Atomistry » Calcium » PDB 2o8o-2ovu » 2ork
Atomistry »
  Calcium »
    PDB 2o8o-2ovu »
      2ork »

Calcium in PDB 2ork: Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Inositol-1-Phosphate

Protein crystallography data

The structure of Crystal Structure of the Trimeric Neck and Carbohydrate Recognition Domain of Human Surfactant Protein D in Complex with Inositol-1-Phosphate, PDB code: 2ork 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) 38.66 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.403, 108.010, 55.701, 90.00, 91.83, 90.00
R / Rfree (%) 18.6 / 22.6

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 Inositol-1-Phosphate (pdb code 2ork). 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 Inositol-1-Phosphate, PDB code: 2ork:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2ork

Go back to Calcium Binding Sites List in 2ork
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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:15.0
occ:1.00
 OD1 A:ASN341 2.4 12.2 1.0
OD1 A:ASP342 2.4 13.4 1.0
OE1 A:GLU329 2.5 15.5 1.0
OD1 A:ASN323 2.5 14.8 1.0
O A:HOH610 2.6 22.7 1.0
OE1 A:GLU321 2.6 15.6 1.0
O A:ASP342 2.7 12.4 1.0
O A:HOH609 2.7 22.6 1.0
CG A:ASN341 3.4 13.3 1.0
CD A:GLU321 3.4 16.7 1.0
CG A:ASP342 3.5 13.7 1.0
CG A:ASN323 3.5 18.5 1.0
CD A:GLU329 3.5 12.0 1.0
C A:ASP342 3.7 12.8 1.0
OE2 A:GLU321 3.7 18.5 1.0
OE2 A:GLU329 3.8 11.5 1.0
N A:ASP342 3.8 12.7 1.0
ND2 A:ASN341 3.8 13.4 1.0
ND2 A:ASN323 3.9 21.3 1.0
CA A:ASP342 4.1 13.3 1.0
N A:ASN323 4.2 16.7 1.0
OD2 A:ASP342 4.2 14.1 1.0
CB A:ASP342 4.4 13.5 1.0
CB A:ASP325 4.4 18.0 1.0
C A:ASN341 4.6 13.3 1.0
CG A:GLU321 4.7 15.8 1.0
CB A:ASN323 4.7 16.3 1.0
CB A:ASN341 4.7 13.1 1.0
N A:ASP325 4.7 16.3 1.0
N A:ASP324 4.8 15.0 1.0
CG A:GLU329 4.8 14.9 1.0
N A:ARG343 4.8 12.9 1.0
CA A:ASN323 4.8 16.7 1.0
CA A:ASN341 4.9 13.5 1.0
CB A:GLU329 4.9 14.2 1.0

Calcium binding site 2 out of 9 in 2ork

Go back to Calcium Binding Sites List in 2ork
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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:13.9
occ:1.00
 OD1 A:ASP330 2.3 12.9 1.0
OD1 A:ASP324 2.4 12.3 1.0
OE2 A:GLU301 2.5 14.3 1.0
O A:GLU329 2.5 12.1 1.0
OD2 A:ASP297 2.5 14.9 1.0
OE1 A:GLU301 2.5 11.4 1.0
O A:HOH588 2.6 13.8 1.0
OD1 A:ASP297 2.6 13.0 1.0
CD A:GLU301 2.8 12.4 1.0
CG A:ASP297 2.9 15.4 1.0
CG A:ASP324 3.3 14.8 1.0
C A:GLU329 3.4 13.5 1.0
CG A:ASP330 3.4 12.3 1.0
CA A:ASP330 3.8 13.0 1.0
CA A:CA403 3.8 23.6 1.0
CB A:ASP324 3.9 15.5 1.0
N A:ASP330 4.0 12.5 1.0
CB A:ASP330 4.1 12.2 1.0
OD2 A:ASP324 4.2 12.2 1.0
N A:GLU329 4.2 17.1 1.0
CG A:GLU301 4.4 15.6 1.0
CA A:GLU329 4.4 14.9 1.0
OD2 A:ASP330 4.4 14.1 1.0
O A:HOH590 4.4 22.8 1.0
CZ A:PHE304 4.5 16.9 1.0
CB A:ASP297 4.5 16.0 1.0
CA A:ASP324 4.5 15.4 1.0
OD2 A:ASP342 4.6 14.1 1.0
N A:GLY302 4.7 17.7 1.0
O A:HOH587 4.7 15.7 1.0
O A:ASP297 4.8 17.4 1.0
O A:HOH436 4.9 19.6 1.0
CE1 A:PHE304 4.9 16.3 1.0
O A:HOH414 5.0 21.7 1.0
CB A:GLU329 5.0 14.2 1.0

Calcium binding site 3 out of 9 in 2ork

Go back to Calcium Binding Sites List in 2ork
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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:23.6
occ:1.00
 O A:HOH604 2.1 35.3 1.0
OE1 A:GLU301 2.3 11.4 1.0
OD2 A:ASP330 2.4 14.1 1.0
OD1 A:ASP330 2.4 12.9 1.0
O A:HOH590 2.5 22.8 1.0
O A:HOH605 2.5 22.9 1.0
O A:HOH587 2.6 15.7 1.0
CG A:ASP330 2.8 12.3 1.0
CD A:GLU301 3.5 12.4 1.0
O A:HOH589 3.7 31.4 1.0
CA A:CA402 3.8 13.9 1.0
OD1 A:ASP324 4.0 12.3 1.0
CB A:ASP330 4.3 12.2 1.0
CG A:GLU301 4.3 15.6 1.0
OE2 A:GLU301 4.4 14.3 1.0
O A:HOH477 4.5 32.0 1.0
CB A:GLU301 4.5 17.3 1.0
OD2 A:ASP324 4.6 12.2 1.0
O A:ASP297 4.7 17.4 1.0
CG A:ASP324 4.7 14.8 1.0
O A:GLY327 4.7 25.3 1.0
OD1 A:ASP297 4.8 13.0 1.0
O A:HOH472 4.9 24.7 1.0

Calcium binding site 4 out of 9 in 2ork

Go back to Calcium Binding Sites List in 2ork
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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:14.7
occ:1.00
 OD1 B:ASP342 2.2 12.6 1.0
OD1 B:ASN341 2.3 15.7 1.0
OD1 B:ASN323 2.5 16.7 1.0
OE1 B:GLU329 2.5 14.7 1.0
OE1 B:GLU321 2.5 13.0 1.0
O B:ASP342 2.6 13.3 1.0
O4 B:IPD995 2.6 16.9 1.0
O5 B:IPD995 2.7 21.2 1.0
CG B:ASP342 3.3 12.5 1.0
CD B:GLU321 3.3 14.1 1.0
CG B:ASN341 3.4 15.3 1.0
CG B:ASN323 3.4 16.8 1.0
CD B:GLU329 3.4 15.0 1.0
C5 B:IPD995 3.5 24.0 1.0
C4 B:IPD995 3.5 24.8 1.0
C B:ASP342 3.6 13.9 1.0
OE2 B:GLU321 3.6 14.2 1.0
N B:ASP342 3.7 13.7 1.0
OE2 B:GLU329 3.7 16.5 1.0
ND2 B:ASN341 3.8 16.7 1.0
ND2 B:ASN323 3.9 16.9 1.0
CA B:ASP342 4.0 13.1 1.0
OD2 B:ASP342 4.0 16.4 1.0
N B:ASN323 4.2 15.5 1.0
CB B:ASP342 4.2 13.3 1.0
C B:ASN341 4.5 13.6 1.0
CB B:ASN323 4.6 15.3 1.0
CG B:GLU321 4.6 14.9 1.0
CB B:ASP325 4.6 21.0 1.0
CB B:ASN341 4.6 13.9 1.0
N B:ASP324 4.7 17.1 1.0
CG B:GLU329 4.7 15.4 1.0
N B:ASP325 4.7 19.3 1.0
N B:ARG343 4.8 13.5 1.0
CA B:ASN323 4.8 16.1 1.0
CA B:ASN341 4.8 13.4 1.0
CB B:GLU329 4.9 16.0 1.0
C3 B:IPD995 4.9 29.9 1.0
C6 B:IPD995 5.0 28.0 1.0
C B:ASN323 5.0 16.9 1.0
CB B:GLU321 5.0 14.9 1.0

Calcium binding site 5 out of 9 in 2ork

Go back to Calcium Binding Sites List in 2ork
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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:19.7
occ:1.00
 O B:HOH1137 2.4 18.5 1.0
O B:GLU329 2.4 15.2 1.0
OD1 B:ASP330 2.4 14.2 1.0
OE1 B:GLU301 2.5 21.1 1.0
OD1 B:ASP324 2.6 15.7 1.0
OD2 B:ASP297 2.6 23.4 1.0
OE2 B:GLU301 2.6 20.8 1.0
OD1 B:ASP297 2.6 18.0 1.0
CD B:GLU301 2.9 22.5 1.0
CG B:ASP297 3.0 21.1 1.0
CG B:ASP324 3.3 20.1 1.0
C B:GLU329 3.4 15.7 1.0
CG B:ASP330 3.6 17.9 1.0
O B:HOH1136 3.8 16.7 1.0
CA B:ASP330 3.8 14.8 1.0
CB B:ASP324 3.9 16.9 1.0
CA B:CA403 4.0 36.4 1.0
N B:ASP330 4.0 14.8 1.0
OD2 B:ASP324 4.1 16.4 1.0
CB B:ASP330 4.3 15.1 1.0
N B:GLU329 4.4 17.9 1.0
CG B:GLU301 4.4 25.2 1.0
CA B:GLU329 4.4 16.8 1.0
CB B:ASP297 4.5 20.5 1.0
CZ B:PHE304 4.5 18.3 1.0
CA B:ASP324 4.5 18.2 1.0
OD2 B:ASP342 4.6 16.4 1.0
OD2 B:ASP330 4.6 18.5 1.0
N B:GLY302 4.8 27.8 1.0
O B:HOH1139 4.8 22.6 1.0
O B:ASP297 4.9 21.8 1.0
O B:HOH1141 4.9 30.1 1.0
CE1 B:PHE304 5.0 18.5 1.0
CA B:GLU301 5.0 27.5 1.0

Calcium binding site 6 out of 9 in 2ork

Go back to Calcium Binding Sites List in 2ork
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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:36.4
occ:1.00
 O B:HOH1139 2.2 22.6 1.0
O B:HOH1136 2.2 16.7 1.0
O B:HOH1143 2.5 33.5 1.0
OE1 B:GLU301 2.5 21.1 1.0
OD1 B:ASP330 2.5 14.2 1.0
O B:HOH1030 2.5 29.5 1.0
OD2 B:ASP330 2.6 18.5 1.0
CG B:ASP330 2.9 17.9 1.0
CD B:GLU301 3.7 22.5 1.0
CA B:CA402 4.0 19.7 1.0
O B:ASP297 4.3 21.8 1.0
O B:HOH1111 4.3 42.3 1.0
OD1 B:ASP324 4.4 15.7 1.0
CB B:GLU301 4.4 27.1 1.0
CB B:ASP330 4.4 15.1 1.0
CG B:GLU301 4.5 25.2 1.0
OE2 B:GLU301 4.7 20.8 1.0
OD1 B:ASP297 4.7 18.0 1.0
CA B:GLU301 4.8 27.5 1.0
O B:GLY327 4.8 20.0 1.0
OD2 B:ASP324 4.8 16.4 1.0
O B:HOH1032 4.9 22.3 1.0
OD2 B:ASP297 5.0 23.4 1.0

Calcium binding site 7 out of 9 in 2ork

Go back to Calcium Binding Sites List in 2ork
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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:14.3
occ:1.00
 OD1 C:ASP342 2.2 12.8 1.0
OE1 C:GLU329 2.3 13.5 1.0
OD1 C:ASN341 2.4 14.1 1.0
OD1 C:ASN323 2.5 15.1 1.0
O4 C:IPD995 2.6 19.1 1.0
O C:ASP342 2.6 13.6 1.0
O5 C:IPD995 2.6 21.9 1.0
OE1 C:GLU321 2.7 14.7 1.0
CG C:ASP342 3.3 13.5 1.0
CD C:GLU329 3.4 14.1 1.0
CG C:ASN341 3.4 15.4 1.0
C5 C:IPD995 3.4 24.0 1.0
CG C:ASN323 3.5 15.7 1.0
C4 C:IPD995 3.5 22.4 1.0
CD C:GLU321 3.5 14.2 1.0
C C:ASP342 3.6 14.5 1.0
OE2 C:GLU329 3.7 15.1 1.0
N C:ASP342 3.7 14.5 1.0
OE2 C:GLU321 3.8 14.9 1.0
ND2 C:ASN341 3.9 15.9 1.0
ND2 C:ASN323 4.0 19.8 1.0
CA C:ASP342 4.0 13.8 1.0
OD2 C:ASP342 4.1 12.7 1.0
N C:ASN323 4.2 14.3 1.0
CB C:ASP342 4.3 13.7 1.0
C C:ASN341 4.6 14.2 1.0
CG C:GLU329 4.6 15.5 1.0
CB C:ASN323 4.7 15.3 1.0
CB C:ASP325 4.7 18.8 1.0
CG C:GLU321 4.7 14.2 1.0
N C:ASP325 4.7 16.6 1.0
CB C:ASN341 4.7 13.3 1.0
N C:ASP324 4.8 15.4 1.0
N C:ARG343 4.8 15.6 1.0
CB C:GLU329 4.8 16.7 1.0
CA C:ASN323 4.8 14.6 1.0
C3 C:IPD995 4.8 25.2 1.0
CA C:ASN341 4.9 14.1 1.0
C6 C:IPD995 4.9 25.4 1.0

Calcium binding site 8 out of 9 in 2ork

Go back to Calcium Binding Sites List in 2ork
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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:19.2
occ:1.00
 O C:HOH1126 2.4 12.7 1.0
O C:GLU329 2.4 16.8 1.0
OD1 C:ASP330 2.5 16.1 1.0
OE1 C:GLU301 2.5 17.4 1.0
OE2 C:GLU301 2.5 19.1 1.0
OD2 C:ASP297 2.6 18.7 1.0
OD1 C:ASP324 2.6 14.3 1.0
OD1 C:ASP297 2.7 16.0 1.0
CD C:GLU301 2.9 19.1 1.0
CG C:ASP297 3.0 19.7 1.0
CG C:ASP324 3.4 16.4 1.0
C C:GLU329 3.4 16.9 1.0
CG C:ASP330 3.6 18.4 1.0
O C:HOH1127 3.7 19.5 1.0
CA C:ASP330 3.8 16.5 1.0
CB C:ASP324 3.9 14.8 1.0
CA C:CA403 3.9 28.9 1.0
N C:ASP330 4.0 16.1 1.0
OD2 C:ASP324 4.2 15.0 1.0
CB C:ASP330 4.3 16.0 1.0
CG C:GLU301 4.4 22.1 1.0
CA C:ASP324 4.4 15.6 1.0
N C:GLU329 4.4 18.6 1.0
CA C:GLU329 4.5 17.2 1.0
CZ C:PHE304 4.5 17.9 1.0
OD2 C:ASP342 4.5 12.7 1.0
CB C:ASP297 4.5 19.9 1.0
OD2 C:ASP330 4.6 19.3 1.0
N C:GLY302 4.7 22.8 1.0
O C:ASP297 4.8 22.3 1.0
O C:HOH1130 4.8 19.3 1.0
O C:HOH1000 4.8 15.3 1.0
CE1 C:PHE304 4.9 15.8 1.0
CA C:GLU301 5.0 23.7 1.0

Calcium binding site 9 out of 9 in 2ork

Go back to Calcium Binding Sites List in 2ork
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 Inositol-1-Phosphate


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 Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:28.9
occ:1.00
 O C:HOH1130 2.2 19.3 1.0
O C:HOH1127 2.2 19.5 1.0
OE1 C:GLU301 2.3 17.4 1.0
O C:HOH1088 2.5 32.7 1.0
O C:HOH1129 2.5 23.2 1.0
OD1 C:ASP330 2.6 16.1 1.0
OD2 C:ASP330 2.6 19.3 1.0
CG C:ASP330 2.9 18.4 1.0
CD C:GLU301 3.5 19.1 1.0
CA C:CA402 3.9 19.2 1.0
O C:HOH1025 4.1 22.6 1.0
CB C:GLU301 4.1 22.8 1.0
CG C:GLU301 4.2 22.1 1.0
O C:ASP297 4.3 22.3 1.0
OD1 C:ASP324 4.3 14.3 1.0
CB C:ASP330 4.4 16.0 1.0
OE2 C:GLU301 4.5 19.1 1.0
OD1 C:ASP297 4.7 16.0 1.0
CA C:GLU301 4.7 23.7 1.0
O C:HOH1143 4.8 42.4 1.0
OD2 C:ASP324 4.8 15.0 1.0
CG C:ASP324 4.9 16.4 1.0
O C:HOH1060 5.0 26.2 1.0

Reference:

E.Crouch, B.Mcdonald, K.Smith, M.Roberts, T.Mealy, B.Seaton, J.Head. Critical Role of Arg/LYS343 in the Species-Dependent Recognition of Phosphatidylinositol By Pulmonary Surfactant Protein D. Biochemistry V. 46 5160 2007.
ISSN: ISSN 0006-2960
PubMed: 17417879
DOI: 10.1021/BI700037X
Page generated: Sat Dec 12 03:48:48 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy