Calcium in PDB 1k9i: Complex of Dc-Sign and GLCNAC2MAN3

The structure of Complex of Dc-Sign and GLCNAC2MAN3, PDB code: 1k9i was solved by H.Feinberg, D.A.Mitchell, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.68 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.805, 148.161, 112.991, 90.00, 91.03, 90.00
R / Rfree (%)	21.3 / 25.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Calcium atom in the Complex of Dc-Sign and GLCNAC2MAN3 (pdb code 1k9i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 30 binding sites of Calcium where determined in the Complex of Dc-Sign and GLCNAC2MAN3, PDB code: 1k9i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 30 in the Complex of Dc-Sign and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Dc-Sign and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:56.9 occ:1.00 O A:HOH408 2.3 37.4 1.0 OD1 A:ASN350 2.3 48.2 1.0 OD1 A:ASP355 2.4 52.4 1.0 OE2 A:GLU324 2.4 69.2 1.0 OD2 A:ASP320 2.4 61.2 1.0 O A:GLU354 2.5 47.1 1.0 OE1 A:GLU324 2.5 66.4 1.0 CD A:GLU324 2.8 69.0 1.0 OD1 A:ASP320 2.8 58.7 1.0 CG A:ASP320 3.0 61.1 1.0 CG A:ASN350 3.1 45.7 1.0 C A:GLU354 3.4 46.2 1.0 CG A:ASP355 3.5 52.5 1.0 CB A:ASN350 3.8 43.3 1.0 CA A:CA407 3.9 64.9 1.0 CA A:ASP355 3.9 48.9 1.0 ND2 A:ASN350 4.0 45.2 1.0 N A:ASP355 4.0 48.0 1.0 CB A:ASP355 4.2 50.8 1.0 N A:GLU354 4.2 46.4 1.0 CZ2 A:TRP327 4.3 72.1 1.0 CG A:GLU324 4.3 69.5 1.0 O A:HOH409 4.4 48.6 1.0 CB A:ASP320 4.5 60.3 1.0 CA A:GLU354 4.5 45.9 1.0 OE2 A:GLU353 4.5 59.3 1.0 OD2 A:ASP355 4.5 54.6 1.0 CA A:ASN350 4.5 43.7 1.0 CH2 A:TRP327 4.5 72.2 1.0 O A:HOH416 4.6 33.4 1.0 OD2 A:ASP366 4.7 39.7 1.0 O A:ASP320 4.9 62.9 1.0 CA A:GLU324 5.0 69.1 1.0

Calcium binding site 2 out of 30 in the Complex of Dc-Sign and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Dc-Sign and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:41.2 occ:1.00 OD1 A:ASN349 2.3 43.1 1.0 OE1 A:GLU354 2.3 39.7 1.0 OE1 A:GLU347 2.4 60.7 1.0 O A:ASP366 2.4 37.4 1.0 OD1 A:ASN365 2.5 37.1 1.0 OD1 A:ASP366 2.5 37.0 1.0 O3 A:MAN2 2.6 39.6 1.0 O4 A:MAN2 2.7 42.5 1.0 CD A:GLU354 3.2 43.2 1.0 CG A:ASN349 3.2 45.6 1.0 CG A:ASP366 3.3 39.7 1.0 CG A:ASN365 3.3 39.5 1.0 CD A:GLU347 3.4 60.2 1.0 C3 A:MAN2 3.4 44.1 1.0 C4 A:MAN2 3.4 44.3 1.0 OE2 A:GLU354 3.5 42.0 1.0 C A:ASP366 3.5 40.9 1.0 ND2 A:ASN365 3.6 39.2 1.0 ND2 A:ASN349 3.6 44.1 1.0 N A:ASP366 3.6 39.6 1.0 OE2 A:GLU347 3.7 61.2 1.0 OD2 A:ASP366 3.8 39.7 1.0 CA A:ASP366 4.0 40.5 1.0 CB A:ASP366 4.2 40.1 1.0 N A:ASN349 4.2 47.2 1.0 CG2 A:VAL351 4.4 45.2 1.0 CG A:GLU354 4.4 42.4 1.0 N A:ASN350 4.6 43.8 1.0 CB A:ASN349 4.6 44.5 1.0 C A:ASN365 4.6 39.4 1.0 CB A:ASN365 4.6 40.0 1.0 CB A:GLU354 4.6 43.7 1.0 CG A:GLU347 4.6 59.3 1.0 N A:ASP367 4.7 42.9 1.0 C2 A:MAN2 4.8 47.9 1.0 CA A:ASN365 4.8 41.0 1.0 CA A:ASN349 4.9 45.4 1.0 C5 A:MAN2 4.9 45.1 1.0

Calcium binding site 3 out of 30 in the Complex of Dc-Sign and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Dc-Sign and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:64.9 occ:1.00 OE2 A:GLU353 2.2 59.3 1.0 OE1 A:GLU324 2.3 66.4 1.0 O A:HOH409 2.4 48.6 1.0 OD1 A:ASP355 2.6 52.4 1.0 OD2 A:ASP355 2.8 54.6 1.0 CG A:ASP355 3.0 52.5 1.0 CD A:GLU353 3.2 57.9 1.0 CD A:GLU324 3.5 69.0 1.0 CG A:GLU353 3.6 55.1 1.0 CA A:CA405 3.9 56.9 1.0 OD1 A:ASN350 4.1 48.2 1.0 CG A:GLU324 4.3 69.5 1.0 CB A:GLU324 4.3 68.8 1.0 OE1 A:GLU353 4.3 59.9 1.0 OE2 A:GLU324 4.4 69.2 1.0 CB A:ASP355 4.5 50.8 1.0 ND2 A:ASN350 4.6 45.2 1.0 OD1 A:ASP320 4.7 58.7 1.0 OD2 A:ASP320 4.7 61.2 1.0 O A:ASP320 4.7 62.9 1.0 CG A:ASN350 4.8 45.7 1.0 CB A:GLU353 4.9 50.1 1.0 CA A:GLU324 4.9 69.1 1.0

Calcium binding site 4 out of 30 in the Complex of Dc-Sign and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Dc-Sign and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:32.3 occ:1.00 O B:GLU354 2.3 37.6 1.0 OE2 B:GLU324 2.5 32.1 1.0 OD2 B:ASP320 2.5 26.8 1.0 O B:HOH504 2.5 26.3 1.0 OE1 B:GLU324 2.6 33.8 1.0 OD1 B:ASP320 2.7 31.5 1.0 OD1 B:ASP355 2.8 40.9 1.0 CD B:GLU324 2.9 34.6 1.0 OD1 B:ASN350 2.9 38.6 1.0 CG B:ASP320 3.0 31.3 1.0 C B:GLU354 3.3 39.2 1.0 CG B:ASN350 3.3 38.2 1.0 CB B:ASN350 3.7 38.6 1.0 CG B:ASP355 3.7 42.1 1.0 O B:HOH525 3.7 48.5 1.0 CA B:ASP355 3.8 38.2 1.0 CA B:CA503 3.9 49.8 1.0 N B:ASP355 4.0 38.5 1.0 ND2 B:ASN350 4.1 34.7 1.0 OE2 B:GLU353 4.2 46.5 1.0 N B:GLU354 4.2 43.1 1.0 CB B:ASP355 4.3 40.6 1.0 CA B:GLU354 4.4 40.5 1.0 CG B:GLU324 4.4 36.1 1.0 CZ2 B:TRP327 4.4 39.2 1.0 CA B:ASN350 4.4 40.1 1.0 CB B:ASP320 4.5 31.8 1.0 OD2 B:ASP366 4.6 31.1 1.0 OD2 B:ASP355 4.6 42.7 1.0 O B:HOH505 4.7 31.4 1.0 N B:GLY325 4.8 37.7 1.0 O B:ASP320 4.9 34.3 1.0 CA B:GLU324 4.9 39.3 1.0

Calcium binding site 5 out of 30 in the Complex of Dc-Sign and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Complex of Dc-Sign and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:28.0 occ:1.00 OE1 B:GLU354 2.3 30.4 1.0 OD1 B:ASN365 2.3 27.8 1.0 O4 E:NAG1 2.3 39.0 1.0 OD1 B:ASN349 2.3 37.5 1.0 OD1 B:ASP366 2.4 32.3 1.0 OE1 B:GLU347 2.5 40.1 1.0 O3 E:NAG1 2.6 31.3 1.0 O B:ASP366 2.6 32.9 1.0 C4 E:NAG1 3.1 35.6 1.0 CG B:ASN349 3.2 36.4 1.0 C3 E:NAG1 3.2 34.3 1.0 CD B:GLU354 3.3 36.6 1.0 CG B:ASN365 3.4 28.3 1.0 CG B:ASP366 3.4 33.9 1.0 CD B:GLU347 3.4 40.0 1.0 ND2 B:ASN349 3.6 32.2 1.0 OE2 B:GLU354 3.7 36.9 1.0 C B:ASP366 3.7 33.4 1.0 N B:ASP366 3.8 31.8 1.0 OE2 B:GLU347 3.8 42.9 1.0 ND2 B:ASN365 3.9 26.2 1.0 OD2 B:ASP366 4.1 31.1 1.0 N B:ASN349 4.2 37.7 1.0 CA B:ASP366 4.2 31.9 1.0 CB B:ASP366 4.4 31.1 1.0 CB B:ASN349 4.5 36.5 1.0 C5 E:NAG1 4.5 36.4 1.0 CG B:GLU354 4.6 37.4 1.0 CG B:GLU347 4.7 39.4 1.0 CB B:ASN365 4.7 29.3 1.0 C2 E:NAG1 4.7 34.9 1.0 C B:ASN365 4.7 31.1 1.0 CA B:ASN349 4.7 38.4 1.0 CG2 B:VAL351 4.8 43.4 1.0 N B:ASN350 4.8 40.5 1.0 CB B:GLU354 4.8 39.2 1.0 N B:ASP367 4.9 33.4 1.0 CA B:ASN365 4.9 30.3 1.0

Calcium binding site 6 out of 30 in the Complex of Dc-Sign and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Complex of Dc-Sign and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:49.8 occ:1.00 OE2 B:GLU353 2.2 46.5 1.0 O B:HOH507 2.3 43.0 1.0 OE1 B:GLU324 2.3 33.8 1.0 O B:HOH506 2.3 43.3 1.0 O B:HOH505 2.4 31.4 1.0 OD2 B:ASP355 2.7 42.7 1.0 OD1 B:ASP355 2.7 40.9 1.0 CG B:ASP355 3.0 42.1 1.0 CD B:GLU353 3.2 47.3 1.0 CD B:GLU324 3.5 34.6 1.0 CG B:GLU353 3.6 45.1 1.0 CA B:CA501 3.9 32.3 1.0 CB B:GLU324 4.2 39.4 1.0 OD1 B:ASN350 4.2 38.6 1.0 OE1 B:GLU353 4.3 47.9 1.0 CG B:GLU324 4.3 36.1 1.0 O B:HOH516 4.4 47.0 1.0 OE2 B:GLU324 4.4 32.1 1.0 CB B:ASP355 4.5 40.6 1.0 O B:ASP320 4.5 34.3 1.0 CA B:GLU324 4.6 39.3 1.0 ND2 B:ASN350 4.7 34.7 1.0 OD2 B:ASP320 4.8 26.8 1.0 CG B:ASN350 4.8 38.2 1.0 CB B:GLU353 5.0 44.5 1.0 OD1 B:ASP320 5.0 31.5 1.0

Calcium binding site 7 out of 30 in the Complex of Dc-Sign and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Complex of Dc-Sign and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:54.5 occ:1.00 OD1 C:ASN350 2.2 49.1 1.0 O C:HOH604 2.4 42.5 1.0 OE2 C:GLU324 2.4 52.3 1.0 OD1 C:ASP355 2.4 41.1 1.0 OD2 C:ASP320 2.5 43.5 1.0 O C:GLU354 2.5 42.9 1.0 OD1 C:ASP320 2.7 41.9 1.0 OE1 C:GLU324 2.8 52.5 1.0 CD C:GLU324 2.9 54.6 1.0 CG C:ASP320 3.0 43.5 1.0 CG C:ASN350 3.2 51.0 1.0 C C:GLU354 3.4 43.4 1.0 CG C:ASP355 3.6 43.4 1.0 CA C:ASP355 3.6 45.0 1.0 OE2 C:GLU353 3.8 53.4 1.0 N C:ASP355 3.9 43.6 1.0 O C:HOH633 3.9 40.7 1.0 ND2 C:ASN350 4.1 51.5 1.0 CB C:ASP355 4.1 44.9 1.0 CB C:ASN350 4.2 50.2 1.0 CA C:CA603 4.2 59.2 1.0 N C:GLU354 4.3 47.8 1.0 CG C:GLU324 4.4 56.1 1.0 CZ2 C:TRP327 4.4 40.8 1.0 O C:HOH605 4.4 49.4 1.0 CB C:ASP320 4.5 44.2 1.0 CA C:GLU354 4.5 45.2 1.0 OD2 C:ASP355 4.6 40.9 1.0 CA C:ASN350 4.8 49.8 1.0 C C:ASP355 4.8 46.2 1.0 O C:ASP320 4.8 47.4 1.0 CH2 C:TRP327 4.9 41.1 1.0 N C:GLY325 4.9 59.1 1.0 CD C:GLU353 4.9 54.9 1.0 OD2 C:ASP366 4.9 36.8 1.0 CA C:GLU324 5.0 59.3 1.0

Calcium binding site 8 out of 30 in the Complex of Dc-Sign and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Complex of Dc-Sign and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca602 b:35.0 occ:1.00 O C:ASP366 2.3 35.8 1.0 OD1 C:ASN349 2.3 41.9 1.0 O3 C:MAN2 2.4 30.9 1.0 OE1 C:GLU354 2.5 45.5 1.0 OD1 C:ASP366 2.5 35.1 1.0 OD1 C:ASN365 2.5 34.8 1.0 O4 C:MAN2 2.6 38.3 1.0 OE1 C:GLU347 2.6 48.6 1.0 CG C:ASP366 3.1 36.7 1.0 C3 C:MAN2 3.3 36.5 1.0 CD C:GLU354 3.3 46.6 1.0 C4 C:MAN2 3.3 36.2 1.0 CG C:ASN349 3.3 44.2 1.0 C C:ASP366 3.3 37.6 1.0 CG C:ASN365 3.5 32.3 1.0 N C:ASP366 3.5 34.7 1.0 CD C:GLU347 3.5 49.0 1.0 OE2 C:GLU354 3.6 45.8 1.0 OD2 C:ASP366 3.6 36.8 1.0 ND2 C:ASN349 3.8 42.5 1.0 CA C:ASP366 3.8 37.0 1.0 OE2 C:GLU347 3.9 47.1 1.0 ND2 C:ASN365 3.9 34.1 1.0 CB C:ASP366 4.0 35.3 1.0 N C:ASN349 4.4 48.3 1.0 N C:ASP367 4.5 38.7 1.0 C C:ASN365 4.5 33.8 1.0 CG2 C:VAL351 4.5 54.3 1.0 CG C:GLU354 4.6 45.6 1.0 N C:ASN350 4.6 48.4 1.0 CB C:ASN349 4.6 44.4 1.0 C2 C:MAN2 4.7 38.4 1.0 CB C:ASN365 4.7 33.2 1.0 CB C:GLU354 4.7 45.7 1.0 C5 C:MAN2 4.7 36.9 1.0 CG C:GLU347 4.8 46.9 1.0 CA C:ASN365 4.9 34.7 1.0 CA C:ASN349 4.9 47.6 1.0 CA C:ASP367 4.9 42.1 1.0 O2 C:MAN2 5.0 41.1 1.0

Calcium binding site 9 out of 30 in the Complex of Dc-Sign and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Complex of Dc-Sign and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:59.2 occ:1.00 OE2 C:GLU353 2.0 53.4 1.0 OE1 C:GLU324 2.2 52.5 1.0 O C:HOH605 2.3 49.4 1.0 OD1 C:ASP355 2.6 41.1 1.0 OD2 C:ASP355 2.8 40.9 1.0 CD C:GLU353 2.9 54.9 1.0 CG C:ASP355 3.0 43.4 1.0 CD C:GLU324 3.4 54.6 1.0 CG C:GLU353 3.6 52.1 1.0 OE1 C:GLU353 3.8 56.9 1.0 CA C:CA601 4.2 54.5 1.0 OE2 C:GLU324 4.2 52.3 1.0 CG C:GLU324 4.2 56.1 1.0 CB C:GLU324 4.3 58.0 1.0 CB C:ASP355 4.4 44.9 1.0 OD1 C:ASN350 4.6 49.1 1.0 O C:ASP320 4.8 47.4 1.0 CA C:GLU324 4.8 59.3 1.0 ND2 C:ASN350 4.9 51.5 1.0 CB C:GLU353 5.0 50.1 1.0

Calcium binding site 10 out of 30 in the Complex of Dc-Sign and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Complex of Dc-Sign and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca701 b:37.9 occ:1.00 O D:HOH704 2.3 40.7 1.0 OD1 D:ASP355 2.3 33.7 1.0 O D:GLU354 2.3 31.1 1.0 OD1 D:ASN350 2.3 41.1 1.0 OD2 D:ASP320 2.5 32.1 1.0 OD1 D:ASP320 2.6 32.2 1.0 OE2 D:GLU324 2.6 41.6 1.0 OE1 D:GLU324 2.6 41.5 1.0 CG D:ASP320 2.9 34.4 1.0 CD D:GLU324 2.9 43.8 1.0 C D:GLU354 3.3 30.8 1.0 CG D:ASN350 3.3 39.7 1.0 CG D:ASP355 3.5 36.9 1.0 CA D:ASP355 3.7 36.2 1.0 N D:ASP355 3.9 31.9 1.0 CA D:CA703 4.0 50.2 1.0 ND2 D:ASN350 4.1 38.9 1.0 CB D:ASP355 4.1 35.2 1.0 CB D:ASN350 4.1 35.1 1.0 CZ2 D:TRP327 4.2 33.9 1.0 N D:GLU354 4.2 32.4 1.0 CA D:GLU354 4.3 32.0 1.0 OE2 D:GLU353 4.3 44.5 1.0 CB D:ASP320 4.4 33.9 1.0 CG D:GLU324 4.4 44.8 1.0 OD2 D:ASP355 4.5 36.9 1.0 CH2 D:TRP327 4.6 32.9 1.0 OD2 D:ASP366 4.6 33.9 1.0 CA D:ASN350 4.7 35.5 1.0 O D:HOH705 4.8 43.8 1.0 O D:ASP320 5.0 39.5 1.0 C D:ASP355 5.0 37.4 1.0 CA D:GLU324 5.0 47.9 1.0 N D:GLY325 5.0 48.0 1.0

H.Feinberg, D.A.Mitchell, K.Drickamer, W.I.Weis. Structural Basis For Selective Recognition of Oligosaccharides By Dc-Sign and Dc-Signr. Science V. 294 2163 2001.
ISSN: ISSN 0036-8075
PubMed: 11739956
DOI: 10.1126/SCIENCE.1066371