Calcium in PDB 1rdk: Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose

The structure of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose, PDB code: 1rdk was solved by K.K.-S.Ng, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.700, 75.300, 57.400, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.5

The structure of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose (pdb code 1rdk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose, PDB code: 1rdk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca227 b:12.8 occ:1.00 O 1:HOH274 2.4 7.3 1.0 OD1 1:ASN199 2.4 10.9 1.0 O 1:GLU198 2.4 8.0 1.0 OD1 1:ASN193 2.5 10.3 1.0 OE1 1:GLU170 2.6 11.2 1.0 OD2 1:ASP166 2.6 7.5 1.0 OD1 1:ASP166 2.7 10.5 1.0 OE2 1:GLU170 2.8 12.0 1.0 CG 1:ASP166 3.0 8.0 1.0 CD 1:GLU170 3.0 9.6 1.0 C 1:GLU198 3.3 8.0 1.0 CG 1:ASN193 3.4 11.9 1.0 CG 1:ASN199 3.5 6.0 1.0 CA 1:ASN199 3.7 8.2 1.0 N 1:ASN199 3.9 8.6 1.0 CB 1:ASN193 4.0 14.7 1.0 CB 1:ASN199 4.1 6.0 1.0 N 1:GLU198 4.2 12.4 1.0 ND2 1:ASN193 4.3 14.2 1.0 CA 1:GLU198 4.4 10.6 1.0 CG 1:GLU170 4.5 11.2 1.0 CB 1:ASP166 4.5 9.3 1.0 OD2 1:ASP211 4.6 11.0 1.0 O 1:HOH273 4.6 18.5 1.0 ND2 1:ASN199 4.6 7.9 1.0 CA 1:ASN193 4.7 13.8 1.0 CZ 1:PHE173 4.7 10.6 1.0 O 1:ASP166 4.8 8.7 1.0 N 1:ASN171 4.9 12.6 1.0 C 1:ASN199 4.9 8.0 1.0

Calcium binding site 2 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca2 b:12.3 occ:1.00 OD1 1:ASP211 2.4 8.8 1.0 OE1 1:GLU198 2.4 9.9 1.0 OD1 1:ASN192 2.5 15.9 1.0 OE1 1:GLU190 2.5 16.6 1.0 O1 1:GAL1 2.5 14.5 1.0 OD1 1:ASN210 2.5 9.8 1.0 O2 1:GAL1 2.6 16.4 1.0 O 1:ASP211 2.6 10.7 1.0 C1 1:GAL1 3.3 19.0 1.0 CD 1:GLU198 3.4 7.3 1.0 CG 1:ASP211 3.4 10.6 1.0 C2 1:GAL1 3.4 18.1 1.0 CG 1:ASN192 3.4 16.4 1.0 CD 1:GLU190 3.4 14.5 1.0 CG 1:ASN210 3.5 13.4 1.0 C 1:ASP211 3.6 8.2 1.0 OE2 1:GLU198 3.7 9.1 1.0 N 1:ASP211 3.7 9.4 1.0 OE2 1:GLU190 3.8 12.8 1.0 ND2 1:ASN192 3.9 18.7 1.0 ND2 1:ASN210 4.0 10.2 1.0 OD2 1:ASP211 4.1 11.0 1.0 CA 1:ASP211 4.1 9.8 1.0 N 1:ASN192 4.2 15.3 1.0 CB 1:ASP211 4.3 8.5 1.0 CG 1:GLU198 4.6 8.4 1.0 C 1:ASN210 4.6 6.5 1.0 O5 1:GAL1 4.6 19.2 1.0 N 1:ASN193 4.6 11.0 1.0 CB 1:ASN192 4.7 17.9 1.0 CG 1:GLU190 4.7 12.3 1.0 CB 1:GLU198 4.7 8.1 1.0 CG2 1:VAL194 4.8 22.1 1.0 C3 1:GAL1 4.8 20.1 1.0 N 1:VAL212 4.8 6.7 1.0 CA 1:ASN192 4.8 13.7 1.0 CB 1:ASN210 4.8 11.5 1.0 CA 1:ASN210 4.9 10.8 1.0

Calcium binding site 3 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca227 b:13.1 occ:1.00 OD1 2:ASN199 2.3 14.4 1.0 O 2:HOH232 2.3 10.5 1.0 O 2:GLU198 2.4 7.6 1.0 OE1 2:GLU170 2.5 10.4 1.0 OD2 2:ASP166 2.5 7.9 1.0 OD1 2:ASN193 2.5 11.2 1.0 OD1 2:ASP166 2.7 11.1 1.0 OE2 2:GLU170 2.7 13.7 1.0 CG 2:ASP166 2.9 11.6 1.0 CD 2:GLU170 3.0 15.2 1.0 C 2:GLU198 3.3 7.7 1.0 CG 2:ASN193 3.4 14.2 1.0 CG 2:ASN199 3.4 10.6 1.0 CA 2:ASN199 3.7 10.7 1.0 N 2:ASN199 3.9 9.1 1.0 CB 2:ASN193 4.0 13.5 1.0 CB 2:ASN199 4.1 10.6 1.0 N 2:GLU198 4.3 13.3 1.0 ND2 2:ASN193 4.3 16.8 1.0 O 2:HOH233 4.3 29.9 1.0 O 2:HOH235 4.4 12.4 1.0 O 2:HOH231 4.4 16.4 1.0 CA 2:GLU198 4.4 9.9 1.0 CG 2:GLU170 4.5 17.0 1.0 CB 2:ASP166 4.5 12.4 1.0 OD2 2:ASP211 4.5 8.6 1.0 ND2 2:ASN199 4.5 15.0 1.0 CA 2:ASN193 4.7 17.9 1.0 O 2:ASP166 4.8 13.5 1.0 N 2:ASN171 4.9 14.6 1.0 CZ 2:PHE173 4.9 11.5 1.0 C 2:ASN199 4.9 9.5 1.0

Calcium binding site 4 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca2 b:12.5 occ:1.00 OD1 2:ASN192 2.3 14.0 1.0 OE1 2:GLU198 2.4 11.6 1.0 OD1 2:ASP211 2.4 10.5 1.0 O2 2:GAL1 2.5 12.7 1.0 OE1 2:GLU190 2.5 16.4 1.0 OD1 2:ASN210 2.6 11.3 1.0 O1 2:GAL1 2.6 16.4 1.0 O 2:ASP211 2.6 10.5 1.0 C1 2:GAL1 3.3 18.8 1.0 CG 2:ASN192 3.3 13.8 1.0 CG 2:ASP211 3.4 12.1 1.0 C2 2:GAL1 3.4 16.9 1.0 CD 2:GLU198 3.4 9.2 1.0 CD 2:GLU190 3.4 15.6 1.0 CG 2:ASN210 3.6 9.8 1.0 C 2:ASP211 3.7 8.7 1.0 OE2 2:GLU190 3.7 15.0 1.0 OE2 2:GLU198 3.7 10.0 1.0 N 2:ASP211 3.7 7.7 1.0 ND2 2:ASN192 3.8 15.8 1.0 OD2 2:ASP211 4.0 8.6 1.0 ND2 2:ASN210 4.0 10.3 1.0 CA 2:ASP211 4.1 9.8 1.0 N 2:ASN192 4.2 16.7 1.0 CB 2:ASP211 4.3 10.6 1.0 CG1 2:VAL194 4.5 23.5 1.0 CB 2:ASN192 4.6 15.7 1.0 C 2:ASN210 4.6 4.7 1.0 CG 2:GLU198 4.6 10.4 1.0 CG 2:GLU190 4.6 14.4 1.0 O5 2:GAL1 4.7 16.9 1.0 N 2:ASN193 4.7 13.6 1.0 C3 2:GAL1 4.7 19.1 1.0 CA 2:ASN192 4.8 14.6 1.0 CB 2:GLU198 4.8 8.9 1.0 N 2:VAL212 4.8 6.7 1.0 CB 2:ASN210 4.9 7.8 1.0 CA 2:ASN210 4.9 9.6 1.0 C 2:ASN192 5.0 14.6 1.0

K.K.Ng, K.Drickamer, W.I.Weis. Structural Analysis of Monosaccharide Recognition By Rat Liver Mannose-Binding Protein. J.Biol.Chem. V. 271 663 1996.
ISSN: ISSN 0021-9258
PubMed: 8557671
DOI: 10.1074/JBC.271.2.663