Calcium in PDB 1kzd: Complex of Mbp-C and Glcnac-Terminated Core

The structure of Complex of Mbp-C and Glcnac-Terminated Core, PDB code: 1kzd 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)	40.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.650, 75.050, 57.350, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.9

The binding sites of Calcium atom in the Complex of Mbp-C and Glcnac-Terminated Core (pdb code 1kzd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Complex of Mbp-C and Glcnac-Terminated Core, PDB code: 1kzd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Complex of Mbp-C and Glcnac-Terminated Core


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Mbp-C and Glcnac-Terminated Core within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca501 b:13.3 occ:1.00 O 1:HOH1060 2.3 13.4 1.0 OD1 1:ASN194 2.3 10.9 1.0 OD1 1:ASP161 2.4 8.6 1.0 O 1:GLU193 2.5 11.7 1.0 OD1 1:ASN188 2.5 17.9 1.0 OE1 1:GLU165 2.6 13.6 1.0 OE2 1:GLU165 2.6 13.9 1.0 OD2 1:ASP161 2.6 12.0 1.0 CG 1:ASP161 2.9 15.1 1.0 CD 1:GLU165 2.9 12.0 1.0 CG 1:ASN188 3.4 19.9 1.0 C 1:GLU193 3.4 12.4 1.0 CG 1:ASN194 3.5 10.3 1.0 CA 1:ASN194 3.7 10.0 1.0 N 1:ASN194 3.9 11.6 1.0 CB 1:ASN188 4.0 20.4 1.0 CB 1:ASN194 4.1 10.2 1.0 N 1:GLU193 4.3 14.3 1.0 ND2 1:ASN188 4.3 15.6 1.0 O 1:HOH1061 4.4 15.4 1.0 CB 1:ASP161 4.4 12.9 1.0 CG 1:GLU165 4.4 12.8 1.0 CA 1:GLU193 4.5 13.4 1.0 ND2 1:ASN194 4.6 10.8 1.0 CA 1:ASN188 4.7 20.1 1.0 O 1:ASP161 4.7 13.9 1.0 OD1 1:ASP206 4.7 9.4 1.0 N 1:ASN166 4.8 14.7 1.0 CZ 1:PHE168 4.8 19.5 1.0 C 1:ASN194 4.9 10.5 1.0

Calcium binding site 2 out of 4 in the Complex of Mbp-C and Glcnac-Terminated Core


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Mbp-C and Glcnac-Terminated Core within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca502 b:14.1 occ:1.00 OD1 1:ASN205 2.4 16.0 1.0 OD1 1:ASN187 2.4 19.0 1.0 OD2 1:ASP206 2.4 10.0 1.0 OE2 1:GLU193 2.4 10.5 1.0 O3 1:NAG1001 2.4 24.8 1.0 OE2 1:GLU185 2.5 20.8 1.0 O4 1:NAG1001 2.5 25.5 1.0 O 1:ASP206 2.6 11.3 1.0 C3 1:NAG1001 3.3 30.4 1.0 C4 1:NAG1001 3.3 29.3 1.0 CG 1:ASP206 3.3 12.0 1.0 CG 1:ASN205 3.3 14.0 1.0 CD 1:GLU193 3.4 9.3 1.0 CG 1:ASN187 3.4 21.5 1.0 CD 1:GLU185 3.4 19.8 1.0 C 1:ASP206 3.6 11.8 1.0 OE1 1:GLU185 3.7 18.2 1.0 OE1 1:GLU193 3.7 9.0 1.0 N 1:ASP206 3.7 11.5 1.0 ND2 1:ASN205 3.8 15.0 1.0 ND2 1:ASN187 3.9 18.8 1.0 OD1 1:ASP206 4.0 9.4 1.0 CA 1:ASP206 4.1 11.0 1.0 N 1:ASN187 4.1 19.2 1.0 CB 1:ASP206 4.3 9.8 1.0 CG2 1:VAL189 4.4 25.6 1.0 C 1:ASN205 4.6 10.9 1.0 N 1:ASN188 4.6 19.2 1.0 CB 1:ASN187 4.6 19.6 1.0 CB 1:ASN205 4.7 14.6 1.0 C2 1:NAG1001 4.7 33.4 1.0 CG 1:GLU193 4.7 10.4 1.0 CG 1:GLU185 4.7 17.0 1.0 C5 1:NAG1001 4.7 33.2 1.0 CA 1:ASN187 4.7 20.0 1.0 N 1:VAL207 4.8 9.2 1.0 CB 1:GLU193 4.8 11.3 1.0 CA 1:ASN205 4.8 13.2 1.0 C 1:ASN187 5.0 21.0 1.0

Calcium binding site 3 out of 4 in the Complex of Mbp-C and Glcnac-Terminated Core


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Mbp-C and Glcnac-Terminated Core within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca601 b:14.5 occ:1.00 OD1 2:ASN194 2.3 16.8 1.0 O 2:HOH2012 2.3 16.2 1.0 OD2 2:ASP161 2.4 12.2 1.0 OE2 2:GLU165 2.5 16.2 1.0 OD1 2:ASN188 2.5 16.2 1.0 O 2:GLU193 2.5 12.4 1.0 OE1 2:GLU165 2.6 17.4 1.0 OD1 2:ASP161 2.7 10.2 1.0 CG 2:ASP161 2.9 13.8 1.0 CD 2:GLU165 2.9 15.4 1.0 CG 2:ASN188 3.4 20.5 1.0 CG 2:ASN194 3.4 13.6 1.0 C 2:GLU193 3.4 13.5 1.0 CA 2:ASN194 3.8 10.0 1.0 N 2:ASN194 4.0 11.9 1.0 CB 2:ASN188 4.0 19.1 1.0 CB 2:ASN194 4.1 10.7 1.0 O 2:HOH2003 4.2 45.7 1.0 ND2 2:ASN188 4.3 19.4 1.0 O 2:HOH2006 4.3 15.1 1.0 N 2:GLU193 4.3 17.9 1.0 O 2:HOH2011 4.3 13.8 1.0 CB 2:ASP161 4.4 13.6 1.0 CG 2:GLU165 4.4 16.0 1.0 ND2 2:ASN194 4.5 16.2 1.0 CA 2:GLU193 4.5 15.3 1.0 OD1 2:ASP206 4.6 10.7 1.0 CA 2:ASN188 4.7 20.9 1.0 O 2:ASP161 4.7 19.2 1.0 N 2:ASN166 4.7 16.1 1.0 CZ 2:PHE168 4.8 15.7 1.0 CA 2:GLU165 4.9 17.2 1.0 C 2:ASN194 5.0 9.9 1.0

Calcium binding site 4 out of 4 in the Complex of Mbp-C and Glcnac-Terminated Core


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Mbp-C and Glcnac-Terminated Core within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca602 b:14.4 occ:1.00 OD1 2:ASN187 2.3 16.8 1.0 OD2 2:ASP206 2.3 12.7 1.0 O4 2:NAG2001 2.4 22.3 1.0 OD1 2:ASN205 2.4 11.4 1.0 OE2 2:GLU193 2.4 9.7 1.0 O3 2:NAG2001 2.6 24.7 1.0 OE1 2:GLU185 2.6 17.3 1.0 O 2:ASP206 2.7 11.9 1.0 C4 2:NAG2001 3.2 28.4 1.0 C3 2:NAG2001 3.3 30.0 1.0 CG 2:ASN187 3.3 19.6 1.0 CG 2:ASP206 3.3 13.2 1.0 CD 2:GLU185 3.4 15.9 1.0 CD 2:GLU193 3.4 13.3 1.0 CG 2:ASN205 3.5 13.1 1.0 OE2 2:GLU185 3.7 13.7 1.0 C 2:ASP206 3.7 12.2 1.0 OE1 2:GLU193 3.7 12.2 1.0 N 2:ASP206 3.8 10.7 1.0 ND2 2:ASN187 3.8 18.5 1.0 ND2 2:ASN205 4.0 14.4 1.0 OD1 2:ASP206 4.0 10.7 1.0 CA 2:ASP206 4.1 11.5 1.0 N 2:ASN187 4.2 18.5 1.0 CB 2:ASP206 4.3 11.5 1.0 CG1 2:VAL189 4.4 29.5 1.0 CB 2:ASN187 4.6 17.9 1.0 N 2:ASN188 4.6 18.1 1.0 CG 2:GLU185 4.6 16.0 1.0 C5 2:NAG2001 4.6 31.7 1.0 C 2:ASN205 4.6 9.8 1.0 CG 2:GLU193 4.7 14.2 1.0 C2 2:NAG2001 4.7 32.8 1.0 CB 2:ASN205 4.8 12.5 1.0 CA 2:ASN187 4.8 19.1 1.0 CB 2:GLU193 4.9 13.8 1.0 N 2:VAL207 4.9 10.6 1.0 CA 2:ASN205 4.9 11.2 1.0 C 2:ASN187 5.0 18.9 1.0 N 2:VAL189 5.0 24.1 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