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

The structure of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-Methyl-L-Fucopyranoside, PDB code: 1rdi 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, 75.100, 57.300, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.4

The structure of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-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 Alpha-Methyl-L-Fucopyranoside (pdb code 1rdi). 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 Alpha-Methyl-L-Fucopyranoside, PDB code: 1rdi:
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 Alpha-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 Alpha-Methyl-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca227 b:12.7 occ:1.00 O 1:HOH274 2.3 9.3 1.0 O 1:GLU198 2.5 10.8 1.0 OD1 1:ASN199 2.5 11.3 1.0 OD2 1:ASP166 2.5 10.8 1.0 OD1 1:ASN193 2.5 11.8 1.0 OE1 1:GLU170 2.5 11.7 1.0 OD1 1:ASP166 2.7 11.4 1.0 OE2 1:GLU170 2.7 13.4 1.0 CG 1:ASP166 2.9 11.8 1.0 CD 1:GLU170 3.0 10.2 1.0 CG 1:ASN193 3.4 12.6 1.0 C 1:GLU198 3.4 11.1 1.0 CG 1:ASN199 3.6 10.6 1.0 CA 1:ASN199 3.8 9.4 1.0 N 1:ASN199 4.0 11.9 1.0 CB 1:ASN193 4.0 15.4 1.0 O 1:HOH273 4.1 17.4 1.0 CB 1:ASN199 4.1 10.8 1.0 N 1:GLU198 4.3 13.8 1.0 ND2 1:ASN193 4.3 16.2 1.0 CB 1:ASP166 4.5 11.1 1.0 CG 1:GLU170 4.5 10.8 1.0 CA 1:GLU198 4.5 13.1 1.0 OD2 1:ASP211 4.6 12.0 1.0 CA 1:ASN193 4.6 17.5 1.0 ND2 1:ASN199 4.7 10.6 1.0 CZ 1:PHE173 4.7 13.5 1.0 N 1:ASN171 4.8 13.3 1.0 O 1:ASP166 4.9 12.4 1.0 C 1:ASN199 5.0 8.5 1.0

Calcium binding site 2 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-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 Alpha-Methyl-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca2 b:13.6 occ:1.00 OD1 1:ASP211 2.3 10.6 1.0 OD1 1:ASN192 2.3 17.9 1.0 OD1 1:ASN210 2.4 13.9 1.0 O2 1:MFU1 2.5 17.6 1.0 OE1 1:GLU198 2.5 14.6 1.0 OE1 1:GLU190 2.5 16.6 1.0 O3 1:MFU1 2.6 17.4 1.0 O 1:ASP211 2.6 11.1 1.0 C3 1:MFU1 3.3 20.5 1.0 CG 1:ASP211 3.3 11.3 1.0 CG 1:ASN192 3.3 18.3 1.0 C2 1:MFU1 3.4 19.4 1.0 CD 1:GLU190 3.4 17.6 1.0 CD 1:GLU198 3.4 12.7 1.0 CG 1:ASN210 3.5 15.3 1.0 C 1:ASP211 3.6 9.4 1.0 OE2 1:GLU190 3.7 17.0 1.0 OE2 1:GLU198 3.7 12.3 1.0 N 1:ASP211 3.7 9.2 1.0 ND2 1:ASN192 3.9 19.4 1.0 ND2 1:ASN210 3.9 13.4 1.0 OD2 1:ASP211 4.1 12.0 1.0 CA 1:ASP211 4.1 10.3 1.0 N 1:ASN192 4.1 14.7 1.0 CB 1:ASP211 4.3 10.3 1.0 CB 1:ASN192 4.6 18.1 1.0 CG2 1:VAL194 4.6 24.9 1.0 C 1:ASN210 4.6 8.6 1.0 CG 1:GLU190 4.6 14.4 1.0 N 1:ASN193 4.6 16.4 1.0 CG 1:GLU198 4.7 10.4 1.0 C1 1:MFU1 4.7 22.9 1.0 CA 1:ASN192 4.7 15.4 1.0 C4 1:MFU1 4.8 22.0 1.0 CB 1:ASN210 4.8 13.2 1.0 N 1:VAL212 4.8 8.7 1.0 CB 1:GLU198 4.8 9.9 1.0 O1 1:MFU1 4.9 24.7 1.0 CA 1:ASN210 4.9 12.7 1.0 C 1:ASN192 5.0 17.0 1.0

Calcium binding site 3 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-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 Alpha-Methyl-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca227 b:15.4 occ:1.00 OD1 2:ASN199 2.4 15.7 1.0 O 2:HOH232 2.4 13.6 1.0 OE1 2:GLU170 2.5 10.4 1.0 OD2 2:ASP166 2.5 11.1 1.0 O 2:GLU198 2.5 11.0 1.0 OD1 2:ASN193 2.5 14.6 1.0 OE2 2:GLU170 2.6 16.8 1.0 OD1 2:ASP166 2.7 11.6 1.0 CD 2:GLU170 2.9 13.2 1.0 CG 2:ASP166 2.9 13.7 1.0 CG 2:ASN193 3.4 17.9 1.0 C 2:GLU198 3.4 11.6 1.0 CG 2:ASN199 3.5 12.6 1.0 CA 2:ASN199 3.8 10.4 1.0 N 2:ASN199 4.0 10.5 1.0 CB 2:ASN193 4.1 15.3 1.0 CB 2:ASN199 4.2 10.6 1.0 ND2 2:ASN193 4.2 19.7 1.0 O 2:HOH233 4.3 32.3 1.0 O 2:HOH231 4.3 17.9 1.0 N 2:GLU198 4.3 16.9 1.0 CG 2:GLU170 4.4 16.5 1.0 O 2:HOH235 4.4 15.2 1.0 CB 2:ASP166 4.4 11.8 1.0 OD2 2:ASP211 4.5 12.8 1.0 CA 2:GLU198 4.5 13.9 1.0 ND2 2:ASN199 4.6 20.3 1.0 CA 2:ASN193 4.7 17.8 1.0 O 2:ASP166 4.8 13.4 1.0 N 2:ASN171 4.8 16.0 1.0 CZ 2:PHE173 4.9 17.9 1.0 C 2:ASN199 5.0 9.6 1.0 CA 2:GLU170 5.0 17.6 1.0

Calcium binding site 4 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-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 Alpha-Methyl-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca2 b:13.5 occ:1.00 OD1 2:ASN192 2.3 15.0 1.0 OD1 2:ASP211 2.4 10.5 1.0 OE1 2:GLU198 2.4 12.7 1.0 O2 2:MFU1 2.5 16.1 1.0 OD1 2:ASN210 2.5 11.4 1.0 OE1 2:GLU190 2.5 13.1 1.0 O3 2:MFU1 2.6 14.6 1.0 O 2:ASP211 2.7 12.6 1.0 C3 2:MFU1 3.3 20.2 1.0 C2 2:MFU1 3.3 18.0 1.0 CG 2:ASN192 3.4 14.2 1.0 CG 2:ASP211 3.4 12.1 1.0 CD 2:GLU190 3.4 15.2 1.0 CD 2:GLU198 3.4 12.5 1.0 CG 2:ASN210 3.6 10.9 1.0 C 2:ASP211 3.7 11.3 1.0 OE2 2:GLU190 3.7 14.3 1.0 OE2 2:GLU198 3.7 15.9 1.0 N 2:ASP211 3.8 8.6 1.0 ND2 2:ASN192 3.9 18.3 1.0 OD2 2:ASP211 4.1 12.8 1.0 ND2 2:ASN210 4.1 15.7 1.0 CA 2:ASP211 4.1 10.2 1.0 N 2:ASN192 4.2 17.0 1.0 CB 2:ASP211 4.3 11.1 1.0 CG1 2:VAL194 4.6 24.9 1.0 CB 2:ASN192 4.6 16.3 1.0 CG 2:GLU190 4.6 13.7 1.0 C 2:ASN210 4.6 8.1 1.0 N 2:ASN193 4.6 15.2 1.0 CG 2:GLU198 4.7 14.7 1.0 C1 2:MFU1 4.7 20.9 1.0 C4 2:MFU1 4.7 21.4 1.0 CA 2:ASN192 4.8 17.6 1.0 CB 2:GLU198 4.8 13.2 1.0 CB 2:ASN210 4.8 10.1 1.0 N 2:VAL212 4.9 10.5 1.0 O1 2:MFU1 4.9 22.0 1.0 CA 2:ASN210 4.9 9.2 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