Manganese in PDB 1tei: Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man
Protein crystallography data
The structure of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man, PDB code: 1tei
was solved by
J.H.Naismith,
D.N.Moothoo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
2.70
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
176.500,
122.800,
124.600,
90.00,
134.20,
90.00
|
R / Rfree (%)
|
17.9 /
21.9
|
Other elements in 1tei:
The structure of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man
(pdb code 1tei). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man, PDB code: 1tei:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 1tei
Go back to
Manganese Binding Sites List in 1tei
Manganese binding site 1 out
of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn238
b:28.7
occ:1.00
|
OD2
|
A:ASP10
|
2.0
|
9.4
|
1.0
|
O
|
A:HOH247
|
2.1
|
21.8
|
1.0
|
O
|
A:HOH246
|
2.2
|
32.6
|
1.0
|
OD1
|
A:ASP19
|
2.2
|
27.9
|
1.0
|
OE2
|
A:GLU8
|
2.4
|
21.4
|
1.0
|
NE2
|
A:HIS24
|
2.4
|
16.5
|
1.0
|
CG
|
A:ASP19
|
3.1
|
25.0
|
1.0
|
CG
|
A:ASP10
|
3.1
|
15.8
|
1.0
|
CE1
|
A:HIS24
|
3.3
|
14.9
|
1.0
|
CD
|
A:GLU8
|
3.3
|
20.0
|
1.0
|
CD2
|
A:HIS24
|
3.3
|
17.6
|
1.0
|
OD2
|
A:ASP19
|
3.3
|
24.0
|
1.0
|
OE1
|
A:GLU8
|
3.5
|
16.6
|
1.0
|
CB
|
A:ASP10
|
3.5
|
13.1
|
1.0
|
O
|
A:HOH245
|
4.0
|
4.5
|
1.0
|
OG
|
A:SER34
|
4.1
|
19.1
|
1.0
|
OD1
|
A:ASP10
|
4.2
|
19.0
|
1.0
|
CA
|
A:CA239
|
4.3
|
18.9
|
1.0
|
CB
|
A:ASP19
|
4.4
|
26.8
|
1.0
|
ND1
|
A:HIS24
|
4.4
|
16.8
|
1.0
|
CG
|
A:HIS24
|
4.5
|
17.9
|
1.0
|
CG
|
A:GLU8
|
4.7
|
13.8
|
1.0
|
O
|
A:VAL32
|
4.7
|
16.4
|
1.0
|
CA
|
A:ASP19
|
4.8
|
25.4
|
1.0
|
|
Manganese binding site 2 out
of 8 in 1tei
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Manganese Binding Sites List in 1tei
Manganese binding site 2 out
of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn238
b:24.1
occ:1.00
|
OD2
|
B:ASP10
|
1.9
|
20.5
|
1.0
|
O
|
B:HOH247
|
2.3
|
15.1
|
1.0
|
O
|
B:HOH246
|
2.3
|
24.7
|
1.0
|
OD1
|
B:ASP19
|
2.3
|
36.5
|
1.0
|
OE2
|
B:GLU8
|
2.4
|
36.3
|
1.0
|
NE2
|
B:HIS24
|
2.4
|
29.2
|
1.0
|
CG
|
B:ASP10
|
3.0
|
24.7
|
1.0
|
CG
|
B:ASP19
|
3.1
|
32.7
|
1.0
|
CE1
|
B:HIS24
|
3.2
|
28.6
|
1.0
|
OD2
|
B:ASP19
|
3.3
|
27.8
|
1.0
|
CD
|
B:GLU8
|
3.3
|
28.9
|
1.0
|
CB
|
B:ASP10
|
3.4
|
21.2
|
1.0
|
CD2
|
B:HIS24
|
3.4
|
28.9
|
1.0
|
OE1
|
B:GLU8
|
3.6
|
26.9
|
1.0
|
O
|
B:HOH245
|
3.9
|
27.5
|
1.0
|
CA
|
B:CA239
|
4.0
|
27.0
|
1.0
|
OD1
|
B:ASP10
|
4.1
|
20.0
|
1.0
|
OG
|
B:SER34
|
4.2
|
22.0
|
1.0
|
ND1
|
B:HIS24
|
4.4
|
31.5
|
1.0
|
CB
|
B:ASP19
|
4.4
|
33.9
|
1.0
|
CG
|
B:HIS24
|
4.5
|
28.2
|
1.0
|
O
|
B:VAL32
|
4.7
|
24.6
|
1.0
|
CG
|
B:GLU8
|
4.7
|
24.3
|
1.0
|
CA
|
B:ASP19
|
4.9
|
35.3
|
1.0
|
CA
|
B:ASP10
|
4.9
|
22.7
|
1.0
|
|
Manganese binding site 3 out
of 8 in 1tei
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Manganese Binding Sites List in 1tei
Manganese binding site 3 out
of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn238
b:24.4
occ:1.00
|
O
|
C:HOH247
|
2.0
|
19.8
|
1.0
|
O
|
C:HOH246
|
2.0
|
21.1
|
1.0
|
OD2
|
C:ASP10
|
2.1
|
9.4
|
1.0
|
OE2
|
C:GLU8
|
2.3
|
24.1
|
1.0
|
NE2
|
C:HIS24
|
2.4
|
20.2
|
1.0
|
OD1
|
C:ASP19
|
2.4
|
28.8
|
1.0
|
CG
|
C:ASP10
|
3.1
|
16.7
|
1.0
|
CG
|
C:ASP19
|
3.2
|
30.1
|
1.0
|
CE1
|
C:HIS24
|
3.3
|
23.1
|
1.0
|
CD
|
C:GLU8
|
3.3
|
21.4
|
1.0
|
CD2
|
C:HIS24
|
3.4
|
24.5
|
1.0
|
OD2
|
C:ASP19
|
3.4
|
21.1
|
1.0
|
CB
|
C:ASP10
|
3.5
|
15.8
|
1.0
|
OE1
|
C:GLU8
|
3.7
|
21.8
|
1.0
|
O
|
C:HOH245
|
4.0
|
9.2
|
1.0
|
OG
|
C:SER34
|
4.1
|
22.4
|
1.0
|
OD1
|
C:ASP10
|
4.2
|
15.3
|
1.0
|
CA
|
C:CA239
|
4.3
|
22.3
|
1.0
|
ND1
|
C:HIS24
|
4.4
|
23.3
|
1.0
|
CB
|
C:ASP19
|
4.5
|
31.0
|
1.0
|
CG
|
C:HIS24
|
4.5
|
26.6
|
1.0
|
O
|
C:VAL32
|
4.7
|
25.9
|
1.0
|
CG
|
C:GLU8
|
4.7
|
18.9
|
1.0
|
CA
|
C:ASP19
|
4.8
|
33.9
|
1.0
|
CA
|
C:ASP10
|
5.0
|
20.3
|
1.0
|
|
Manganese binding site 4 out
of 8 in 1tei
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Manganese Binding Sites List in 1tei
Manganese binding site 4 out
of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn238
b:32.9
occ:1.00
|
O
|
D:HOH245
|
2.0
|
28.6
|
1.0
|
OD2
|
D:ASP10
|
2.1
|
13.4
|
1.0
|
OD1
|
D:ASP19
|
2.3
|
32.1
|
1.0
|
OE2
|
D:GLU8
|
2.4
|
25.2
|
1.0
|
NE2
|
D:HIS24
|
2.4
|
18.5
|
1.0
|
CG
|
D:ASP19
|
3.1
|
29.7
|
1.0
|
CG
|
D:ASP10
|
3.2
|
19.1
|
1.0
|
CE1
|
D:HIS24
|
3.3
|
23.3
|
1.0
|
CD
|
D:GLU8
|
3.4
|
26.2
|
1.0
|
OD2
|
D:ASP19
|
3.4
|
24.2
|
1.0
|
CD2
|
D:HIS24
|
3.4
|
24.1
|
1.0
|
CB
|
D:ASP10
|
3.6
|
18.5
|
1.0
|
OE1
|
D:GLU8
|
3.6
|
26.8
|
1.0
|
OG
|
D:SER34
|
4.1
|
16.5
|
1.0
|
CA
|
D:CA239
|
4.2
|
33.0
|
1.0
|
OD1
|
D:ASP10
|
4.3
|
19.2
|
1.0
|
CB
|
D:ASP19
|
4.4
|
32.6
|
1.0
|
ND1
|
D:HIS24
|
4.4
|
28.3
|
1.0
|
CG
|
D:HIS24
|
4.5
|
30.4
|
1.0
|
O
|
D:VAL32
|
4.6
|
23.3
|
1.0
|
CG
|
D:GLU8
|
4.7
|
25.2
|
1.0
|
CA
|
D:ASP19
|
4.7
|
33.2
|
1.0
|
CD
|
D:PRO20
|
5.0
|
41.0
|
1.0
|
|
Manganese binding site 5 out
of 8 in 1tei
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Manganese Binding Sites List in 1tei
Manganese binding site 5 out
of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn238
b:24.2
occ:1.00
|
O
|
E:HOH247
|
2.0
|
12.3
|
1.0
|
O
|
E:HOH246
|
2.1
|
34.0
|
1.0
|
OD1
|
E:ASP19
|
2.2
|
27.3
|
1.0
|
OD2
|
E:ASP10
|
2.2
|
8.4
|
1.0
|
OE2
|
E:GLU8
|
2.3
|
22.9
|
1.0
|
NE2
|
E:HIS24
|
2.5
|
20.1
|
1.0
|
CG
|
E:ASP19
|
3.1
|
25.4
|
1.0
|
CD
|
E:GLU8
|
3.3
|
21.3
|
1.0
|
CG
|
E:ASP10
|
3.3
|
16.2
|
1.0
|
O
|
E:HOH245
|
3.3
|
14.5
|
1.0
|
OD2
|
E:ASP19
|
3.4
|
22.4
|
1.0
|
CE1
|
E:HIS24
|
3.4
|
22.6
|
1.0
|
OE1
|
E:GLU8
|
3.5
|
16.7
|
1.0
|
CD2
|
E:HIS24
|
3.5
|
21.7
|
1.0
|
CB
|
E:ASP10
|
3.7
|
15.7
|
1.0
|
OG
|
E:SER34
|
4.0
|
10.3
|
1.0
|
CA
|
E:CA239
|
4.1
|
13.3
|
1.0
|
OD1
|
E:ASP10
|
4.4
|
12.5
|
1.0
|
CB
|
E:ASP19
|
4.4
|
25.5
|
1.0
|
O
|
E:VAL32
|
4.5
|
24.6
|
1.0
|
ND1
|
E:HIS24
|
4.6
|
24.4
|
1.0
|
CG
|
E:HIS24
|
4.7
|
22.1
|
1.0
|
CG
|
E:GLU8
|
4.7
|
17.3
|
1.0
|
CA
|
E:ASP19
|
4.8
|
28.6
|
1.0
|
|
Manganese binding site 6 out
of 8 in 1tei
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Manganese Binding Sites List in 1tei
Manganese binding site 6 out
of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn238
b:50.1
occ:1.00
|
O
|
F:HOH246
|
1.9
|
16.0
|
1.0
|
OD2
|
F:ASP10
|
2.2
|
23.2
|
1.0
|
O
|
F:HOH245
|
2.2
|
29.4
|
1.0
|
OE2
|
F:GLU8
|
2.3
|
40.2
|
1.0
|
OD1
|
F:ASP19
|
2.4
|
48.0
|
1.0
|
NE2
|
F:HIS24
|
2.4
|
36.4
|
1.0
|
CG
|
F:ASP19
|
3.2
|
47.9
|
1.0
|
CG
|
F:ASP10
|
3.2
|
29.9
|
1.0
|
CD
|
F:GLU8
|
3.3
|
34.8
|
1.0
|
CE1
|
F:HIS24
|
3.3
|
40.4
|
1.0
|
CD2
|
F:HIS24
|
3.4
|
38.3
|
1.0
|
OD2
|
F:ASP19
|
3.5
|
46.2
|
1.0
|
OE1
|
F:GLU8
|
3.5
|
33.1
|
1.0
|
CB
|
F:ASP10
|
3.7
|
28.1
|
1.0
|
OG
|
F:SER34
|
3.9
|
24.3
|
1.0
|
CA
|
F:CA239
|
4.3
|
52.5
|
1.0
|
OD1
|
F:ASP10
|
4.4
|
31.4
|
1.0
|
ND1
|
F:HIS24
|
4.4
|
42.8
|
1.0
|
O
|
F:VAL32
|
4.5
|
34.4
|
1.0
|
CB
|
F:ASP19
|
4.5
|
48.5
|
1.0
|
CG
|
F:HIS24
|
4.5
|
39.9
|
1.0
|
CG
|
F:GLU8
|
4.6
|
32.5
|
1.0
|
CA
|
F:ASP19
|
4.8
|
48.2
|
1.0
|
CD
|
F:PRO20
|
5.0
|
51.8
|
1.0
|
|
Manganese binding site 7 out
of 8 in 1tei
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Manganese Binding Sites List in 1tei
Manganese binding site 7 out
of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn238
b:32.7
occ:1.00
|
O
|
G:HOH247
|
2.1
|
13.9
|
1.0
|
OD2
|
G:ASP10
|
2.1
|
19.1
|
1.0
|
OE2
|
G:GLU8
|
2.2
|
32.8
|
1.0
|
NE2
|
G:HIS24
|
2.3
|
26.6
|
1.0
|
O
|
G:HOH246
|
2.4
|
17.4
|
1.0
|
OD1
|
G:ASP19
|
2.4
|
31.7
|
1.0
|
CG
|
G:ASP10
|
3.1
|
19.3
|
1.0
|
CD
|
G:GLU8
|
3.2
|
29.1
|
1.0
|
CD2
|
G:HIS24
|
3.2
|
30.5
|
1.0
|
CG
|
G:ASP19
|
3.3
|
31.4
|
1.0
|
CE1
|
G:HIS24
|
3.3
|
25.9
|
1.0
|
OE1
|
G:GLU8
|
3.5
|
28.6
|
1.0
|
CB
|
G:ASP10
|
3.5
|
20.8
|
1.0
|
OD2
|
G:ASP19
|
3.6
|
30.7
|
1.0
|
OG
|
G:SER34
|
4.0
|
26.6
|
1.0
|
O
|
G:HOH245
|
4.1
|
29.3
|
1.0
|
OD1
|
G:ASP10
|
4.3
|
23.1
|
1.0
|
CG
|
G:HIS24
|
4.4
|
32.3
|
1.0
|
ND1
|
G:HIS24
|
4.4
|
31.2
|
1.0
|
CA
|
G:CA239
|
4.4
|
31.6
|
1.0
|
CG
|
G:GLU8
|
4.6
|
25.4
|
1.0
|
CB
|
G:ASP19
|
4.6
|
28.3
|
1.0
|
O
|
G:VAL32
|
4.6
|
21.9
|
1.0
|
CA
|
G:ASP19
|
4.9
|
33.5
|
1.0
|
|
Manganese binding site 8 out
of 8 in 1tei
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Manganese Binding Sites List in 1tei
Manganese binding site 8 out
of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mn245
b:42.6
occ:1.00
|
OD2
|
H:ASP10
|
2.2
|
25.9
|
1.0
|
OD1
|
H:ASP19
|
2.2
|
47.0
|
1.0
|
OE2
|
H:GLU8
|
2.3
|
35.5
|
1.0
|
NE2
|
H:HIS24
|
2.4
|
33.0
|
1.0
|
O
|
H:HOH248
|
2.6
|
15.9
|
1.0
|
CG
|
H:ASP19
|
3.2
|
41.5
|
1.0
|
CD
|
H:GLU8
|
3.2
|
33.3
|
1.0
|
CE1
|
H:HIS24
|
3.3
|
36.2
|
1.0
|
CG
|
H:ASP10
|
3.3
|
27.7
|
1.0
|
CD2
|
H:HIS24
|
3.4
|
36.2
|
1.0
|
OE1
|
H:GLU8
|
3.4
|
33.5
|
1.0
|
OD2
|
H:ASP19
|
3.5
|
35.8
|
1.0
|
CB
|
H:ASP10
|
3.7
|
28.1
|
1.0
|
OG
|
H:SER34
|
3.9
|
42.4
|
1.0
|
O
|
H:HOH247
|
4.1
|
18.7
|
1.0
|
CA
|
H:CA246
|
4.3
|
47.6
|
1.0
|
OD1
|
H:ASP10
|
4.4
|
25.1
|
1.0
|
ND1
|
H:HIS24
|
4.4
|
38.4
|
1.0
|
CB
|
H:ASP19
|
4.5
|
41.8
|
1.0
|
CG
|
H:HIS24
|
4.5
|
36.4
|
1.0
|
O
|
H:VAL32
|
4.5
|
36.4
|
1.0
|
CG
|
H:GLU8
|
4.6
|
31.9
|
1.0
|
CA
|
H:ASP19
|
4.8
|
41.9
|
1.0
|
CD
|
H:PRO20
|
5.0
|
45.5
|
1.0
|
|
Reference:
D.N.Moothoo,
J.H.Naismith.
Concanavalin A Distorts the Beta-Glcnac-(1-->2)-Man Linkage of Beta-Glcnac-(1-->2)-Alpha-Man-(1-->3)-[Beta-Glcnac-(1-- >2)-Alpha-Man- (1-->6)]-Man Upon Binding. Glycobiology V. 8 173 1998.
ISSN: ISSN 0959-6658
PubMed: 9451027
DOI: 10.1093/GLYCOB/8.2.173
Page generated: Sat Oct 5 12:34:18 2024
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