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Calcium in PDB 1rdm: Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-Methyl-D-Mannopyranoside (1.3 M)

Protein crystallography data

The structure of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-Methyl-D-Mannopyranoside (1.3 M), PDB code: 1rdm 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.600, 75.400, 57.400, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 24

Other elements in 1rdm:

The structure of Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-Methyl-D-Mannopyranoside (1.3 M) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-Methyl-D-Mannopyranoside (1.3 M) (pdb code 1rdm). 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-D-Mannopyranoside (1.3 M), PDB code: 1rdm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1rdm

Go back to Calcium Binding Sites List in 1rdm
Calcium binding site 1 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-Methyl-D-Mannopyranoside (1.3 M)


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-D-Mannopyranoside (1.3 M) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca227

b:13.3
occ:1.00
 O 1:HOH276 2.4 8.6 1.0
OD2 1:ASP166 2.5 9.2 1.0
OD1 1:ASN199 2.5 10.0 1.0
O 1:GLU198 2.5 11.2 1.0
OD1 1:ASN193 2.5 9.3 1.0
OE1 1:GLU170 2.6 9.0 1.0
OE2 1:GLU170 2.7 11.1 1.0
OD1 1:ASP166 2.7 13.2 1.0
CG 1:ASP166 2.9 9.8 1.0
CD 1:GLU170 3.0 9.9 1.0
C 1:GLU198 3.4 10.7 1.0
CG 1:ASN193 3.4 11.2 1.0
CG 1:ASN199 3.6 8.1 1.0
CA 1:ASN199 3.7 9.0 1.0
N 1:ASN199 3.9 9.2 1.0
CB 1:ASN193 4.0 13.3 1.0
CB 1:ASN199 4.1 9.1 1.0
N 1:GLU198 4.3 13.6 1.0
ND2 1:ASN193 4.3 8.6 1.0
O 1:HOH275 4.4 20.0 1.0
CB 1:ASP166 4.4 8.4 1.0
CG 1:GLU170 4.5 10.6 1.0
CA 1:GLU198 4.5 10.9 1.0
OD2 1:ASP211 4.6 11.1 1.0
CA 1:ASN193 4.7 14.6 1.0
O 1:ASP166 4.7 10.0 1.0
ND2 1:ASN199 4.7 11.2 1.0
CZ 1:PHE173 4.7 16.6 1.0
O 1:HOH248 4.8 32.4 0.9
N 1:ASN171 4.8 12.8 1.0
C 1:ASN199 5.0 8.9 1.0

Calcium binding site 2 out of 4 in 1rdm

Go back to Calcium Binding Sites List in 1rdm
Calcium binding site 2 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-Methyl-D-Mannopyranoside (1.3 M)


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-D-Mannopyranoside (1.3 M) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca228

b:11.9
occ:1.00
 OD1 1:ASN192 2.4 16.8 1.0
OD1 1:ASP211 2.4 9.3 1.0
OE1 1:GLU198 2.4 10.6 1.0
O4 1:MMA1 2.5 21.1 1.0
OD1 1:ASN210 2.5 12.3 1.0
OE1 1:GLU190 2.5 16.3 1.0
O 1:ASP211 2.6 9.9 1.0
O3 1:MMA1 2.6 16.5 1.0
C4 1:MMA1 3.3 20.7 1.0
CG 1:ASP211 3.3 10.7 1.0
C3 1:MMA1 3.4 20.7 1.0
CD 1:GLU198 3.4 5.6 1.0
CG 1:ASN192 3.4 16.7 1.0
CD 1:GLU190 3.5 18.6 1.0
CG 1:ASN210 3.5 14.3 1.0
C 1:ASP211 3.6 9.0 1.0
N 1:ASP211 3.7 10.2 1.0
OE2 1:GLU198 3.7 8.4 1.0
OE2 1:GLU190 3.8 16.4 1.0
ND2 1:ASN210 3.9 10.4 1.0
ND2 1:ASN192 3.9 16.1 1.0
OD2 1:ASP211 4.0 11.1 1.0
CA 1:ASP211 4.1 9.2 1.0
N 1:ASN192 4.2 14.1 1.0
CB 1:ASP211 4.3 5.3 1.0
CG2 1:VAL194 4.5 21.8 1.0
C 1:ASN210 4.6 8.4 1.0
N 1:ASN193 4.6 13.7 1.0
CB 1:ASN192 4.6 14.2 1.0
CG 1:GLU198 4.7 10.4 1.0
C5 1:MMA1 4.7 25.7 1.0
CG 1:GLU190 4.7 15.4 1.0
N 1:VAL212 4.8 9.0 1.0
CA 1:ASN192 4.8 14.1 1.0
C2 1:MMA1 4.8 21.0 1.0
CB 1:ASN210 4.8 12.4 1.0
CB 1:GLU198 4.8 9.9 1.0
CA 1:ASN210 4.9 10.0 1.0
C 1:ASN192 5.0 15.2 1.0

Calcium binding site 3 out of 4 in 1rdm

Go back to Calcium Binding Sites List in 1rdm
Calcium binding site 3 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-Methyl-D-Mannopyranoside (1.3 M)


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-D-Mannopyranoside (1.3 M) within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca227

b:15.1
occ:1.00
 O 2:HOH232 2.3 13.5 1.0
O 2:GLU198 2.4 11.3 1.0
OD2 2:ASP166 2.4 7.8 1.0
OD1 2:ASN199 2.5 16.6 1.0
OE1 2:GLU170 2.5 12.8 1.0
OE2 2:GLU170 2.6 17.6 1.0
OD1 2:ASN193 2.6 15.5 1.0
OD1 2:ASP166 2.6 10.0 1.0
CD 2:GLU170 2.9 15.7 1.0
CG 2:ASP166 2.9 12.2 1.0
C 2:GLU198 3.4 10.6 1.0
CG 2:ASN193 3.5 19.2 1.0
CG 2:ASN199 3.6 12.4 1.0
CA 2:ASN199 3.7 10.8 1.0
N 2:ASN199 3.9 10.1 1.0
CB 2:ASN193 4.1 16.8 1.0
CB 2:ASN199 4.2 12.4 1.0
O 2:HOH231 4.2 11.9 1.0
N 2:GLU198 4.3 14.0 1.0
CG 2:GLU170 4.4 16.2 1.0
ND2 2:ASN193 4.4 19.5 1.0
CB 2:ASP166 4.4 11.6 1.0
O 2:HOH235 4.4 13.2 1.0
CA 2:GLU198 4.5 12.1 1.0
OD2 2:ASP211 4.5 12.0 1.0
O 2:HOH233 4.6 40.5 1.0
CA 2:ASN193 4.7 18.7 1.0
ND2 2:ASN199 4.7 17.4 1.0
N 2:ASN171 4.8 14.5 1.0
O 2:ASP166 4.9 13.3 1.0
CZ 2:PHE173 4.9 12.3 1.0
C 2:ASN199 4.9 9.2 1.0

Calcium binding site 4 out of 4 in 1rdm

Go back to Calcium Binding Sites List in 1rdm
Calcium binding site 4 out of 4 in the Mannose-Binding Protein, Subtilisin Digest Fragment Complex with Alpha-Methyl-D-Mannopyranoside (1.3 M)


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-D-Mannopyranoside (1.3 M) within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca2

b:13.3
occ:1.00
 OD1 2:ASN192 2.3 11.6 1.0
OD1 2:ASP211 2.4 10.4 1.0
OE1 2:GLU198 2.4 12.0 1.0
OD1 2:ASN210 2.5 14.5 1.0
O4 2:MMA1 2.5 14.4 1.0
OE1 2:GLU190 2.5 12.9 1.0
O3 2:MMA1 2.6 14.8 1.0
O 2:ASP211 2.7 11.4 1.0
C3 2:MMA1 3.3 16.5 1.0
CG 2:ASP211 3.3 10.5 1.0
C4 2:MMA1 3.3 17.4 1.0
CG 2:ASN192 3.3 10.6 1.0
CD 2:GLU198 3.4 9.6 1.0
CD 2:GLU190 3.4 15.9 1.0
CG 2:ASN210 3.6 10.9 1.0
C 2:ASP211 3.7 10.1 1.0
OE2 2:GLU198 3.7 10.0 1.0
OE2 2:GLU190 3.8 15.2 1.0
N 2:ASP211 3.8 8.0 1.0
ND2 2:ASN192 3.8 13.2 1.0
OD2 2:ASP211 3.9 12.0 1.0
ND2 2:ASN210 4.0 12.4 1.0
N 2:ASN192 4.1 16.9 1.0
CA 2:ASP211 4.2 10.2 1.0
CB 2:ASP211 4.3 10.2 1.0
CG1 2:VAL194 4.5 24.0 1.0
CB 2:ASN192 4.6 13.1 1.0
N 2:ASN193 4.6 15.3 1.0
CG 2:GLU198 4.6 12.0 1.0
CG 2:GLU190 4.7 12.1 1.0
C5 2:MMA1 4.7 24.2 1.0
C 2:ASN210 4.7 7.0 1.0
CA 2:ASN192 4.7 15.2 1.0
C2 2:MMA1 4.7 19.7 1.0
CB 2:GLU198 4.8 9.7 1.0
CB 2:ASN210 4.8 10.2 1.0
N 2:VAL212 4.9 9.6 1.0
CA 2:ASN210 5.0 9.7 1.0
C 2:ASN192 5.0 15.5 1.0

Reference:

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
Page generated: Thu Jul 11 22:06:48 2024

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