Calcium in PDB 1rdj: Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Beta-Methyl-L-Fucopyranoside

The structure of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Beta-Methyl-L-Fucopyranoside, PDB code: 1rdj 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, 74.900, 57.100, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.6

The structure of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Beta-Methyl-L-Fucopyranoside 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 Beta-Methyl-L-Fucopyranoside (pdb code 1rdj). 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 Beta-Methyl-L-Fucopyranoside, PDB code: 1rdj:
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 Beta-Methyl-L-Fucopyranoside


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 Beta-Methyl-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca227 b:12.8 occ:1.00 O 1:HOH274 2.3 11.7 1.0 OD2 1:ASP166 2.4 10.6 1.0 OD1 1:ASN199 2.5 13.2 1.0 O 1:GLU198 2.5 9.2 1.0 OD1 1:ASN193 2.5 14.5 1.0 OE1 1:GLU170 2.5 12.0 1.0 OE2 1:GLU170 2.7 14.8 1.0 OD1 1:ASP166 2.7 10.9 1.0 CG 1:ASP166 2.9 11.9 1.0 CD 1:GLU170 2.9 12.1 1.0 CG 1:ASN193 3.3 16.4 1.0 C 1:GLU198 3.4 10.3 1.0 CG 1:ASN199 3.6 11.8 1.0 CA 1:ASN199 3.8 9.9 1.0 CB 1:ASN193 4.0 16.3 1.0 N 1:ASN199 4.0 9.5 1.0 CB 1:ASN199 4.1 11.5 1.0 ND2 1:ASN193 4.2 16.0 1.0 O 1:HOH273 4.3 20.9 1.0 N 1:GLU198 4.3 16.1 1.0 CG 1:GLU170 4.4 10.4 1.0 CB 1:ASP166 4.4 11.3 1.0 CA 1:GLU198 4.5 14.1 1.0 OD2 1:ASP211 4.6 12.6 1.0 CA 1:ASN193 4.6 17.2 1.0 ND2 1:ASN199 4.7 14.4 1.0 CZ 1:PHE173 4.7 13.7 1.0 N 1:ASN171 4.8 13.9 1.0 O 1:ASP166 4.8 13.4 1.0 C 1:ASN199 5.0 9.4 1.0

Calcium binding site 2 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Beta-Methyl-L-Fucopyranoside


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 Beta-Methyl-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca2 b:15.1 occ:1.00 OD1 1:ASN192 2.4 19.0 1.0 OD1 1:ASP211 2.4 12.1 1.0 OD1 1:ASN210 2.4 13.9 1.0 OE1 1:GLU198 2.4 12.0 1.0 OE1 1:GLU190 2.5 15.7 1.0 O3 1:MFB1 2.5 17.1 1.0 O2 1:MFB1 2.6 15.1 1.0 O 1:ASP211 2.6 13.6 1.0 C3 1:MFB1 3.3 20.7 1.0 C2 1:MFB1 3.4 18.5 1.0 CD 1:GLU198 3.4 10.1 1.0 CG 1:ASP211 3.4 12.9 1.0 CD 1:GLU190 3.4 19.0 1.0 CG 1:ASN192 3.4 19.8 1.0 CG 1:ASN210 3.5 15.2 1.0 C 1:ASP211 3.6 9.8 1.0 OE2 1:GLU190 3.7 15.4 1.0 OE2 1:GLU198 3.7 13.3 1.0 N 1:ASP211 3.8 10.0 1.0 ND2 1:ASN192 3.9 20.9 1.0 ND2 1:ASN210 3.9 13.1 1.0 OD2 1:ASP211 4.1 12.6 1.0 CA 1:ASP211 4.1 10.9 1.0 N 1:ASN192 4.2 16.9 1.0 CB 1:ASP211 4.3 8.0 1.0 CG2 1:VAL194 4.4 21.8 1.0 CB 1:ASN192 4.6 17.4 1.0 C 1:ASN210 4.6 9.9 1.0 CG 1:GLU198 4.6 9.4 1.0 CG 1:GLU190 4.6 12.2 1.0 N 1:ASN193 4.7 15.0 1.0 C4 1:MFB1 4.7 23.1 1.0 CA 1:ASN192 4.7 15.9 1.0 C1 1:MFB1 4.7 23.5 1.0 CB 1:ASN210 4.8 13.1 1.0 N 1:VAL212 4.8 9.5 1.0 CB 1:GLU198 4.8 11.3 1.0 CA 1:ASN210 4.9 12.1 1.0 C 1:ASN192 5.0 16.4 1.0

Calcium binding site 3 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Beta-Methyl-L-Fucopyranoside


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 Beta-Methyl-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca227 b:16.0 occ:1.00 O 2:HOH232 2.3 15.4 1.0 OD1 2:ASN199 2.4 15.8 1.0 OD2 2:ASP166 2.4 12.8 1.0 OE1 2:GLU170 2.4 11.1 1.0 O 2:GLU198 2.5 11.5 1.0 OD1 2:ASN193 2.5 14.2 1.0 OE2 2:GLU170 2.5 16.6 1.0 OD1 2:ASP166 2.7 14.4 1.0 CD 2:GLU170 2.8 13.9 1.0 CG 2:ASP166 2.9 14.9 1.0 CG 2:ASN193 3.3 18.1 1.0 C 2:GLU198 3.4 11.9 1.0 CG 2:ASN199 3.5 14.2 1.0 CA 2:ASN199 3.8 10.1 1.0 N 2:ASN199 4.0 9.7 1.0 CB 2:ASN193 4.1 15.5 1.0 ND2 2:ASN193 4.2 18.0 1.0 CB 2:ASN199 4.2 11.1 1.0 N 2:GLU198 4.3 16.3 1.0 O 2:HOH233 4.3 31.6 1.0 O 2:HOH231 4.3 15.8 1.0 CG 2:GLU170 4.3 16.8 1.0 O 2:HOH235 4.4 14.5 1.0 CB 2:ASP166 4.4 14.0 1.0 OD2 2:ASP211 4.5 14.8 1.0 CA 2:GLU198 4.5 14.2 1.0 ND2 2:ASN199 4.6 21.4 1.0 CA 2:ASN193 4.7 19.4 1.0 O 2:ASP166 4.8 15.1 1.0 N 2:ASN171 4.8 14.3 1.0 CZ 2:PHE173 4.9 19.4 1.0 C 2:ASN199 5.0 9.6 1.0

Calcium binding site 4 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Beta-Methyl-L-Fucopyranoside


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 Beta-Methyl-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca2 b:14.7 occ:1.00 OD1 2:ASN192 2.3 16.3 1.0 OD1 2:ASP211 2.4 13.0 1.0 OD1 2:ASN210 2.4 12.1 1.0 OE1 2:GLU198 2.4 13.3 1.0 O2 2:MFB1 2.5 13.6 1.0 O3 2:MFB1 2.6 18.4 1.0 OE1 2:GLU190 2.6 15.2 1.0 O 2:ASP211 2.6 15.4 1.0 C3 2:MFB1 3.3 20.7 1.0 C2 2:MFB1 3.3 18.1 1.0 CG 2:ASP211 3.3 14.2 1.0 CD 2:GLU198 3.4 11.9 1.0 CG 2:ASN192 3.4 15.2 1.0 CD 2:GLU190 3.4 17.3 1.0 CG 2:ASN210 3.5 12.8 1.0 C 2:ASP211 3.6 12.2 1.0 OE2 2:GLU198 3.7 16.7 1.0 N 2:ASP211 3.7 9.3 1.0 OE2 2:GLU190 3.8 13.6 1.0 ND2 2:ASN192 3.9 20.9 1.0 ND2 2:ASN210 4.0 14.2 1.0 OD2 2:ASP211 4.1 14.8 1.0 CA 2:ASP211 4.1 11.3 1.0 N 2:ASN192 4.2 18.0 1.0 CB 2:ASP211 4.3 10.4 1.0 CG1 2:VAL194 4.5 22.9 1.0 C 2:ASN210 4.6 8.8 1.0 CG 2:GLU198 4.6 16.5 1.0 CB 2:ASN192 4.6 18.2 1.0 N 2:ASN193 4.6 16.7 1.0 CG 2:GLU190 4.7 14.7 1.0 C1 2:MFB1 4.7 23.4 1.0 C4 2:MFB1 4.7 21.6 1.0 CB 2:ASN210 4.8 12.5 1.0 CB 2:GLU198 4.8 13.7 1.0 N 2:VAL212 4.8 11.8 1.0 CA 2:ASN192 4.8 18.9 1.0 CA 2:ASN210 4.9 10.6 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