 23.3 1.0
CD A:GLU301 3.5 23.5 1.0
CA A:CA402 4.0 21.4 1.0
CG A:GLU301 4.2 25.2 1.0
CB A:GLU301 4.3 26.6 1.0
OD1 A:ASP324 4.4 22.3 1.0
O A:ASP297 4.4 29.1 1.0
OE2 A:GLU301 4.4 19.5 1.0
CB A:ASP330 4.5 22.4 1.0
CA A:GLU301 4.7 28.1 1.0
OD1 A:ASP297 4.8 26.7 1.0
O A:HOH58 4.8 22.5 1.0
OD2 A:ASP324 4.8 25.2 1.0
O A:GLY327 4.9 25.1 1.0
OD2 A:ASP297 4.9 25.5 1.0
CG A:ASP324 5.0 22.9 1.0

Calcium binding site 4 out of 10 in 3ikq

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Calcium binding site 4 out of 10 in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D


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 Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:26.5
occ:1.00
OE1 A:GLU232 2.2 19.7 1.0
OE1 C:GLU232 2.2 19.1 1.0
OE1 B:GLU232 2.3 20.0 1.0
O C:HOH160 2.4 27.4 1.0
O A:HOH156 2.5 14.7 1.0
O B:HOH157 2.5 16.3 1.0
CD A:GLU232 3.2 20.4 1.0
CD C:GLU232 3.2 17.8 1.0
CD B:GLU232 3.3 19.4 1.0
OE2 C:GLU232 3.7 19.3 1.0
OE2 A:GLU232 3.7 20.1 1.0
OE2 B:GLU232 3.8 19.1 1.0
CA A:GLU232 4.2 14.6 1.0
NZ C:LYS246 4.3 14.9 1.0
CA B:GLU232 4.3 14.0 1.0
CG A:GLU232 4.4 17.8 1.0
CB A:GLU232 4.4 16.2 1.0
CA C:GLU232 4.4 14.7 1.0
O A:GLU232 4.4 14.7 1.0
CG C:GLU232 4.4 17.4 1.0
O B:GLU232 4.4 14.1 1.0
NZ B:LYS246 4.5 15.0 1.0
CG B:GLU232 4.5 15.8 1.0
CB C:GLU232 4.5 15.2 1.0
CB B:GLU232 4.5 14.1 1.0
O C:GLU232 4.6 14.2 1.0
NZ A:LYS246 4.7 10.6 1.0
C A:GLU232 4.8 14.5 1.0
C B:GLU232 4.9 14.5 1.0
C C:GLU232 5.0 15.1 1.0

Calcium binding site 5 out of 10 in 3ikq

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Calcium binding site 5 out of 10 in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D


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 Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:17.4
occ:1.00
OD1 B:ASP342 2.2 11.1 1.0
OD1 B:ASN323 2.4 20.5 1.0
OE1 B:GLU329 2.4 16.6 1.0
O3 B:MAN405 2.4 29.7 1.0
OD1 B:ASN341 2.5 12.8 1.0
OE1 B:GLU321 2.6 13.9 1.0
O B:ASP342 2.6 14.9 1.0
O4 B:MAN405 2.9 32.1 1.0
CG B:ASP342 3.3 13.0 1.0
CG B:ASN323 3.4 18.5 1.0
CD B:GLU329 3.4 19.1 1.0
C3 B:MAN405 3.4 34.6 1.0
CD B:GLU321 3.4 13.2 1.0
CG B:ASN341 3.4 16.4 1.0
C4 B:MAN405 3.5 34.9 1.0
C B:ASP342 3.7 15.0 1.0
OE2 B:GLU329 3.7 21.9 1.0
OE2 B:GLU321 3.7 12.6 1.0
N B:ASP342 3.8 14.1 1.0
ND2 B:ASN341 3.9 14.8 1.0
ND2 B:ASN323 3.9 16.8 1.0
OD2 B:ASP342 4.0 12.3 1.0
N B:ASN323 4.1 16.7 1.0
CA B:ASP342 4.1 13.5 1.0
CB B:ASP342 4.3 11.8 1.0
C B:ASN341 4.5 15.5 1.0
CB B:ASN323 4.6 18.2 1.0
CB B:ASP325 4.6 24.9 1.0
CG B:GLU321 4.6 14.1 1.0
N B:ASP325 4.7 20.4 1.0
N B:ASP324 4.7 17.3 1.0
CG B:GLU329 4.7 18.0 1.0
CB B:ASN341 4.7 15.7 1.0
CA B:ASN323 4.7 18.2 1.0
C2 B:MAN405 4.8 37.3 1.0
N B:ARG343 4.8 16.5 1.0
CA B:ASN341 4.9 15.8 1.0
CB B:GLU329 4.9 18.9 1.0
O2 B:MAN405 4.9 39.8 1.0
C B:ASN323 4.9 17.8 1.0
C5 B:MAN405 5.0 37.2 1.0

Calcium binding site 6 out of 10 in 3ikq

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Calcium binding site 6 out of 10 in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D


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 Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:20.4
occ:1.00
OD1 B:ASP330 2.3 19.2 1.0
O B:HOH8 2.4 21.5 1.0
OD2 B:ASP297 2.4 25.8 1.0
O B:GLU329 2.4 18.0 1.0
OE1 B:GLU301 2.5 20.4 1.0
OD1 B:ASP324 2.6 21.6 1.0
OE2 B:GLU301 2.6 25.2 1.0
OD1 B:ASP297 2.9 29.3 1.0
CD B:GLU301 2.9 25.8 1.0
CG B:ASP297 3.0 27.3 1.0
CG B:ASP324 3.4 22.4 1.0
C B:GLU329 3.4 19.3 1.0
CG B:ASP330 3.5 19.9 1.0
CA B:ASP330 3.8 18.3 1.0
CA B:CA403 3.9 30.8 1.0
CB B:ASP324 3.9 18.6 1.0
N B:ASP330 4.0 18.0 1.0
CB B:ASP330 4.2 19.6 1.0
OD2 B:ASP324 4.3 24.8 1.0
CG B:GLU301 4.4 26.9 1.0
OD2 B:ASP330 4.5 21.3 1.0
N B:GLU329 4.5 22.2 1.0
CA B:ASP324 4.5 18.7 1.0
CA B:GLU329 4.5 20.2 1.0
CB B:ASP297 4.5 25.9 1.0
N B:GLY302 4.6 27.7 1.0
CZ B:PHE304 4.6 13.0 1.0
OD2 B:ASP342 4.7 12.3 1.0
O B:ASP297 4.9 26.1 1.0
O B:HOH66 5.0 29.1 1.0

Calcium binding site 7 out of 10 in 3ikq

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Calcium binding site 7 out of 10 in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D


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 Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:30.8
occ:1.00
OE1 B:GLU301 2.3 20.4 1.0
O B:HOH165 2.5 26.4 1.0
OD2 B:ASP330 2.6 21.3 1.0
O B:HOH169 2.6 28.5 1.0
OD1 B:ASP330 2.7 19.2 1.0
CG B:ASP330 3.0 19.9 1.0
CD B:GLU301 3.5 25.8 1.0
CA B:CA402 3.9 20.4 1.0
O B:HOH102 4.0 32.1 1.0
CB B:GLU301 4.1 26.5 1.0
CG B:GLU301 4.2 26.9 1.0
OD1 B:ASP324 4.3 21.6 1.0
O B:ASP297 4.4 26.1 1.0
CB B:ASP330 4.5 19.6 1.0
OE2 B:GLU301 4.5 25.2 1.0
CA B:GLU301 4.6 26.7 1.0
OD2 B:ASP297 4.7 25.8 1.0
O B:HOH110 4.8 38.8 1.0
O B:HOH26 4.8 27.3 1.0
O B:GLY327 4.9 25.3 1.0
OD1 B:ASP297 4.9 29.3 1.0

Calcium binding site 8 out of 10 in 3ikq

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Calcium binding site 8 out of 10 in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D


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 Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:21.8
occ:1.00
OD1 C:ASP342 2.3 16.8 1.0
OE1 C:GLU329 2.3 25.1 1.0
OD1 C:ASN323 2.5 24.6 1.0
O3 C:MAN405 2.5 36.5 1.0
O4 C:MAN405 2.5 38.0 1.0
OD1 C:ASN341 2.6 22.6 1.0
OE1 C:GLU321 2.6 24.2 1.0
O C:ASP342 2.7 20.1 1.0
C4 C:MAN405 3.3 40.3 1.0
C3 C:MAN405 3.3 40.0 1.0
CG C:ASP342 3.3 19.2 1.0
CD C:GLU329 3.3 25.8 1.0
CG C:ASN323 3.5 25.5 1.0
CD C:GLU321 3.5 25.9 1.0
CG C:ASN341 3.5 22.2 1.0
OE2 C:GLU329 3.7 27.4 1.0
C C:ASP342 3.7 21.9 1.0
OE2 C:GLU321 3.8 27.7 1.0
N C:ASP342 3.8 22.2 1.0
ND2 C:ASN341 3.9 22.0 1.0
OD2 C:ASP342 4.0 18.4 1.0
ND2 C:ASN323 4.0 22.9 1.0
CA C:ASP342 4.2 21.4 1.0
N C:ASN323 4.3 24.3 1.0
CB C:ASP342 4.3 19.2 1.0
C C:ASN341 4.6 23.0 1.0
CB C:ASP325 4.6 31.6 1.0
CG C:GLU329 4.6 23.7 1.0
CB C:ASN323 4.7 24.2 1.0
C2 C:MAN405 4.7 42.3 1.0
N C:ASP325 4.7 26.2 1.0
CG C:GLU321 4.7 25.6 1.0
C5 C:MAN405 4.7 42.1 1.0
CB C:ASN341 4.8 21.6 1.0
N C:ASP324 4.8 24.7 1.0
CA C:ASN323 4.8 24.9 1.0
N C:ARG343 4.8 24.4 1.0
CB C:GLU329 4.9 23.8 1.0
CA C:ASN341 4.9 23.0 1.0
O2 C:MAN405 4.9 45.1 1.0
C C:ASN323 5.0 24.8 1.0

Calcium binding site 9 out of 10 in 3ikq

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Calcium binding site 9 out of 10 in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D


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 Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:27.9
occ:1.00
O C:HOH158 2.3 15.4 1.0
OD2 C:ASP297 2.5 35.6 1.0
O C:GLU329 2.5 23.3 1.0
OD1 C:ASP324 2.6 34.1 1.0
OE1 C:GLU301 2.6 32.5 1.0
OE2 C:GLU301 2.6 33.2 1.0
OD1 C:ASP330 2.6 29.7 1.0
OD1 C:ASP297 2.8 35.6 1.0
CD C:GLU301 2.9 34.1 1.0
CG C:ASP297 3.0 35.9 1.0
C C:GLU329 3.4 23.7 1.0
CG C:ASP324 3.4 32.8 1.0
CG C:ASP330 3.7 29.1 1.0
O C:HOH23 3.8 30.2 1.0
CA C:ASP330 3.8 25.6 1.0
CB C:ASP324 3.9 27.9 1.0
N C:ASP330 4.0 24.8 1.0
CA C:CA403 4.1 35.2 1.0
N C:GLU329 4.3 26.5 1.0
OD2 C:ASP324 4.3 34.3 1.0
CB C:ASP330 4.4 26.5 1.0
O C:HOH175 4.4 36.6 1.0
CA C:GLU329 4.4 24.6 1.0
CA C:ASP324 4.4 26.1 1.0
CG C:GLU301 4.4 34.8 1.0
CZ C:PHE304 4.5 27.2 1.0
CB C:ASP297 4.5 34.9 1.0
OD2 C:ASP342 4.6 18.4 1.0
N C:GLY302 4.7 38.7 1.0
OD2 C:ASP330 4.7 28.6 1.0
O C:ASP297 4.8 37.1 1.0
O C:HOH129 4.9 31.4 1.0
CB C:GLU329 4.9 23.8 1.0
CE1 C:PHE304 5.0 29.0 1.0

Calcium binding site 10 out of 10 in 3ikq

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Calcium binding site 10 out of 10 in the Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Alpha 1-2 Mannobiose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:35.2
occ:1.00
OE1 C:GLU301 2.4 32.5 1.0
O C:HOH166 2.4 29.8 1.0
O C:HOH168 2.5 27.4 1.0
O C:HOH23 2.6 30.2 1.0
O C:HOH167 2.6 25.1 1.0
OD1 C:ASP330 2.7 29.7 1.0
OD2 C:ASP330 2.8 28.6 1.0
CG C:ASP330 3.1 29.1 1.0
CD C:GLU301 3.4 34.1 1.0
CB C:GLU301 4.0 36.1 1.0
CA C:CA402 4.1 27.9 1.0
CG C:GLU301 4.1 34.8 1.0
O C:HOH150 4.2 40.4 1.0
OD1 C:ASP324 4.4 34.1 1.0
OE2 C:GLU301 4.4 33.2 1.0
O C:ASP297 4.4 37.1 1.0
CA C:GLU301 4.6 37.7 1.0
CB C:ASP330 4.6 26.5 1.0
OD2 C:ASP297 4.8 35.6 1.0
OD1 C:ASP297 5.0 35.6 1.0

Reference:

A.K.Shrive, C.Martin, I.Burns, J.M.Paterson, J.D.Martin, J.P.Townsend, P.Waters, H.W.Clark, U.Kishore, K.B.M.Reid, T.J.Greenhough. Structural Characterisation of Ligand-Binding Determinants in Human Lung Surfactant Protein D: Influence of ASP325 J.Mol.Biol. V. 394 776 2009.
ISSN: ISSN 0022-2836
PubMed: 19799916
DOI: 10.1016/J.JMB.2009.09.057
Page generated: Sat Dec 12 04:15:36 2020

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