Calcium in PDB 1kzb: Complex of Mbp-C and Trimannosyl Core

The structure of Complex of Mbp-C and Trimannosyl Core, PDB code: 1kzb 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 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.720, 75.330, 57.440, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.9

The binding sites of Calcium atom in the Complex of Mbp-C and Trimannosyl Core (pdb code 1kzb). 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 Trimannosyl Core, PDB code: 1kzb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Complex of Mbp-C and Trimannosyl 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 Trimannosyl Core within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca501 b:12.0 occ:1.00 O 1:HOH1558 2.3 12.4 1.0 OD2 1:ASP161 2.4 14.2 1.0 OD1 1:ASN188 2.4 17.2 1.0 O 1:GLU193 2.4 11.4 1.0 OD1 1:ASN194 2.4 11.7 1.0 OE1 1:GLU165 2.5 14.6 1.0 OE2 1:GLU165 2.6 16.1 1.0 OD1 1:ASP161 2.6 12.5 1.0 CG 1:ASP161 2.9 16.8 1.0 CD 1:GLU165 2.9 14.5 1.0 CG 1:ASN188 3.3 18.8 1.0 C 1:GLU193 3.4 12.4 1.0 CG 1:ASN194 3.5 12.4 1.0 CA 1:ASN194 3.7 10.4 1.0 N 1:ASN194 4.0 11.6 1.0 CB 1:ASN188 4.0 18.8 1.0 CB 1:ASN194 4.1 11.9 1.0 ND2 1:ASN188 4.2 15.7 1.0 N 1:GLU193 4.3 13.9 1.0 CB 1:ASP161 4.4 15.2 1.0 CG 1:GLU165 4.4 16.5 1.0 CA 1:GLU193 4.5 14.4 1.0 O 1:HOH1557 4.5 18.6 1.0 ND2 1:ASN194 4.7 14.5 1.0 CA 1:ASN188 4.7 18.7 1.0 OD2 1:ASP206 4.7 13.8 1.0 O 1:ASP161 4.7 14.0 1.0 CZ 1:PHE168 4.7 18.5 1.0 N 1:ASN166 4.8 15.3 1.0 C 1:ASN194 4.9 11.3 1.0 CA 1:GLU165 5.0 16.4 1.0

Calcium binding site 2 out of 4 in the Complex of Mbp-C and Trimannosyl 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 Trimannosyl Core within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca502 b:13.8 occ:1.00 OD1 1:ASP206 2.3 11.3 1.0 OE1 1:GLU193 2.3 10.8 1.0 OD1 1:ASN187 2.4 16.4 1.0 OD1 1:ASN205 2.5 15.6 1.0 O3 1:MAN1501 2.5 17.2 1.0 O4 1:MAN1501 2.5 18.4 1.0 OE1 1:GLU185 2.5 15.5 1.0 O 1:ASP206 2.6 12.5 1.0 CG 1:ASP206 3.3 13.0 1.0 C3 1:MAN1501 3.3 20.3 1.0 C4 1:MAN1501 3.3 20.0 1.0 CD 1:GLU193 3.3 9.9 1.0 CG 1:ASN187 3.4 19.6 1.0 CD 1:GLU185 3.4 17.3 1.0 CG 1:ASN205 3.5 17.3 1.0 C 1:ASP206 3.6 11.8 1.0 OE2 1:GLU193 3.7 11.7 1.0 N 1:ASP206 3.7 11.5 1.0 OE2 1:GLU185 3.8 17.1 1.0 ND2 1:ASN187 3.9 19.6 1.0 OD2 1:ASP206 3.9 13.8 1.0 ND2 1:ASN205 4.0 13.8 1.0 CA 1:ASP206 4.1 11.9 1.0 N 1:ASN187 4.2 18.9 1.0 CB 1:ASP206 4.3 9.9 1.0 CG2 1:VAL189 4.5 24.0 1.0 CG 1:GLU193 4.6 14.4 1.0 N 1:ASN188 4.6 17.9 1.0 C 1:ASN205 4.6 12.3 1.0 CG 1:GLU185 4.7 14.7 1.0 CB 1:ASN187 4.7 19.5 1.0 C2 1:MAN1501 4.7 20.8 1.0 C5 1:MAN1501 4.7 23.1 1.0 N 1:VAL207 4.8 11.8 1.0 CB 1:GLU193 4.8 13.0 1.0 CA 1:ASN187 4.8 18.1 1.0 CB 1:ASN205 4.8 14.5 1.0 CA 1:ASN205 4.9 13.4 1.0

Calcium binding site 3 out of 4 in the Complex of Mbp-C and Trimannosyl 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 Trimannosyl Core within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca601 b:14.4 occ:1.00 O 2:HOH1721 2.2 13.2 1.0 OD1 2:ASN194 2.3 17.3 1.0 OE1 2:GLU165 2.4 13.8 1.0 O 2:GLU193 2.5 10.9 1.0 OD2 2:ASP161 2.5 13.4 1.0 OE2 2:GLU165 2.5 16.2 1.0 OD1 2:ASN188 2.5 14.5 1.0 OD1 2:ASP161 2.7 12.4 1.0 CD 2:GLU165 2.8 13.7 1.0 CG 2:ASP161 2.9 13.5 1.0 CG 2:ASN188 3.4 17.6 1.0 C 2:GLU193 3.4 12.3 1.0 CG 2:ASN194 3.4 15.5 1.0 CA 2:ASN194 3.7 12.7 1.0 N 2:ASN194 4.0 11.9 1.0 CB 2:ASN188 4.0 17.0 1.0 CB 2:ASN194 4.1 13.6 1.0 O 2:HOH1645 4.1 16.2 1.0 ND2 2:ASN188 4.2 17.5 1.0 O 2:HOH1644 4.3 30.2 1.0 N 2:GLU193 4.3 16.6 1.0 O 2:HOH1722 4.3 19.6 1.0 CG 2:GLU165 4.3 16.1 1.0 CB 2:ASP161 4.4 13.4 1.0 CA 2:GLU193 4.5 13.4 1.0 ND2 2:ASN194 4.5 19.8 1.0 OD2 2:ASP206 4.6 11.8 1.0 CA 2:ASN188 4.7 18.5 1.0 O 2:ASP161 4.7 18.3 1.0 N 2:ASN166 4.8 17.3 1.0 CA 2:GLU165 4.9 17.0 1.0 C 2:ASN194 4.9 11.2 1.0 CZ 2:PHE168 5.0 17.2 1.0

Calcium binding site 4 out of 4 in the Complex of Mbp-C and Trimannosyl 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 Trimannosyl Core within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca602 b:13.2 occ:1.00 OD1 2:ASP206 2.3 13.2 1.0 OE1 2:GLU193 2.4 14.8 1.0 OD1 2:ASN187 2.4 14.2 1.0 OD1 2:ASN205 2.4 12.0 1.0 O4 2:MAN1601 2.5 14.6 1.0 O 2:ASP206 2.6 13.3 1.0 O3 2:MAN1601 2.6 13.6 1.0 OE1 2:GLU185 2.6 12.4 1.0 CG 2:ASP206 3.3 11.9 1.0 C3 2:MAN1601 3.3 18.7 1.0 C4 2:MAN1601 3.4 18.5 1.0 CD 2:GLU193 3.4 12.7 1.0 CD 2:GLU185 3.4 14.3 1.0 CG 2:ASN187 3.4 18.1 1.0 CG 2:ASN205 3.5 14.7 1.0 C 2:ASP206 3.6 13.4 1.0 N 2:ASP206 3.7 10.7 1.0 OE2 2:GLU185 3.8 13.5 1.0 OE2 2:GLU193 3.8 10.8 1.0 ND2 2:ASN187 3.9 16.5 1.0 ND2 2:ASN205 3.9 14.6 1.0 OD2 2:ASP206 3.9 11.8 1.0 CA 2:ASP206 4.1 11.3 1.0 CG1 2:VAL189 4.2 25.1 1.0 N 2:ASN187 4.2 18.9 1.0 CB 2:ASP206 4.3 10.5 1.0 C 2:ASN205 4.6 10.8 1.0 CG 2:GLU193 4.6 14.5 1.0 CG 2:GLU185 4.6 13.6 1.0 N 2:ASN188 4.7 17.6 1.0 CB 2:ASN187 4.7 17.8 1.0 C5 2:MAN1601 4.7 21.2 1.0 CB 2:ASN205 4.8 12.4 1.0 C2 2:MAN1601 4.8 19.7 1.0 N 2:VAL207 4.8 11.5 1.0 CB 2:GLU193 4.8 13.5 1.0 CA 2:ASN187 4.8 18.0 1.0 CA 2:ASN205 4.9 11.4 1.0 N 2:VAL189 5.0 20.2 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