Atomistry » Calcium » PDB 3fyi-3ghg » 3g81
Atomistry »
  Calcium »
    PDB 3fyi-3ghg »
      3g81 »

Calcium in PDB 3g81: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha Methyl Mannoside

Protein crystallography data

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Alpha Methyl Mannoside, PDB code: 3g81 was solved by J.F.Head, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.29 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.384, 107.980, 55.668, 90.00, 92.20, 90.00
R / Rfree (%) 17.8 / 20

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 Alpha Methyl Mannoside (pdb code 3g81). 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 Alpha Methyl Mannoside, PDB code: 3g81:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 3g81

Go back to Calcium Binding Sites List in 3g81
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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:13.2
occ:1.00
 OD1 A:ASP342 2.2 16.3 1.0
OD1 A:ASN341 2.2 16.9 1.0
O3 A:MMA500 2.4 18.6 1.0
OE1 A:GLU321 2.4 17.2 1.0
OD1 A:ASN323 2.5 17.1 1.0
OE1 A:GLU329 2.5 17.6 1.0
O A:ASP342 2.7 15.6 1.0
O4 A:MMA500 2.7 20.3 1.0
CG A:ASP342 3.3 16.5 1.0
CG A:ASN341 3.3 15.8 1.0
CD A:GLU321 3.3 18.4 1.0
C3 A:MMA500 3.3 23.1 1.0
C4 A:MMA500 3.4 21.9 1.0
CG A:ASN323 3.4 21.0 1.0
CD A:GLU329 3.5 17.4 1.0
OE2 A:GLU321 3.6 19.1 1.0
C A:ASP342 3.6 16.0 1.0
N A:ASP342 3.7 14.7 1.0
ND2 A:ASN341 3.8 18.4 1.0
OE2 A:GLU329 3.8 17.5 1.0
ND2 A:ASN323 3.9 21.0 1.0
CA A:ASP342 4.0 14.7 1.0
OD2 A:ASP342 4.0 16.2 1.0
N A:ASN323 4.1 19.0 1.0
CB A:ASP342 4.2 14.2 1.0
C A:ASN341 4.5 16.9 1.0
CG A:GLU321 4.6 17.9 1.0
CB A:ASN323 4.6 18.5 1.0
CB A:ASN341 4.6 16.6 1.0
N A:ASP324 4.7 16.6 1.0
N A:ASP325 4.7 17.4 1.0
C2 A:MMA500 4.7 27.3 1.0
CB A:ASP325 4.8 20.3 1.0
CA A:ASN323 4.8 19.0 1.0
CG A:GLU329 4.8 17.6 1.0
N A:ARG343 4.8 15.1 1.0
CA A:ASN341 4.8 15.9 1.0
C5 A:MMA500 4.9 26.1 1.0
CB A:GLU329 5.0 17.1 1.0

Calcium binding site 2 out of 9 in 3g81

Go back to Calcium Binding Sites List in 3g81
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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:13.5
occ:1.00
 OD1 A:ASP330 2.3 17.1 1.0
OE1 A:GLU301 2.4 16.9 1.0
O A:HOH538 2.4 16.2 1.0
OD1 A:ASP324 2.4 17.1 1.0
OE2 A:GLU301 2.5 17.6 1.0
OD2 A:ASP297 2.5 18.3 1.0
O A:GLU329 2.5 16.8 1.0
OD1 A:ASP297 2.7 16.7 1.0
CD A:GLU301 2.7 19.0 1.0
CG A:ASP297 2.9 17.9 1.0
CG A:ASP324 3.3 19.2 1.0
CG A:ASP330 3.4 18.9 1.0
C A:GLU329 3.4 16.5 1.0
CA A:ASP330 3.7 15.1 1.0
CA A:CA403 3.8 30.6 1.0
O A:HOH476 3.8 21.0 1.0
N A:ASP330 4.0 16.6 1.0
CB A:ASP324 4.0 16.4 1.0
CB A:ASP330 4.0 16.8 1.0
OD2 A:ASP324 4.1 19.3 1.0
CG A:GLU301 4.2 21.1 1.0
OD2 A:ASP330 4.3 20.0 1.0
N A:GLU329 4.3 18.3 1.0
CA A:GLU329 4.4 17.4 1.0
CZ A:PHE304 4.4 17.4 1.0
CB A:ASP297 4.5 19.0 1.0
O A:HOH505 4.5 22.1 1.0
CA A:ASP324 4.6 15.8 1.0
N A:GLY302 4.6 20.9 1.0
O A:ASP297 4.7 21.2 1.0
OD2 A:ASP342 4.8 16.2 1.0
O A:HOH42 4.9 19.9 1.0
CA A:GLU301 4.9 21.0 1.0
CB A:GLU301 5.0 21.8 1.0
O A:HOH56 5.0 23.2 1.0
CE1 A:PHE304 5.0 16.8 1.0

Calcium binding site 3 out of 9 in 3g81

Go back to Calcium Binding Sites List in 3g81
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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:30.6
occ:1.00
 O A:HOH476 2.3 21.0 1.0
O A:HOH505 2.3 22.1 1.0
OD2 A:ASP330 2.4 20.0 1.0
OE1 A:GLU301 2.5 16.9 1.0
OD1 A:ASP330 2.5 17.1 1.0
CG A:ASP330 2.8 18.9 1.0
CD A:GLU301 3.7 19.0 1.0
O A:HOH547 3.7 31.7 1.0
CA A:CA402 3.8 13.5 1.0
OD1 A:ASP324 4.1 17.1 1.0
CB A:ASP330 4.3 16.8 1.0
O A:HOH592 4.4 33.1 1.0
O A:GLY327 4.4 22.4 1.0
CB A:GLU301 4.4 21.8 1.0
CG A:GLU301 4.5 21.1 1.0
O A:ASP297 4.5 21.2 1.0
OE2 A:GLU301 4.5 17.6 1.0
OD2 A:ASP324 4.6 19.3 1.0
OD1 A:ASP297 4.7 16.7 1.0
CG A:ASP324 4.8 19.2 1.0
CA A:SER328 4.9 21.3 1.0
CA A:GLU301 5.0 21.0 1.0

Calcium binding site 4 out of 9 in 3g81

Go back to Calcium Binding Sites List in 3g81
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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:12.5
occ:1.00
 OD1 B:ASP342 2.2 14.7 1.0
OD1 B:ASN341 2.3 16.0 1.0
OE1 B:GLU329 2.3 16.3 1.0
OD1 B:ASN323 2.4 14.3 1.0
O3 B:MMA500 2.5 16.4 1.0
O B:ASP342 2.5 14.5 1.0
OE1 B:GLU321 2.6 15.0 1.0
O4 B:MMA500 2.6 17.4 1.0
CG B:ASP342 3.3 14.2 1.0
CG B:ASN341 3.3 16.5 1.0
C4 B:MMA500 3.3 21.2 1.0
CD B:GLU329 3.4 17.6 1.0
CG B:ASN323 3.4 16.1 1.0
C3 B:MMA500 3.4 19.2 1.0
CD B:GLU321 3.4 15.3 1.0
C B:ASP342 3.6 14.4 1.0
OE2 B:GLU321 3.7 16.4 1.0
N B:ASP342 3.7 15.3 1.0
OE2 B:GLU329 3.7 16.2 1.0
ND2 B:ASN341 3.7 15.4 1.0
ND2 B:ASN323 4.0 16.8 1.0
CA B:ASP342 4.0 14.5 1.0
OD2 B:ASP342 4.0 16.0 1.0
N B:ASN323 4.1 14.5 1.0
CB B:ASP342 4.2 13.6 1.0
C B:ASN341 4.5 14.6 1.0
CB B:ASN323 4.5 16.1 1.0
CB B:ASP325 4.6 20.3 1.0
CB B:ASN341 4.7 14.7 1.0
CG B:GLU329 4.7 16.5 1.0
CG B:GLU321 4.7 14.7 1.0
N B:ASP325 4.7 18.2 1.0
N B:ARG343 4.7 14.8 1.0
CA B:ASN323 4.7 14.9 1.0
C2 B:MMA500 4.7 23.8 1.0
N B:ASP324 4.7 16.1 1.0
CA B:ASN341 4.9 13.9 1.0
C5 B:MMA500 4.9 27.0 1.0
CB B:GLU329 4.9 18.9 1.0
C B:ASN323 4.9 16.5 1.0
O2 B:MMA500 5.0 26.8 1.0

Calcium binding site 5 out of 9 in 3g81

Go back to Calcium Binding Sites List in 3g81
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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:17.5
occ:1.00
 O B:HOH536 2.2 18.6 1.0
OD1 B:ASP330 2.2 21.3 1.0
OD2 B:ASP297 2.3 23.9 1.0
O B:GLU329 2.4 16.4 1.0
OD1 B:ASP324 2.7 21.4 1.0
OE1 B:GLU301 2.7 25.1 1.0
OD1 B:ASP297 2.7 21.4 1.0
OE2 B:GLU301 2.7 24.9 1.0
CG B:ASP297 2.8 22.6 1.0
CD B:GLU301 3.0 27.6 1.0
C B:GLU329 3.4 17.5 1.0
CG B:ASP324 3.4 23.1 1.0
CG B:ASP330 3.4 24.9 1.0
CA B:ASP330 3.7 17.8 1.0
O B:HOH464 3.7 29.1 1.0
CA B:CA403 3.9 44.7 1.0
N B:ASP330 4.0 18.2 1.0
CB B:ASP324 4.0 19.2 1.0
CB B:ASP330 4.1 19.6 1.0
OD2 B:ASP324 4.1 22.8 1.0
O B:HOH373 4.3 29.4 1.0
CB B:ASP297 4.3 20.6 1.0
N B:GLU329 4.4 19.8 1.0
OD2 B:ASP330 4.4 23.7 1.0
CA B:GLU329 4.4 17.9 1.0
CZ B:PHE304 4.5 18.1 1.0
CG B:GLU301 4.5 28.9 1.0
CA B:ASP324 4.6 17.5 1.0
O B:HOH443 4.7 29.6 1.0
OD2 B:ASP342 4.7 16.0 1.0
N B:GLY302 4.8 27.2 1.0
O B:ASP297 4.9 25.6 1.0
CE1 B:PHE304 5.0 18.0 1.0
C B:ASP330 5.0 17.0 1.0
CA B:GLU301 5.0 28.3 1.0

Calcium binding site 6 out of 9 in 3g81

Go back to Calcium Binding Sites List in 3g81
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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:44.7
occ:1.00
 O B:HOH464 2.3 29.1 1.0
O B:HOH443 2.4 29.6 1.0
O B:HOH542 2.5 41.1 1.0
OE1 B:GLU301 2.6 25.1 1.0
OD2 B:ASP330 2.6 23.7 1.0
OD1 B:ASP330 2.7 21.3 1.0
O B:HOH558 2.8 43.5 1.0
CG B:ASP330 2.9 24.9 1.0
CD B:GLU301 3.8 27.6 1.0
CA B:CA402 3.9 17.5 1.0
O B:HOH412 3.9 34.5 1.0
OD1 B:ASP324 4.3 21.4 1.0
CB B:ASP330 4.4 19.6 1.0
O B:GLY327 4.5 26.0 1.0
O B:ASP297 4.5 25.6 1.0
CB B:GLU301 4.5 30.0 1.0
O B:HOH531 4.6 39.9 1.0
CG B:GLU301 4.6 28.9 1.0
OE2 B:GLU301 4.7 24.9 1.0
OD2 B:ASP297 4.7 23.9 1.0
OD1 B:ASP297 4.7 21.4 1.0
OD2 B:ASP324 4.7 22.8 1.0
CA B:GLU301 4.9 28.3 1.0
CG B:ASP324 4.9 23.1 1.0
CG B:ASP297 5.0 22.6 1.0

Calcium binding site 7 out of 9 in 3g81

Go back to Calcium Binding Sites List in 3g81
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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:14.0
occ:1.00
 OD1 C:ASP342 2.1 17.1 1.0
OE1 C:GLU329 2.3 17.6 1.0
OD1 C:ASN341 2.3 17.7 1.0
OD1 C:ASN323 2.4 17.8 1.0
O3 C:MMA500 2.4 18.6 1.0
OE1 C:GLU321 2.5 17.5 1.0
O C:ASP342 2.6 16.7 1.0
O4 C:MMA500 2.7 21.3 1.0
CG C:ASP342 3.3 15.9 1.0
CG C:ASN341 3.3 18.3 1.0
CD C:GLU329 3.3 20.1 1.0
C3 C:MMA500 3.3 22.4 1.0
CD C:GLU321 3.4 17.3 1.0
CG C:ASN323 3.4 19.0 1.0
C4 C:MMA500 3.4 24.8 1.0
C C:ASP342 3.6 16.7 1.0
OE2 C:GLU321 3.7 18.4 1.0
N C:ASP342 3.7 15.3 1.0
OE2 C:GLU329 3.8 20.4 1.0
ND2 C:ASN341 3.8 18.9 1.0
ND2 C:ASN323 4.0 20.4 1.0
CA C:ASP342 4.0 16.1 1.0
OD2 C:ASP342 4.0 16.5 1.0
N C:ASN323 4.1 16.7 1.0
CB C:ASP342 4.2 15.6 1.0
C C:ASN341 4.5 17.5 1.0
CB C:ASN323 4.6 18.2 1.0
CB C:ASN341 4.6 15.6 1.0
CG C:GLU329 4.6 18.9 1.0
CG C:GLU321 4.6 16.4 1.0
C2 C:MMA500 4.7 26.9 1.0
CB C:ASP325 4.7 22.3 1.0
CA C:ASN323 4.7 16.8 1.0
N C:ASP325 4.8 18.9 1.0
N C:ARG343 4.8 17.9 1.0
N C:ASP324 4.8 17.6 1.0
CB C:GLU329 4.8 17.9 1.0
CA C:ASN341 4.9 15.4 1.0
C5 C:MMA500 4.9 30.0 1.0
O2 C:MMA500 5.0 31.0 1.0
C C:ASN323 5.0 19.6 1.0

Calcium binding site 8 out of 9 in 3g81

Go back to Calcium Binding Sites List in 3g81
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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:20.6
occ:1.00
 O C:HOH507 2.1 20.4 1.0
OD2 C:ASP297 2.4 27.1 1.0
OD1 C:ASP330 2.5 23.4 1.0
OE2 C:GLU301 2.5 24.9 1.0
O C:GLU329 2.5 21.3 1.0
OE1 C:GLU301 2.6 27.5 1.0
OD1 C:ASP297 2.6 23.5 1.0
OD1 C:ASP324 2.7 21.6 1.0
CG C:ASP297 2.9 26.8 1.0
CD C:GLU301 2.9 28.1 1.0
CG C:ASP324 3.4 25.7 1.0
C C:GLU329 3.4 19.2 1.0
CG C:ASP330 3.6 27.6 1.0
CA C:ASP330 3.8 21.7 1.0
O C:HOH527 3.8 29.9 1.0
CA C:CA403 3.9 43.9 1.0
O C:HOH545 3.9 35.6 1.0
N C:ASP330 4.0 19.8 1.0
CB C:ASP324 4.1 22.1 1.0
OD2 C:ASP324 4.1 21.2 1.0
CB C:ASP330 4.2 22.9 1.0
CZ C:PHE304 4.3 23.0 1.0
CB C:ASP297 4.4 26.6 1.0
CG C:GLU301 4.4 30.1 1.0
N C:GLU329 4.4 21.7 1.0
CA C:GLU329 4.5 20.2 1.0
OD2 C:ASP330 4.6 28.6 1.0
CA C:ASP324 4.6 20.0 1.0
OD2 C:ASP342 4.6 16.5 1.0
N C:GLY302 4.7 29.3 1.0
CE1 C:PHE304 4.7 21.0 1.0
O C:ASP297 4.9 31.5 1.0
O C:HOH416 4.9 32.2 1.0
CA C:GLU301 4.9 32.4 1.0
C C:ASP330 5.0 20.6 1.0

Calcium binding site 9 out of 9 in 3g81

Go back to Calcium Binding Sites List in 3g81
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 Alpha Methyl Mannoside


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 Alpha Methyl Mannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:43.9
occ:1.00
 O C:HOH416 2.2 32.2 1.0
OE1 C:GLU301 2.3 27.5 1.0
O C:HOH527 2.5 29.9 1.0
OD1 C:ASP330 2.6 23.4 1.0
OD2 C:ASP330 2.7 28.6 1.0
O C:HOH569 2.8 39.5 1.0
O C:HOH544 2.8 46.0 1.0
CG C:ASP330 2.9 27.6 1.0
CD C:GLU301 3.6 28.1 1.0
CA C:CA402 3.9 20.6 1.0
CB C:GLU301 4.1 34.3 1.0
O C:HOH392 4.2 36.9 1.0
O C:ASP297 4.2 31.5 1.0
CB C:ASP330 4.3 22.9 1.0
CG C:GLU301 4.3 30.1 1.0
O C:HOH555 4.4 42.1 1.0
OE2 C:GLU301 4.5 24.9 1.0
OD1 C:ASP324 4.5 21.6 1.0
OD1 C:ASP297 4.5 23.5 1.0
CA C:GLU301 4.6 32.4 1.0
OD2 C:ASP297 4.7 27.1 1.0
O C:GLY327 4.8 27.2 1.0
OD2 C:ASP324 4.8 21.2 1.0
CG C:ASP297 4.8 26.8 1.0
O C:HOH378 4.9 32.8 1.0

Reference:

E.Crouch, K.Hartshorn, T.Horlacher, B.Mcdonald, K.Smith, T.Cafarella, B.Seaton, P.H.Seeberger, J.Head. Recognition of Mannosylated Ligands and Influenza A Virus By Human Surfactant Protein D: Contributions of An Extended Site and Residue 343. Biochemistry V. 48 3335 2009.
ISSN: ISSN 0006-2960
PubMed: 19249874
DOI: 10.1021/BI8022703
Page generated: Sat Jul 13 10:30:31 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy