Manganese in PDB 1qdo: Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex
Protein crystallography data
The structure of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdo
was solved by
J.Bouckaert,
R.Loris,
L.Wyns,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
2.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.410,
64.530,
126.960,
90.00,
93.21,
90.00
|
R / Rfree (%)
|
16.4 /
25.7
|
Other elements in 1qdo:
The structure of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex
(pdb code 1qdo). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdo:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 1qdo
Go back to
Manganese Binding Sites List in 1qdo
Manganese binding site 1 out
of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn240
b:43.9
occ:1.00
|
OE2
|
A:GLU8
|
1.9
|
38.3
|
1.0
|
OD2
|
A:ASP10
|
2.2
|
15.8
|
1.0
|
OD1
|
A:ASP19
|
2.2
|
41.6
|
1.0
|
NE2
|
A:HIS24
|
2.6
|
17.3
|
1.0
|
CD
|
A:GLU8
|
3.0
|
45.8
|
1.0
|
CG
|
A:ASP19
|
3.2
|
38.0
|
1.0
|
CG
|
A:ASP10
|
3.3
|
27.9
|
1.0
|
OG
|
A:SER34
|
3.4
|
15.3
|
1.0
|
OE1
|
A:GLU8
|
3.5
|
27.0
|
1.0
|
CD2
|
A:HIS24
|
3.5
|
17.4
|
1.0
|
OD2
|
A:ASP19
|
3.7
|
44.7
|
1.0
|
CE1
|
A:HIS24
|
3.7
|
15.2
|
1.0
|
CB
|
A:ASP10
|
3.7
|
22.8
|
1.0
|
O
|
A:VAL32
|
4.2
|
24.1
|
1.0
|
CG
|
A:GLU8
|
4.3
|
38.1
|
1.0
|
OD1
|
A:ASP10
|
4.3
|
43.7
|
1.0
|
CB
|
A:ASP19
|
4.4
|
16.6
|
1.0
|
CA
|
A:ASP19
|
4.5
|
51.2
|
1.0
|
CG
|
A:HIS24
|
4.7
|
31.3
|
1.0
|
ND1
|
A:HIS24
|
4.8
|
20.9
|
1.0
|
CB
|
A:SER34
|
4.8
|
16.2
|
1.0
|
|
Manganese binding site 2 out
of 4 in 1qdo
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Manganese Binding Sites List in 1qdo
Manganese binding site 2 out
of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn242
b:42.3
occ:1.00
|
OE2
|
B:GLU8
|
2.0
|
37.9
|
1.0
|
OD2
|
B:ASP10
|
2.0
|
25.0
|
1.0
|
O
|
B:HOH1242
|
2.1
|
23.4
|
1.0
|
OD1
|
B:ASP19
|
2.2
|
45.5
|
1.0
|
NE2
|
B:HIS24
|
2.5
|
15.7
|
1.0
|
CG
|
B:ASP10
|
3.1
|
36.8
|
1.0
|
CG
|
B:ASP19
|
3.1
|
33.0
|
1.0
|
CD
|
B:GLU8
|
3.2
|
34.9
|
1.0
|
CD2
|
B:HIS24
|
3.4
|
28.9
|
1.0
|
OD2
|
B:ASP19
|
3.5
|
32.4
|
1.0
|
CE1
|
B:HIS24
|
3.5
|
27.6
|
1.0
|
CB
|
B:ASP10
|
3.5
|
20.8
|
1.0
|
O
|
B:HOH1240
|
3.6
|
16.4
|
1.0
|
OE1
|
B:GLU8
|
3.9
|
18.2
|
1.0
|
OG
|
B:SER34
|
4.2
|
32.0
|
1.0
|
OD1
|
B:ASP10
|
4.2
|
46.8
|
1.0
|
CG
|
B:GLU8
|
4.3
|
29.7
|
1.0
|
CB
|
B:ASP19
|
4.4
|
21.4
|
1.0
|
CA
|
B:CA243
|
4.5
|
39.4
|
1.0
|
CG
|
B:HIS24
|
4.6
|
31.6
|
1.0
|
CA
|
B:ASP19
|
4.6
|
46.0
|
1.0
|
ND1
|
B:HIS24
|
4.6
|
16.2
|
1.0
|
O
|
B:VAL32
|
4.7
|
28.4
|
1.0
|
|
Manganese binding site 3 out
of 4 in 1qdo
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Manganese Binding Sites List in 1qdo
Manganese binding site 3 out
of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn244
b:42.8
occ:1.00
|
OE2
|
C:GLU8
|
1.8
|
30.5
|
1.0
|
OD2
|
C:ASP10
|
2.0
|
10.3
|
1.0
|
OD1
|
C:ASP19
|
2.0
|
44.5
|
1.0
|
NE2
|
C:HIS24
|
2.5
|
23.1
|
1.0
|
CD
|
C:GLU8
|
3.0
|
39.6
|
1.0
|
CG
|
C:ASP19
|
3.2
|
42.0
|
1.0
|
CG
|
C:ASP10
|
3.3
|
23.0
|
1.0
|
CE1
|
C:HIS24
|
3.4
|
14.3
|
1.0
|
OG
|
C:SER34
|
3.4
|
30.8
|
1.0
|
OE1
|
C:GLU8
|
3.6
|
29.4
|
1.0
|
CD2
|
C:HIS24
|
3.6
|
21.4
|
1.0
|
OD2
|
C:ASP19
|
3.7
|
41.1
|
1.0
|
CB
|
C:ASP10
|
3.9
|
10.3
|
1.0
|
O
|
C:VAL32
|
4.0
|
26.6
|
1.0
|
CG
|
C:GLU8
|
4.3
|
37.0
|
1.0
|
OD1
|
C:ASP10
|
4.3
|
36.0
|
1.0
|
CB
|
C:ASP19
|
4.4
|
32.1
|
1.0
|
CA
|
C:ASP19
|
4.6
|
48.5
|
1.0
|
ND1
|
C:HIS24
|
4.6
|
28.4
|
1.0
|
CG
|
C:HIS24
|
4.7
|
32.8
|
1.0
|
CB
|
C:SER34
|
4.8
|
12.3
|
1.0
|
CA
|
C:CA245
|
4.9
|
47.0
|
1.0
|
|
Manganese binding site 4 out
of 4 in 1qdo
Go back to
Manganese Binding Sites List in 1qdo
Manganese binding site 4 out
of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn246
b:48.0
occ:1.00
|
O
|
D:HOH3243
|
1.8
|
29.3
|
1.0
|
OD2
|
D:ASP10
|
1.9
|
20.2
|
1.0
|
OD1
|
D:ASP19
|
2.1
|
33.1
|
1.0
|
OE2
|
D:GLU8
|
2.1
|
31.7
|
1.0
|
NE2
|
D:HIS24
|
2.6
|
13.1
|
1.0
|
CG
|
D:ASP10
|
3.0
|
37.2
|
1.0
|
CG
|
D:ASP19
|
3.0
|
37.5
|
1.0
|
CD
|
D:GLU8
|
3.3
|
28.8
|
1.0
|
OD2
|
D:ASP19
|
3.4
|
42.0
|
1.0
|
CB
|
D:ASP10
|
3.5
|
30.3
|
1.0
|
CE1
|
D:HIS24
|
3.5
|
13.1
|
1.0
|
CD2
|
D:HIS24
|
3.7
|
27.0
|
1.0
|
OE1
|
D:GLU8
|
4.0
|
14.7
|
1.0
|
OD1
|
D:ASP10
|
4.0
|
53.8
|
1.0
|
OG
|
D:SER34
|
4.1
|
23.2
|
1.0
|
CB
|
D:ASP19
|
4.4
|
28.9
|
1.0
|
CG
|
D:GLU8
|
4.4
|
29.4
|
1.0
|
CA
|
D:CA247
|
4.4
|
42.8
|
1.0
|
O
|
D:VAL32
|
4.6
|
23.2
|
1.0
|
ND1
|
D:HIS24
|
4.7
|
18.9
|
1.0
|
CA
|
D:ASP19
|
4.7
|
40.3
|
1.0
|
CG
|
D:HIS24
|
4.8
|
32.8
|
1.0
|
CA
|
D:ASP10
|
4.9
|
15.0
|
1.0
|
|
Reference:
J.Bouckaert,
T.W.Hamelryck,
L.Wyns,
R.Loris.
The Crystal Structures of Man(ALPHA1-3)Man(ALPHA1-O)Me and Man(ALPHA1-6)Man(ALPHA1-O)Me in Complex with Concanavalin A. J.Biol.Chem. V. 274 29188 1999.
ISSN: ISSN 0021-9258
PubMed: 10506175
DOI: 10.1074/JBC.274.41.29188
Page generated: Sat Oct 5 12:11:48 2024
|