Calcium in PDB 1rdo: Mannose-Binding Protein, Subtilisin Digest Fragment

The structure of Mannose-Binding Protein, Subtilisin Digest Fragment, PDB code: 1rdo 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 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.700, 75.300, 57.600, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.8

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

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Mannose-Binding Protein, Subtilisin Digest Fragment (pdb code 1rdo). 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, PDB code: 1rdo:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca1 b:12.4 occ:1.00 O 1:HOH273 2.3 8.4 1.0 OD2 1:ASP166 2.4 11.2 1.0 OE1 1:GLU170 2.5 11.8 1.0 O 1:GLU198 2.5 11.7 1.0 OD1 1:ASN199 2.5 11.1 1.0 OD1 1:ASN193 2.6 12.3 1.0 OE2 1:GLU170 2.7 15.4 1.0 OD1 1:ASP166 2.7 13.0 1.0 CG 1:ASP166 2.9 10.6 1.0 CD 1:GLU170 2.9 11.7 1.0 C 1:GLU198 3.4 12.8 1.0 CG 1:ASN193 3.4 15.1 1.0 CG 1:ASN199 3.6 10.1 1.0 CA 1:ASN199 3.8 11.3 1.0 N 1:ASN199 4.0 11.7 1.0 CB 1:ASN193 4.0 15.3 1.0 CB 1:ASN199 4.2 10.1 1.0 N 1:GLU198 4.3 13.7 1.0 ND2 1:ASN193 4.3 16.7 1.0 CB 1:ASP166 4.4 12.5 1.0 CG 1:GLU170 4.4 13.9 1.0 O 1:HOH272 4.5 17.9 1.0 CA 1:GLU198 4.5 11.7 1.0 CZ 1:PHE173 4.6 17.3 1.0 OD2 1:ASP211 4.7 12.9 1.0 CA 1:ASN193 4.7 17.1 1.0 N 1:ASN171 4.7 14.2 1.0 ND2 1:ASN199 4.7 13.4 1.0 O 1:ASP166 4.8 12.4 1.0 C 1:ASN199 4.9 10.2 1.0 CA 1:GLU170 5.0 13.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca2 b:14.0 occ:1.00 OE1 1:GLU198 2.3 11.4 1.0 OD1 1:ASP211 2.3 12.9 1.0 OD1 1:ASN192 2.4 16.6 1.0 OD1 1:ASN210 2.4 12.6 1.0 O 1:HOH346 2.5 17.3 1.0 O 1:ASP211 2.6 9.5 1.0 O 1:HOH345 2.7 21.1 1.0 OE1 1:GLU190 2.7 15.4 1.0 CD 1:GLU198 3.3 10.6 1.0 CG 1:ASP211 3.3 11.5 1.0 CG 1:ASN192 3.4 18.9 1.0 CG 1:ASN210 3.4 14.6 1.0 CD 1:GLU190 3.5 16.8 1.0 C 1:ASP211 3.6 7.6 1.0 OE2 1:GLU198 3.7 14.0 1.0 N 1:ASP211 3.8 9.7 1.0 OE2 1:GLU190 3.8 16.8 1.0 ND2 1:ASN210 3.8 9.9 1.0 ND2 1:ASN192 3.9 19.1 1.0 OD2 1:ASP211 4.0 12.9 1.0 CA 1:ASP211 4.1 9.3 1.0 N 1:ASN192 4.3 16.5 1.0 CB 1:ASP211 4.3 7.2 1.0 CG2 1:VAL194 4.3 24.2 1.0 O 1:HOH344 4.6 35.0 0.7 CG 1:GLU198 4.6 11.2 1.0 N 1:ASN193 4.6 14.8 1.0 C 1:ASN210 4.7 8.1 1.0 CB 1:ASN192 4.7 17.5 1.0 CG 1:GLU190 4.7 13.9 1.0 CB 1:ASN210 4.7 12.9 1.0 N 1:VAL212 4.8 9.0 1.0 CB 1:GLU198 4.8 9.4 1.0 CA 1:ASN192 4.8 15.7 1.0 N 1:VAL194 4.9 19.7 1.0 CA 1:ASN210 4.9 12.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca1 b:14.4 occ:1.00 O 2:HOH231 2.3 12.9 1.0 OD1 2:ASN199 2.4 14.5 1.0 OE1 2:GLU170 2.4 14.4 1.0 OD1 2:ASN193 2.5 14.2 1.0 OD2 2:ASP166 2.5 10.4 1.0 O 2:GLU198 2.5 10.0 1.0 OE2 2:GLU170 2.6 14.0 1.0 OD1 2:ASP166 2.7 13.2 1.0 CD 2:GLU170 2.9 11.9 1.0 CG 2:ASP166 2.9 11.5 1.0 CG 2:ASN193 3.3 15.2 1.0 C 2:GLU198 3.4 10.7 1.0 CG 2:ASN199 3.5 14.5 1.0 CA 2:ASN199 3.7 11.8 1.0 N 2:ASN199 4.0 11.4 1.0 CB 2:ASN193 4.1 14.3 1.0 CB 2:ASN199 4.1 13.2 1.0 ND2 2:ASN193 4.2 15.7 1.0 N 2:GLU198 4.3 15.8 1.0 O 2:HOH230 4.3 19.1 1.0 O 2:HOH234 4.4 12.8 1.0 CG 2:GLU170 4.4 16.1 1.0 O 2:HOH232 4.4 30.2 1.0 CB 2:ASP166 4.4 12.5 1.0 CA 2:GLU198 4.5 12.3 1.0 OD2 2:ASP211 4.5 13.4 1.0 ND2 2:ASN199 4.6 21.1 1.0 CA 2:ASN193 4.7 18.2 1.0 N 2:ASN171 4.8 15.3 1.0 O 2:ASP166 4.8 16.4 1.0 CZ 2:PHE173 4.9 18.4 1.0 C 2:ASN199 5.0 11.8 1.0 CA 2:GLU170 5.0 16.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca2 b:13.6 occ:1.00 OD1 2:ASP211 2.3 12.2 1.0 OD1 2:ASN192 2.3 14.4 1.0 OE1 2:GLU198 2.4 12.8 1.0 OD1 2:ASN210 2.4 14.1 1.0 OE1 2:GLU190 2.6 15.6 1.0 O 2:ASP211 2.7 11.0 1.0 O 2:HOH364 2.7 16.7 1.0 O 2:HOH363 2.7 17.7 1.0 CD 2:GLU198 3.3 11.9 1.0 CG 2:ASP211 3.3 12.4 1.0 CG 2:ASN192 3.4 15.3 1.0 CG 2:ASN210 3.5 12.2 1.0 CD 2:GLU190 3.5 14.9 1.0 OE2 2:GLU198 3.7 13.8 1.0 C 2:ASP211 3.7 10.3 1.0 OE2 2:GLU190 3.8 13.5 1.0 N 2:ASP211 3.8 9.0 1.0 ND2 2:ASN192 3.8 19.0 1.0 ND2 2:ASN210 3.9 12.8 1.0 OD2 2:ASP211 4.0 13.4 1.0 CA 2:ASP211 4.1 10.5 1.0 N 2:ASN192 4.2 16.7 1.0 CB 2:ASP211 4.3 10.5 1.0 CG1 2:VAL194 4.4 25.8 1.0 O 2:HOH365 4.5 24.3 0.6 CG 2:GLU198 4.6 13.6 1.0 CB 2:ASN192 4.6 16.8 1.0 N 2:ASN193 4.7 16.6 1.0 C 2:ASN210 4.7 8.1 1.0 CG 2:GLU190 4.8 15.1 1.0 CB 2:ASN210 4.8 11.9 1.0 CA 2:ASN192 4.8 16.9 1.0 CB 2:GLU198 4.8 11.7 1.0 N 2:VAL212 4.9 9.4 1.0 N 2:VAL194 5.0 20.7 1.0 CA 2:ASN210 5.0 11.4 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