Calcium in PDB 1kx1: Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn

The structure of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn, PDB code: 1kx1 was solved by K.K.Ng, A.R.Kolatkar, S.Park-Snyder, H.Feinberg, D.A.Clark, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.04 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.800, 255.560, 61.790, 90.00, 119.60, 90.00
R / Rfree (%)	24.2 / 28.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn (pdb code 1kx1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn, PDB code: 1kx1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca222 b:46.3 occ:1.00 OD2 A:ASP161 2.4 40.6 1.0 O A:GLU193 2.4 35.9 1.0 OD2 A:ASP188 2.4 28.5 1.0 OE2 A:GLU165 2.4 36.2 1.0 OD2 A:ASP194 2.5 38.0 1.0 OD1 A:ASP161 2.7 42.8 1.0 CG A:ASP161 2.9 42.2 1.0 OE1 A:GLU165 3.1 32.7 1.0 CD A:GLU165 3.1 35.4 1.0 C A:GLU193 3.3 36.2 1.0 CG A:ASP188 3.3 27.7 1.0 CG A:ASP194 3.5 38.8 1.0 CB A:ASP188 3.7 28.1 1.0 CA A:ASP194 3.7 36.3 1.0 N A:ASP194 3.9 36.1 1.0 N A:GLU193 4.1 36.2 1.0 CA A:ASP188 4.2 28.8 1.0 CB A:ASP194 4.2 36.8 1.0 CA A:CA224 4.2 37.8 1.0 CA A:GLU193 4.4 36.2 1.0 OD1 A:ASP188 4.4 26.2 1.0 CB A:ASP161 4.4 40.8 1.0 OD1 A:ASP194 4.4 38.0 1.0 CZ A:PHE168 4.5 50.2 1.0 CG A:GLU165 4.6 36.0 1.0 OD1 A:ASP206 4.7 32.3 1.0 N A:GLY166 4.8 40.1 1.0 N A:ASP188 4.9 30.1 1.0 C A:ASP194 5.0 36.8 1.0 CE1 A:PHE168 5.0 50.1 1.0

Calcium binding site 2 out of 18 in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca223 b:23.7 occ:1.00 OD1 A:ASN205 2.3 23.3 1.0 OD2 A:ASP206 2.3 35.7 1.0 OE2 A:GLU193 2.3 39.5 1.0 O A:ASP206 2.5 34.4 1.0 OE2 A:GLU185 2.6 37.7 1.0 OD1 A:ASN187 2.8 41.5 1.0 CD A:GLU185 3.1 39.6 1.0 OE1 A:GLU185 3.1 39.0 1.0 CD A:GLU193 3.3 39.8 1.0 CG A:ASN187 3.3 38.6 1.0 CG A:ASP206 3.3 33.9 1.0 ND2 A:ASN187 3.3 38.2 1.0 CG A:ASN205 3.3 25.4 1.0 C A:ASP206 3.5 35.9 1.0 OE1 A:GLU193 3.6 37.0 1.0 N A:ASP206 3.6 30.6 1.0 ND2 A:ASN205 3.8 30.1 1.0 OD1 A:ASP206 4.0 32.3 1.0 CA A:ASP206 4.0 34.0 1.0 N A:ASN187 4.2 36.2 1.0 CB A:ASP206 4.2 33.4 1.0 CG A:GLU185 4.4 39.7 1.0 C A:ASN205 4.5 29.6 1.0 CB A:ASN187 4.6 35.5 1.0 CB A:ASN205 4.6 25.3 1.0 CG A:GLU193 4.6 36.6 1.0 N A:ILE207 4.7 38.1 1.0 CA A:ASN205 4.7 26.8 1.0 CB A:HIS189 4.8 33.6 1.0 CA A:ASN187 4.8 33.5 1.0 CB A:GLU193 4.9 35.7 1.0

Calcium binding site 3 out of 18 in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca224 b:37.8 occ:1.00 OD1 A:ASP194 2.4 38.0 1.0 OE2 A:GLU165 2.7 36.2 1.0 OD2 A:ASP194 2.7 38.0 1.0 O A:HOH8 2.8 17.0 1.0 CG A:ASP194 2.9 38.8 1.0 CD A:GLU165 3.7 35.4 1.0 CB A:GLU165 3.8 39.0 1.0 CG A:GLU165 4.0 36.0 1.0 OD2 A:ASP188 4.2 28.5 1.0 OD2 A:ASP161 4.2 40.6 1.0 CA A:CA222 4.2 46.3 1.0 CA A:GLU165 4.4 39.8 1.0 CB A:ASP194 4.4 36.8 1.0 O A:ASP161 4.5 39.5 1.0 OE1 A:GLU165 4.8 32.7 1.0 N A:GLU165 5.0 40.7 1.0 CA A:GLU162 5.0 44.5 1.0

Calcium binding site 4 out of 18 in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca222 b:13.2 occ:1.00 O B:GLU193 2.1 33.5 1.0 OE2 B:GLU165 2.2 15.1 1.0 OD2 B:ASP194 2.5 23.6 1.0 OE1 B:GLU165 2.6 8.5 1.0 CD B:GLU165 2.7 13.9 1.0 OD1 B:ASP161 2.9 15.7 1.0 OD2 B:ASP161 2.9 16.8 1.0 OD2 B:ASP188 3.0 22.0 1.0 C B:GLU193 3.1 35.3 1.0 CG B:ASP161 3.3 18.6 1.0 CG B:ASP188 3.3 22.5 1.0 CA B:ASP194 3.6 32.1 1.0 CG B:ASP194 3.6 25.8 1.0 CB B:ASP188 3.7 24.3 1.0 N B:ASP194 3.7 33.4 1.0 OD1 B:ASP206 4.0 28.4 1.0 OD1 B:ASP188 4.0 21.8 1.0 CA B:ASP188 4.1 29.9 1.0 N B:GLU193 4.2 40.0 1.0 CB B:ASP194 4.2 30.3 1.0 CA B:GLU193 4.2 37.8 1.0 CZ B:PHE168 4.2 29.6 1.0 CG B:GLU165 4.3 15.6 1.0 CA B:CA224 4.6 29.8 1.0 OD1 B:ASP194 4.7 23.3 1.0 N B:ASP188 4.7 29.5 1.0 C B:ASP194 4.7 32.4 1.0 CB B:ASP161 4.8 23.0 1.0 CB B:GLU193 4.8 37.7 1.0 CE2 B:PHE168 4.9 32.6 1.0 CE1 B:PHE168 4.9 29.1 1.0 N B:GLY166 5.0 24.1 1.0 CG B:ASP206 5.0 30.8 1.0

Calcium binding site 5 out of 18 in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca223 b:30.1 occ:1.00 O3 B:MAN20 2.1 17.9 0.8 O B:ASP206 2.4 35.7 1.0 OD1 B:ASN187 2.5 22.9 1.0 OD2 B:ASP206 2.6 27.1 1.0 OD1 B:ASN205 2.9 30.1 1.0 ND2 B:ASN205 2.9 29.7 1.0 OE2 B:GLU193 2.9 36.3 1.0 OE2 B:GLU185 3.0 29.3 1.0 CG B:ASN205 3.1 30.4 1.0 C3 B:MAN20 3.2 23.1 0.8 O4 B:MAN20 3.3 23.7 0.8 OE1 B:GLU185 3.4 29.9 1.0 CD B:GLU193 3.4 37.3 1.0 CG B:ASN187 3.4 23.9 1.0 CD B:GLU185 3.5 31.0 1.0 C B:ASP206 3.5 35.5 1.0 OE1 B:GLU193 3.6 36.0 1.0 N B:ASP206 3.7 30.4 1.0 CG B:ASP206 3.7 30.8 1.0 C4 B:MAN20 3.7 23.1 0.8 ND2 B:ASN187 3.8 16.2 1.0 CA B:ASP206 4.1 33.4 1.0 C B:ASN205 4.2 30.4 1.0 N B:ASN187 4.4 27.4 1.0 CB B:ASN205 4.4 32.1 1.0 C2 B:MAN20 4.5 24.2 0.8 CB B:ASP206 4.5 32.1 1.0 CA B:ASN205 4.5 31.8 1.0 CG B:GLU193 4.6 36.6 1.0 N B:ILE207 4.6 36.0 1.0 OD1 B:ASP206 4.6 28.4 1.0 CB B:ASN187 4.8 23.0 1.0 CG B:GLU185 4.8 32.1 1.0 CB B:GLU193 4.8 37.7 1.0 O B:ASN205 4.8 30.1 1.0 O2 B:MAN20 4.9 25.8 0.8 CB B:HIS189 4.9 40.5 1.0 CA B:ILE207 5.0 36.9 1.0

Calcium binding site 6 out of 18 in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca224 b:29.8 occ:1.00 OD1 B:ASP194 2.4 23.3 1.0 OE1 B:GLU165 2.6 8.5 1.0 OD2 B:ASP194 2.8 23.6 1.0 CG B:ASP194 2.9 25.8 1.0 CD B:GLU165 3.7 13.9 1.0 CB B:GLU165 4.0 18.0 1.0 CG B:GLU165 4.2 15.6 1.0 CB B:ASP194 4.4 30.3 1.0 O B:ASP161 4.5 23.7 1.0 OD2 B:ASP188 4.6 22.0 1.0 CA B:CA222 4.6 13.2 1.0 CA B:GLU165 4.6 19.8 1.0 OE2 B:GLU165 4.7 15.1 1.0 OD1 B:ASP188 4.8 21.8 1.0 OD2 B:ASP161 4.8 16.8 1.0 O B:GLU162 4.9 26.9 1.0

Calcium binding site 7 out of 18 in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:31.1 occ:1.00 OE1 C:GLU165 2.2 40.3 1.0 O C:GLU193 2.2 52.9 1.0 OD2 C:ASP194 2.5 55.8 1.0 OD2 C:ASP161 2.7 40.4 1.0 OD2 C:ASP188 2.8 41.4 1.0 OD1 C:ASP161 3.1 39.3 1.0 CD C:GLU165 3.2 40.2 1.0 C C:GLU193 3.2 52.5 1.0 CG C:ASP161 3.3 43.5 1.0 OE2 C:GLU165 3.5 38.3 1.0 O C:HOH307 3.5 3.8 1.0 CG C:ASP188 3.6 43.8 1.0 CB C:ASP188 3.7 42.8 1.0 CG C:ASP194 3.7 57.2 1.0 CA C:ASP194 3.7 54.8 1.0 N C:ASP194 3.8 53.4 1.0 CA C:ASP188 3.9 42.9 1.0 OD1 C:ASP206 4.1 55.0 1.0 N C:GLU193 4.2 50.4 1.0 CZ C:PHE168 4.2 42.4 1.0 CA C:GLU193 4.3 51.7 1.0 CB C:ASP194 4.3 56.0 1.0 CA C:CA303 4.4 52.5 1.0 N C:ASP188 4.4 43.3 1.0 CE2 C:PHE168 4.5 41.7 1.0 CG C:GLU165 4.5 41.7 1.0 OD1 C:ASP188 4.7 44.8 1.0 N C:GLY166 4.7 45.1 1.0 OD1 C:ASP194 4.7 58.6 1.0 CB C:ASP161 4.8 42.4 1.0 C C:ASP194 4.8 53.7 1.0 CB C:GLU193 4.9 51.2 1.0

Calcium binding site 8 out of 18 in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:54.7 occ:1.00 O3 C:MAN39 2.2 44.8 0.8 O4 C:MAN39 2.4 47.7 0.8 OD1 C:ASN205 2.5 40.1 1.0 OD1 C:ASN187 2.6 47.5 1.0 OE2 C:GLU193 2.6 46.6 1.0 OE2 C:GLU185 2.7 42.1 1.0 OD2 C:ASP206 2.8 56.1 1.0 OE1 C:GLU185 2.8 45.6 1.0 C3 C:MAN39 3.0 47.1 0.8 C4 C:MAN39 3.0 47.1 0.8 O C:ASP206 3.1 43.4 1.0 CD C:GLU185 3.2 44.8 1.0 CG C:ASN187 3.2 46.6 1.0 ND2 C:ASN187 3.4 48.0 1.0 CD C:GLU193 3.5 49.8 1.0 CG C:ASN205 3.6 39.3 1.0 OE1 C:GLU193 3.7 51.2 1.0 CG C:ASP206 4.0 53.2 1.0 ND2 C:ASN205 4.1 35.5 1.0 C C:ASP206 4.3 44.9 1.0 CB C:HIS189 4.3 45.8 1.0 C2 C:MAN39 4.4 48.5 0.8 N C:ASP206 4.4 45.5 1.0 C5 C:MAN39 4.4 48.2 0.8 CB C:ASN187 4.6 43.8 1.0 O2 C:MAN39 4.6 49.0 0.8 CG C:GLU185 4.7 43.9 1.0 OD1 C:ASP206 4.8 55.0 1.0 CA C:ASP206 4.8 46.6 1.0 N C:ASN187 4.8 43.2 1.0 CB C:ASN205 4.8 40.6 1.0 CG C:GLU193 4.9 50.0 1.0

Calcium binding site 9 out of 18 in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:52.5 occ:1.00 OE2 C:GLU165 1.9 38.3 1.0 OD1 C:ASP194 2.4 58.6 1.0 OD2 C:ASP194 2.7 55.8 1.0 CG C:ASP194 2.9 57.2 1.0 CD C:GLU165 3.0 40.2 1.0 OE1 C:GLU165 3.7 40.3 1.0 OD2 C:ASP188 3.7 41.4 1.0 CG C:GLU165 4.0 41.7 1.0 CB C:GLU165 4.2 44.1 1.0 CA C:CA301 4.4 31.1 1.0 CB C:ASP194 4.4 56.0 1.0 CG C:ASP188 4.6 43.8 1.0 CA C:GLU165 4.6 45.9 1.0 O C:ASP161 4.7 48.4 1.0 OD1 C:ASP188 4.7 44.8 1.0 OD1 C:ASP161 4.8 39.3 1.0

Calcium binding site 10 out of 18 in the Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Rat Mannose Protein A Complexed with MAN6-GLCNAC2-Asn within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:34.8 occ:1.00 O D:GLU193 2.3 36.5 1.0 OD2 D:ASP188 2.3 28.6 1.0 OE2 D:GLU165 2.4 36.7 1.0 OD2 D:ASP161 2.7 31.2 1.0 OD2 D:ASP194 2.9 36.9 1.0 OD1 D:ASP161 2.9 35.7 1.0 OE1 D:GLU165 3.0 37.2 1.0 CG D:ASP188 3.0 28.7 1.0 CD D:GLU165 3.1 38.0 1.0 CG D:ASP161 3.2 35.6 1.0 CB D:ASP188 3.2 27.5 1.0 C D:GLU193 3.2 35.3 1.0 CA D:ASP188 3.7 28.4 1.0 N D:ASP194 4.0 35.4 1.0 CA D:ASP194 4.0 36.0 1.0 N D:GLU193 4.0 34.8 1.0 CG D:ASP194 4.0 38.8 1.0 OD1 D:ASP188 4.2 27.3 1.0 CA D:GLU193 4.2 35.4 1.0 N D:ASP188 4.3 29.7 1.0 OD1 D:ASP206 4.4 37.9 1.0 CZ D:PHE168 4.6 53.5 1.0 CB D:ASP194 4.6 36.4 1.0 CG D:GLU165 4.6 37.6 1.0 CA D:CA403 4.6 38.2 1.0 CB D:ASP161 4.7 36.8 1.0 O D:HOH22 4.7 11.9 1.0 CB D:GLU193 4.7 35.2 1.0 N D:GLY166 4.8 39.6 1.0 O D:HOH7 4.9 6.4 1.0 C D:ASP188 5.0 29.6 1.0

K.K.Ng, A.R.Kolatkar, S.Park-Snyder, H.Feinberg, D.A.Clark, K.Drickamer, W.I.Weis. Orientation of Bound Ligands in Mannose-Binding Proteins. Implications For Multivalent Ligand Recognition. J.Biol.Chem. V. 277 16088 2002.
ISSN: ISSN 0021-9258
PubMed: 11850428
DOI: 10.1074/JBC.M200493200