Manganese in PDB 1qdc: Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex
Protein crystallography data
The structure of Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdc
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)
|
15.00 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
69.510,
117.030,
120.920,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.5 /
21.1
|
Other elements in 1qdc:
The structure of Man(APLHA1-6)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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex
(pdb code 1qdc). 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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdc:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 1qdc
Go back to
Manganese Binding Sites List in 1qdc
Manganese binding site 1 out
of 4 in the Man(APLHA1-6)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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn240
b:33.8
occ:1.00
|
O
|
A:HOH260
|
2.4
|
21.0
|
1.0
|
OE2
|
A:GLU8
|
2.4
|
13.8
|
1.0
|
OD1
|
A:ASP19
|
2.4
|
14.3
|
1.0
|
OD2
|
A:ASP10
|
2.4
|
11.9
|
1.0
|
NE2
|
A:HIS24
|
2.5
|
11.6
|
1.0
|
O
|
A:HOH251
|
2.5
|
16.4
|
1.0
|
CG
|
A:ASP19
|
3.3
|
13.5
|
1.0
|
CD
|
A:GLU8
|
3.3
|
17.2
|
1.0
|
CE1
|
A:HIS24
|
3.4
|
13.0
|
1.0
|
CG
|
A:ASP10
|
3.4
|
13.7
|
1.0
|
OE1
|
A:GLU8
|
3.4
|
13.3
|
1.0
|
CD2
|
A:HIS24
|
3.5
|
14.9
|
1.0
|
OD2
|
A:ASP19
|
3.7
|
13.0
|
1.0
|
CB
|
A:ASP10
|
3.7
|
12.5
|
1.0
|
O
|
A:HOH244
|
4.1
|
11.9
|
1.0
|
OG
|
A:SER34
|
4.2
|
15.2
|
1.0
|
CA
|
A:CA241
|
4.3
|
12.5
|
1.0
|
O
|
A:HOH288
|
4.3
|
33.2
|
1.0
|
CB
|
A:ASP19
|
4.4
|
14.2
|
1.0
|
O
|
A:HOH352
|
4.4
|
81.4
|
1.0
|
OD1
|
A:ASP10
|
4.5
|
17.6
|
1.0
|
O
|
A:VAL32
|
4.5
|
14.0
|
1.0
|
ND1
|
A:HIS24
|
4.6
|
16.3
|
1.0
|
CA
|
A:ASP19
|
4.6
|
19.8
|
1.0
|
CG
|
A:HIS24
|
4.7
|
14.2
|
1.0
|
CG
|
A:GLU8
|
4.7
|
13.0
|
1.0
|
|
Manganese binding site 2 out
of 4 in 1qdc
Go back to
Manganese Binding Sites List in 1qdc
Manganese binding site 2 out
of 4 in the Man(APLHA1-6)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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn243
b:37.0
occ:1.00
|
O
|
B:HOH1242
|
2.0
|
14.6
|
1.0
|
OD1
|
B:ASP19
|
2.4
|
15.4
|
1.0
|
O
|
B:HOH1248
|
2.4
|
17.2
|
1.0
|
NE2
|
B:HIS24
|
2.5
|
14.1
|
1.0
|
OE2
|
B:GLU8
|
2.5
|
20.6
|
1.0
|
OD2
|
B:ASP10
|
2.5
|
16.4
|
1.0
|
CG
|
B:ASP19
|
3.2
|
16.5
|
1.0
|
CD
|
B:GLU8
|
3.3
|
20.2
|
1.0
|
CE1
|
B:HIS24
|
3.4
|
13.2
|
1.0
|
OE1
|
B:GLU8
|
3.4
|
18.6
|
1.0
|
OD2
|
B:ASP19
|
3.4
|
15.4
|
1.0
|
CG
|
B:ASP10
|
3.5
|
17.8
|
1.0
|
CD2
|
B:HIS24
|
3.5
|
14.3
|
1.0
|
CB
|
B:ASP10
|
3.7
|
13.3
|
1.0
|
O
|
B:HOH1241
|
4.1
|
14.2
|
1.0
|
OG
|
B:SER34
|
4.2
|
18.7
|
1.0
|
O
|
B:HOH1333
|
4.2
|
59.8
|
1.0
|
CA
|
B:CA244
|
4.3
|
17.3
|
1.0
|
CB
|
B:ASP19
|
4.4
|
16.6
|
1.0
|
O
|
B:VAL32
|
4.5
|
17.1
|
1.0
|
OD1
|
B:ASP10
|
4.6
|
17.0
|
1.0
|
ND1
|
B:HIS24
|
4.6
|
17.2
|
1.0
|
CG
|
B:HIS24
|
4.6
|
16.9
|
1.0
|
CA
|
B:ASP19
|
4.7
|
22.1
|
1.0
|
CG
|
B:GLU8
|
4.8
|
14.7
|
1.0
|
|
Manganese binding site 3 out
of 4 in 1qdc
Go back to
Manganese Binding Sites List in 1qdc
Manganese binding site 3 out
of 4 in the Man(APLHA1-6)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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn245
b:41.5
occ:1.00
|
O
|
C:HOH2248
|
2.0
|
20.9
|
1.0
|
O
|
C:HOH2254
|
2.1
|
23.9
|
1.0
|
OE2
|
C:GLU8
|
2.4
|
16.6
|
1.0
|
NE2
|
C:HIS24
|
2.5
|
20.0
|
1.0
|
OD1
|
C:ASP19
|
2.6
|
21.0
|
1.0
|
OD2
|
C:ASP10
|
2.6
|
20.4
|
1.0
|
CD
|
C:GLU8
|
3.3
|
19.3
|
1.0
|
CG
|
C:ASP19
|
3.3
|
25.9
|
1.0
|
OE1
|
C:GLU8
|
3.4
|
16.8
|
1.0
|
CE1
|
C:HIS24
|
3.5
|
17.3
|
1.0
|
CD2
|
C:HIS24
|
3.6
|
18.7
|
1.0
|
OD2
|
C:ASP19
|
3.6
|
22.6
|
1.0
|
CG
|
C:ASP10
|
3.7
|
23.1
|
1.0
|
CB
|
C:ASP10
|
3.9
|
24.1
|
1.0
|
OG
|
C:SER34
|
4.0
|
19.6
|
1.0
|
O
|
C:HOH2244
|
4.1
|
18.9
|
1.0
|
O
|
C:HOH2301
|
4.4
|
46.1
|
1.0
|
CA
|
C:CA246
|
4.4
|
21.6
|
1.0
|
O
|
C:VAL32
|
4.5
|
21.3
|
1.0
|
CB
|
C:ASP19
|
4.5
|
25.1
|
1.0
|
ND1
|
C:HIS24
|
4.6
|
18.4
|
1.0
|
CG
|
C:GLU8
|
4.7
|
19.7
|
1.0
|
CA
|
C:ASP19
|
4.7
|
26.1
|
1.0
|
CG
|
C:HIS24
|
4.7
|
17.4
|
1.0
|
OD1
|
C:ASP10
|
4.8
|
24.9
|
1.0
|
CB
|
C:SER34
|
4.9
|
17.6
|
1.0
|
|
Manganese binding site 4 out
of 4 in 1qdc
Go back to
Manganese Binding Sites List in 1qdc
Manganese binding site 4 out
of 4 in the Man(APLHA1-6)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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn247
b:38.4
occ:1.00
|
O
|
D:HOH3256
|
1.9
|
25.7
|
1.0
|
OD1
|
D:ASP19
|
2.4
|
17.6
|
1.0
|
OE2
|
D:GLU8
|
2.4
|
20.8
|
1.0
|
OD2
|
D:ASP10
|
2.5
|
14.4
|
1.0
|
NE2
|
D:HIS24
|
2.5
|
12.5
|
1.0
|
O
|
D:HOH3252
|
2.6
|
23.6
|
1.0
|
CG
|
D:ASP19
|
3.3
|
20.7
|
1.0
|
CD
|
D:GLU8
|
3.3
|
20.4
|
1.0
|
OE1
|
D:GLU8
|
3.4
|
17.3
|
1.0
|
CE1
|
D:HIS24
|
3.4
|
10.9
|
1.0
|
CG
|
D:ASP10
|
3.5
|
18.9
|
1.0
|
CD2
|
D:HIS24
|
3.6
|
13.2
|
1.0
|
OD2
|
D:ASP19
|
3.6
|
18.9
|
1.0
|
CB
|
D:ASP10
|
3.7
|
14.4
|
1.0
|
O
|
D:HOH3242
|
4.0
|
15.9
|
1.0
|
OG
|
D:SER34
|
4.2
|
19.8
|
1.0
|
CA
|
D:CA248
|
4.3
|
17.6
|
1.0
|
CB
|
D:ASP19
|
4.5
|
21.2
|
1.0
|
O
|
D:VAL32
|
4.5
|
15.7
|
1.0
|
OD1
|
D:ASP10
|
4.6
|
19.1
|
1.0
|
ND1
|
D:HIS24
|
4.6
|
13.3
|
1.0
|
CG
|
D:GLU8
|
4.7
|
15.4
|
1.0
|
O
|
D:HOH3274
|
4.7
|
36.1
|
1.0
|
CG
|
D:HIS24
|
4.7
|
12.1
|
1.0
|
CA
|
D:ASP19
|
4.8
|
25.5
|
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 12:11:05 2024
|