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Calcium in PDB 3ikn: Crystal Structure of Galactose Bound Trimeric Human Lung Surfactant Protein D

Protein crystallography data

The structure of Crystal Structure of Galactose Bound Trimeric Human Lung Surfactant Protein D, PDB code: 3ikn 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) 55.86 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.740, 108.580, 55.880, 90.00, 91.41, 90.00
R / Rfree (%) 20.1 / 21.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Galactose Bound Trimeric Human Lung Surfactant Protein D (pdb code 3ikn). 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 Galactose Bound Trimeric Human Lung Surfactant Protein D, PDB code: 3ikn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3ikn

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Calcium binding site 1 out of 10 in the Crystal Structure of Galactose 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 Galactose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:16.3
occ:1.00
 OD1 A:ASP342 2.5 17.0 1.0
OE1 A:GLU329 2.5 17.1 1.0
OD1 A:ASN341 2.6 19.6 1.0
O2 A:GAL405 2.6 21.5 1.0
OD1 A:ASN323 2.6 19.6 1.0
O A:ASP342 2.7 18.1 1.0
O1 A:GAL405 2.7 18.2 1.0
OE1 A:GLU321 2.7 21.9 1.0
CG A:ASP342 3.4 16.3 1.0
C1 A:GAL405 3.4 22.1 1.0
CD A:GLU329 3.4 16.6 1.0
C2 A:GAL405 3.4 22.1 1.0
CG A:ASN323 3.5 20.5 1.0
CD A:GLU321 3.5 21.3 1.0
CG A:ASN341 3.5 19.7 1.0
C A:ASP342 3.7 17.3 1.0
OE2 A:GLU321 3.7 23.1 1.0
OE2 A:GLU329 3.7 18.8 1.0
N A:ASP342 3.8 16.0 1.0
ND2 A:ASN323 3.8 21.6 1.0
ND2 A:ASN341 3.9 19.3 1.0
OD2 A:ASP342 4.0 16.2 1.0
CA A:ASP342 4.1 16.4 1.0
N A:ASN323 4.2 18.1 1.0
CB A:ASP342 4.3 15.2 1.0
CB A:ASP325 4.6 22.2 1.0
C A:ASN341 4.6 18.2 1.0
N A:ASP325 4.7 19.3 1.0
CG A:GLU321 4.7 20.6 1.0
CB A:ASN323 4.7 19.1 1.0
N A:ASP324 4.7 17.4 1.0
O5 A:GAL405 4.7 24.2 1.0
CG A:GLU329 4.7 18.3 1.0
CB A:ASN341 4.8 16.9 1.0
C3 A:GAL405 4.8 24.9 1.0
CA A:ASN323 4.8 17.7 1.0
N A:ARG343 4.9 16.8 1.0
CB A:GLU329 4.9 19.6 1.0
CA A:ASN341 4.9 17.7 1.0

Calcium binding site 2 out of 10 in 3ikn

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Calcium binding site 2 out of 10 in the Crystal Structure of Galactose 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 Galactose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:14.7
occ:1.00
 OD1 A:ASP330 2.5 18.6 1.0
O A:HOH38 2.6 17.4 1.0
O A:GLU329 2.6 17.5 1.0
OE1 A:GLU301 2.6 17.8 1.0
OD2 A:ASP297 2.6 17.8 1.0
OE2 A:GLU301 2.6 18.7 1.0
OD1 A:ASP324 2.6 19.7 1.0
OD1 A:ASP297 2.7 17.1 1.0
CD A:GLU301 3.0 19.7 1.0
CG A:ASP297 3.0 18.7 1.0
CG A:ASP324 3.4 19.2 1.0
C A:GLU329 3.4 17.1 1.0
CG A:ASP330 3.6 19.6 1.0
CA A:ASP330 3.8 16.3 1.0
N A:ASP330 3.9 16.6 1.0
CB A:ASP324 4.0 16.8 1.0
CA A:CA403 4.0 19.6 1.0
OD2 A:ASP324 4.2 19.5 1.0
CB A:ASP330 4.2 16.1 1.0
N A:GLU329 4.3 19.3 1.0
O A:HOH364 4.4 31.9 1.0
CA A:GLU329 4.4 17.5 1.0
CG A:GLU301 4.5 19.9 1.0
CA A:ASP324 4.5 17.1 1.0
CZ A:PHE304 4.5 18.3 1.0
CB A:ASP297 4.5 18.1 1.0
OD2 A:ASP330 4.5 21.4 1.0
N A:GLY302 4.6 20.2 1.0
OD2 A:ASP342 4.6 16.2 1.0
O A:HOH11 4.7 21.2 1.0
O A:ASP297 4.8 19.6 1.0
O A:HOH58 4.9 25.4 1.0
O A:HOH52 5.0 21.3 1.0
C A:ASP330 5.0 15.8 1.0
CB A:GLU329 5.0 19.6 1.0

Calcium binding site 3 out of 10 in 3ikn

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Calcium binding site 3 out of 10 in the Crystal Structure of Galactose 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 Galactose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:19.6
occ:1.00
 OE1 A:GLU301 2.6 17.8 1.0
O A:HOH52 2.6 21.3 1.0
OD2 A:ASP330 2.6 21.4 1.0
OD1 A:ASP330 2.7 18.6 1.0
O A:HOH364 2.7 31.9 1.0
O A:HOH144 2.7 31.1 1.0
CG A:ASP330 3.0 19.6 1.0
CD A:GLU301 3.7 19.7 1.0
CA A:CA402 4.0 14.7 1.0
OD1 A:ASP324 4.3 19.7 1.0
CB A:GLU301 4.4 19.5 1.0
CG A:GLU301 4.4 19.9 1.0
CB A:ASP330 4.5 16.1 1.0
O A:ASP297 4.5 19.6 1.0
OE2 A:GLU301 4.6 18.7 1.0
OD2 A:ASP324 4.8 19.5 1.0
O A:GLY327 4.8 24.1 1.0
OD1 A:ASP297 4.8 17.1 1.0
CA A:GLU301 4.8 19.7 1.0
CG A:ASP324 4.9 19.2 1.0
O A:HOH62 5.0 23.0 1.0

Calcium binding site 4 out of 10 in 3ikn

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Calcium binding site 4 out of 10 in the Crystal Structure of Galactose 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 Galactose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:20.9
occ:1.00
 OE1 C:GLU232 2.4 19.5 1.0
OE1 A:GLU232 2.5 24.2 1.0
OE1 B:GLU232 2.6 26.3 1.0
O B:HOH68 2.6 23.1 1.0
O C:HOH367 2.6 24.8 1.0
O A:HOH80 2.7 27.1 1.0
CD B:GLU232 3.4 24.8 1.0
CD C:GLU232 3.4 19.3 1.0
CD A:GLU232 3.4 23.4 1.0
OE2 B:GLU232 3.8 22.0 1.0
OE2 C:GLU232 3.9 18.2 1.0
OE2 A:GLU232 3.9 24.0 1.0
CA A:GLU232 4.2 15.8 1.0
CA B:GLU232 4.2 16.4 1.0
NZ B:LYS246 4.3 17.4 1.0
NZ C:LYS246 4.3 15.2 1.0
O A:GLU232 4.4 16.2 1.0
CA C:GLU232 4.4 13.9 1.0
O B:GLU232 4.4 16.4 1.0
CB A:GLU232 4.4 15.7 1.0
CB B:GLU232 4.4 19.1 1.0
NZ A:LYS246 4.5 16.8 1.0
CG B:GLU232 4.5 22.1 1.0
CG A:GLU232 4.5 20.5 1.0
CB C:GLU232 4.5 14.9 1.0
O C:GLU232 4.5 16.3 1.0
CG C:GLU232 4.5 16.2 1.0
C A:GLU232 4.8 15.4 1.0
C B:GLU232 4.8 16.5 1.0
O B:HOH24 4.9 19.5 1.0
O C:HOH390 4.9 24.9 1.0
C C:GLU232 4.9 14.8 1.0
O A:HOH27 5.0 22.6 1.0

Calcium binding site 5 out of 10 in 3ikn

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Calcium binding site 5 out of 10 in the Crystal Structure of Galactose 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 Galactose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:14.0
occ:1.00
 OD1 B:ASP342 2.5 16.0 1.0
OD1 B:ASN341 2.5 16.6 1.0
OD1 B:ASN323 2.5 16.8 1.0
OE1 B:GLU329 2.6 15.9 1.0
O2 B:GAL405 2.6 17.6 1.0
O1 B:GAL405 2.6 15.9 1.0
OE1 B:GLU321 2.6 16.9 1.0
O B:ASP342 2.6 15.2 1.0
C1 B:GAL405 3.4 19.0 1.0
C2 B:GAL405 3.4 19.2 1.0
CG B:ASP342 3.4 12.5 1.0
CD B:GLU321 3.4 17.3 1.0
CG B:ASN341 3.4 16.6 1.0
CD B:GLU329 3.5 14.5 1.0
CG B:ASN323 3.5 16.5 1.0
C B:ASP342 3.7 15.6 1.0
OE2 B:GLU321 3.7 19.7 1.0
OE2 B:GLU329 3.7 17.8 1.0
N B:ASP342 3.7 14.0 1.0
ND2 B:ASN341 3.8 15.5 1.0
ND2 B:ASN323 4.0 18.4 1.0
OD2 B:ASP342 4.1 16.9 1.0
CA B:ASP342 4.1 15.0 1.0
N B:ASN323 4.2 15.3 1.0
CB B:ASP342 4.3 13.2 1.0
C B:ASN341 4.5 16.2 1.0
CB B:ASP325 4.5 19.1 1.0
CG B:GLU321 4.7 16.4 1.0
CB B:ASN323 4.7 16.6 1.0
O5 B:GAL405 4.7 21.3 1.0
N B:ASP325 4.7 17.1 1.0
CB B:ASN341 4.7 15.8 1.0
N B:ASP324 4.8 17.0 1.0
C3 B:GAL405 4.8 21.8 1.0
CG B:GLU329 4.8 16.8 1.0
N B:ARG343 4.8 14.8 1.0
CA B:ASN323 4.9 15.9 1.0
CA B:ASN341 4.9 14.8 1.0
CB B:GLU329 5.0 18.6 1.0

Calcium binding site 6 out of 10 in 3ikn

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Calcium binding site 6 out of 10 in the Crystal Structure of Galactose 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 Galactose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:15.3
occ:1.00
 O B:GLU329 2.5 16.6 1.0
O B:HOH21 2.5 16.9 1.0
OD1 B:ASP330 2.5 18.6 1.0
OE1 B:GLU301 2.6 21.9 1.0
OD2 B:ASP297 2.6 19.4 1.0
OD1 B:ASP324 2.7 19.5 1.0
OE2 B:GLU301 2.7 19.8 1.0
OD1 B:ASP297 2.8 18.0 1.0
CD B:GLU301 3.0 22.0 1.0
CG B:ASP297 3.1 18.3 1.0
C B:GLU329 3.4 16.7 1.0
CG B:ASP324 3.5 19.1 1.0
CG B:ASP330 3.6 20.4 1.0
CA B:ASP330 3.8 16.8 1.0
CA B:CA403 3.9 20.0 1.0
O B:HOH44 4.0 23.4 1.0
CB B:ASP324 4.0 17.1 1.0
N B:ASP330 4.0 17.1 1.0
CB B:ASP330 4.3 19.0 1.0
OD2 B:ASP324 4.3 20.7 1.0
O B:HOH154 4.4 28.6 1.0
CG B:GLU301 4.5 22.2 1.0
N B:GLU329 4.5 19.2 1.0
CA B:ASP324 4.5 16.2 1.0
CZ B:PHE304 4.5 19.7 1.0
CA B:GLU329 4.5 18.0 1.0
CB B:ASP297 4.6 18.7 1.0
OD2 B:ASP342 4.6 16.9 1.0
OD2 B:ASP330 4.6 20.9 1.0
N B:GLY302 4.7 21.7 1.0
O B:ASP297 4.8 20.4 1.0
CE1 B:PHE304 4.9 20.2 1.0
O B:HOH112 4.9 25.7 1.0
CA B:GLU301 5.0 23.0 1.0

Calcium binding site 7 out of 10 in 3ikn

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Calcium binding site 7 out of 10 in the Crystal Structure of Galactose 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 Galactose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:20.0
occ:1.00
 OE1 B:GLU301 2.5 21.9 1.0
O B:HOH60 2.6 23.8 1.0
O B:HOH44 2.6 23.4 1.0
OD2 B:ASP330 2.6 20.9 1.0
OD1 B:ASP330 2.6 18.6 1.0
O B:HOH160 2.7 32.8 1.0
O B:HOH61 2.7 25.4 1.0
CG B:ASP330 3.0 20.4 1.0
CD B:GLU301 3.7 22.0 1.0
CA B:CA402 3.9 15.3 1.0
O B:HOH54 4.2 22.6 1.0
CB B:GLU301 4.3 22.7 1.0
O B:ASP297 4.3 20.4 1.0
OD1 B:ASP324 4.4 19.5 1.0
CG B:GLU301 4.5 22.2 1.0
CB B:ASP330 4.5 19.0 1.0
OE2 B:GLU301 4.7 19.8 1.0
O B:HOH432 4.7 36.6 1.0
O B:HOH411 4.7 37.1 1.0
OD1 B:ASP297 4.7 18.0 1.0
CA B:GLU301 4.7 23.0 1.0
O B:HOH57 5.0 27.4 1.0
OD2 B:ASP297 5.0 19.4 1.0
O B:GLY327 5.0 23.6 1.0

Calcium binding site 8 out of 10 in 3ikn

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Calcium binding site 8 out of 10 in the Crystal Structure of Galactose 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 Galactose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:14.7
occ:1.00
 OD1 C:ASP342 2.5 15.2 1.0
OD1 C:ASN341 2.5 16.8 1.0
OE1 C:GLU329 2.5 16.7 1.0
OD1 C:ASN323 2.5 16.9 1.0
O2 C:GAL405 2.5 17.8 1.0
OE1 C:GLU321 2.6 17.1 1.0
O C:ASP342 2.7 15.7 1.0
O1 C:GAL405 2.7 17.6 1.0
C1 C:GAL405 3.4 20.4 1.0
C2 C:GAL405 3.4 20.2 1.0
CD C:GLU321 3.4 17.2 1.0
CG C:ASP342 3.4 14.9 1.0
CD C:GLU329 3.5 18.0 1.0
CG C:ASN341 3.5 14.9 1.0
CG C:ASN323 3.5 18.2 1.0
OE2 C:GLU321 3.7 20.3 1.0
C C:ASP342 3.7 16.6 1.0
OE2 C:GLU329 3.8 19.9 1.0
N C:ASP342 3.8 14.6 1.0
ND2 C:ASN341 3.9 15.2 1.0
ND2 C:ASN323 4.0 20.3 1.0
OD2 C:ASP342 4.1 16.4 1.0
CA C:ASP342 4.1 16.3 1.0
N C:ASN323 4.2 15.7 1.0
CB C:ASP342 4.4 15.5 1.0
C C:ASN341 4.6 16.7 1.0
CB C:ASP325 4.6 20.3 1.0
CG C:GLU321 4.6 16.5 1.0
CB C:ASN323 4.7 17.3 1.0
N C:ASP325 4.7 16.3 1.0
O5 C:GAL405 4.7 21.9 1.0
CB C:ASN341 4.7 15.8 1.0
C3 C:GAL405 4.8 22.4 1.0
CG C:GLU329 4.8 15.9 1.0
N C:ASP324 4.8 15.3 1.0
CA C:ASN323 4.9 16.2 1.0
N C:ARG343 4.9 16.5 1.0
CA C:ASN341 4.9 15.0 1.0
CB C:GLU329 4.9 15.6 1.0

Calcium binding site 9 out of 10 in 3ikn

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Calcium binding site 9 out of 10 in the Crystal Structure of Galactose 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 Galactose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:16.0
occ:1.00
 O C:GLU329 2.5 17.0 1.0
OD1 C:ASP330 2.5 19.8 1.0
O C:HOH14 2.5 17.1 1.0
OE1 C:GLU301 2.6 21.3 1.0
OE2 C:GLU301 2.6 18.6 1.0
OD2 C:ASP297 2.7 20.5 1.0
OD1 C:ASP324 2.7 19.7 1.0
OD1 C:ASP297 2.8 17.4 1.0
CD C:GLU301 3.0 22.9 1.0
CG C:ASP297 3.1 21.1 1.0
CG C:ASP324 3.4 18.6 1.0
C C:GLU329 3.4 16.6 1.0
CG C:ASP330 3.7 22.9 1.0
CA C:ASP330 3.8 18.9 1.0
CB C:ASP324 3.9 16.8 1.0
CA C:CA403 3.9 20.4 1.0
O C:HOH18 3.9 19.6 1.0
N C:ASP330 4.0 18.2 1.0
OD2 C:ASP324 4.3 19.4 1.0
CB C:ASP330 4.3 20.2 1.0
CA C:ASP324 4.4 16.8 1.0
N C:GLU329 4.5 19.0 1.0
CG C:GLU301 4.5 21.3 1.0
CA C:GLU329 4.5 17.2 1.0
CZ C:PHE304 4.5 18.5 1.0
OD2 C:ASP342 4.6 16.4 1.0
CB C:ASP297 4.6 19.3 1.0
OD2 C:ASP330 4.6 23.6 1.0
N C:GLY302 4.7 21.2 1.0
O C:HOH35 4.8 26.3 1.0
O C:ASP297 4.8 21.6 1.0
CE1 C:PHE304 4.9 15.5 1.0
O C:HOH17 5.0 20.2 1.0
CA C:GLU301 5.0 22.5 1.0

Calcium binding site 10 out of 10 in 3ikn

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Calcium binding site 10 out of 10 in the Crystal Structure of Galactose 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 Galactose Bound Trimeric Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:20.4
occ:1.00
 OE1 C:GLU301 2.5 21.3 1.0
OD1 C:ASP330 2.6 19.8 1.0
O C:HOH111 2.6 27.5 1.0
O C:HOH18 2.6 19.6 1.0
O C:HOH64 2.7 23.6 1.0
OD2 C:ASP330 2.7 23.6 1.0
O C:HOH357 2.8 31.6 1.0
CG C:ASP330 3.0 22.9 1.0
CD C:GLU301 3.7 22.9 1.0
CA C:CA402 3.9 16.0 1.0
O C:HOH487 4.1 39.5 1.0
O C:HOH123 4.2 24.5 1.0
CB C:GLU301 4.3 22.7 1.0
OD1 C:ASP324 4.4 19.7 1.0
CG C:GLU301 4.4 21.3 1.0
O C:ASP297 4.4 21.6 1.0
CB C:ASP330 4.5 20.2 1.0
OE2 C:GLU301 4.6 18.6 1.0
O C:HOH463 4.6 40.0 1.0
O C:HOH365 4.7 36.7 1.0
CA C:GLU301 4.7 22.5 1.0
OD1 C:ASP297 4.8 17.4 1.0
OD2 C:ASP324 5.0 19.4 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 Jul 13 11:35:32 2024

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