Calcium 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:
Calcium Binding Sites:
The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the
Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdc:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1qdc
Go back to
Calcium Binding Sites List in 1qdc
Calcium 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 Calcium with other atoms in the Ca 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:Ca241
b:12.5
occ:1.00
|
O
|
A:TYR12
|
2.3
|
14.6
|
1.0
|
OD1
|
A:ASN14
|
2.4
|
15.1
|
1.0
|
OD2
|
A:ASP19
|
2.4
|
13.0
|
1.0
|
OD1
|
A:ASP10
|
2.5
|
17.6
|
1.0
|
OD2
|
A:ASP10
|
2.5
|
11.9
|
1.0
|
O
|
A:HOH246
|
2.5
|
13.4
|
1.0
|
O
|
A:HOH244
|
2.5
|
11.9
|
1.0
|
CG
|
A:ASP10
|
2.8
|
13.7
|
1.0
|
CG
|
A:ASP19
|
3.5
|
13.5
|
1.0
|
CG
|
A:ASN14
|
3.5
|
15.8
|
1.0
|
C
|
A:TYR12
|
3.6
|
16.3
|
1.0
|
OD1
|
A:ASP19
|
3.9
|
14.3
|
1.0
|
N
|
A:ASN14
|
3.9
|
18.9
|
1.0
|
CB
|
A:ASN14
|
4.1
|
17.1
|
1.0
|
CB
|
A:ASP10
|
4.3
|
12.5
|
1.0
|
MN
|
A:MN240
|
4.3
|
33.8
|
1.0
|
CA
|
A:TYR12
|
4.4
|
15.0
|
1.0
|
N
|
A:TYR12
|
4.5
|
14.7
|
1.0
|
CB
|
A:TYR12
|
4.5
|
12.8
|
1.0
|
N
|
A:PRO13
|
4.5
|
19.7
|
1.0
|
CA
|
A:PRO13
|
4.5
|
19.4
|
1.0
|
O
|
A:HOH251
|
4.6
|
16.4
|
1.0
|
ND2
|
A:ASN14
|
4.6
|
16.5
|
1.0
|
C
|
A:PRO13
|
4.6
|
18.7
|
1.0
|
OD1
|
A:ASP208
|
4.7
|
8.7
|
1.0
|
CA
|
A:ASN14
|
4.7
|
17.6
|
1.0
|
CB
|
A:ASP19
|
4.7
|
14.2
|
1.0
|
O
|
A:ASP208
|
4.7
|
11.3
|
1.0
|
CE1
|
A:HIS24
|
4.8
|
13.0
|
1.0
|
CA
|
A:ARG228
|
4.9
|
14.1
|
1.0
|
CB
|
A:ARG228
|
4.9
|
18.6
|
1.0
|
O
|
A:ARG228
|
4.9
|
11.9
|
1.0
|
CD2
|
A:TYR12
|
5.0
|
13.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1qdc
Go back to
Calcium Binding Sites List in 1qdc
Calcium 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 Calcium with other atoms in the Ca 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:Ca244
b:17.3
occ:1.00
|
O
|
B:TYR12
|
2.4
|
19.3
|
1.0
|
OD2
|
B:ASP19
|
2.5
|
15.4
|
1.0
|
OD2
|
B:ASP10
|
2.5
|
16.4
|
1.0
|
OD1
|
B:ASN14
|
2.5
|
19.0
|
1.0
|
OD1
|
B:ASP10
|
2.5
|
17.0
|
1.0
|
O
|
B:HOH1250
|
2.6
|
18.2
|
1.0
|
O
|
B:HOH1241
|
2.6
|
14.2
|
1.0
|
CG
|
B:ASP10
|
2.8
|
17.8
|
1.0
|
C
|
B:TYR12
|
3.6
|
21.3
|
1.0
|
CG
|
B:ASP19
|
3.6
|
16.5
|
1.0
|
CG
|
B:ASN14
|
3.6
|
18.6
|
1.0
|
N
|
B:ASN14
|
4.0
|
21.7
|
1.0
|
OD1
|
B:ASP19
|
4.1
|
15.4
|
1.0
|
CB
|
B:ASN14
|
4.2
|
17.9
|
1.0
|
CB
|
B:ASP10
|
4.3
|
13.3
|
1.0
|
MN
|
B:MN243
|
4.3
|
37.0
|
1.0
|
CA
|
B:TYR12
|
4.4
|
20.9
|
1.0
|
CB
|
B:TYR12
|
4.5
|
20.0
|
1.0
|
N
|
B:PRO13
|
4.5
|
23.5
|
1.0
|
N
|
B:TYR12
|
4.5
|
21.8
|
1.0
|
CA
|
B:PRO13
|
4.6
|
22.6
|
1.0
|
O
|
B:ASP208
|
4.6
|
16.1
|
1.0
|
C
|
B:PRO13
|
4.7
|
23.6
|
1.0
|
O
|
B:HOH1248
|
4.7
|
17.2
|
1.0
|
OD1
|
B:ASP208
|
4.7
|
16.9
|
1.0
|
ND2
|
B:ASN14
|
4.7
|
14.1
|
1.0
|
CA
|
B:ASN14
|
4.7
|
20.8
|
1.0
|
CB
|
B:ASP19
|
4.8
|
16.6
|
1.0
|
CA
|
B:ARG228
|
4.8
|
16.4
|
1.0
|
O
|
B:ARG228
|
4.8
|
15.6
|
1.0
|
CE1
|
B:HIS24
|
4.9
|
13.2
|
1.0
|
CB
|
B:ARG228
|
4.9
|
17.4
|
1.0
|
CD2
|
B:TYR12
|
5.0
|
23.8
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1qdc
Go back to
Calcium Binding Sites List in 1qdc
Calcium 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 Calcium with other atoms in the Ca 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:Ca246
b:21.6
occ:1.00
|
O
|
C:TYR12
|
2.3
|
22.9
|
1.0
|
OD2
|
C:ASP10
|
2.4
|
20.4
|
1.0
|
OD1
|
C:ASN14
|
2.4
|
30.2
|
1.0
|
OD2
|
C:ASP19
|
2.5
|
22.6
|
1.0
|
OD1
|
C:ASP10
|
2.6
|
24.9
|
1.0
|
O
|
C:HOH2244
|
2.6
|
18.9
|
1.0
|
O
|
C:HOH2243
|
2.6
|
18.2
|
1.0
|
CG
|
C:ASP10
|
2.8
|
23.1
|
1.0
|
C
|
C:TYR12
|
3.6
|
26.9
|
1.0
|
CG
|
C:ASN14
|
3.6
|
32.4
|
1.0
|
CG
|
C:ASP19
|
3.7
|
25.9
|
1.0
|
N
|
C:ASN14
|
4.0
|
28.7
|
1.0
|
CB
|
C:ASN14
|
4.1
|
28.5
|
1.0
|
OD1
|
C:ASP19
|
4.1
|
21.0
|
1.0
|
CB
|
C:ASP10
|
4.3
|
24.1
|
1.0
|
CA
|
C:TYR12
|
4.4
|
25.5
|
1.0
|
MN
|
C:MN245
|
4.4
|
41.5
|
1.0
|
O
|
C:HOH2254
|
4.4
|
23.9
|
1.0
|
N
|
C:TYR12
|
4.5
|
23.2
|
1.0
|
CB
|
C:TYR12
|
4.5
|
27.6
|
1.0
|
N
|
C:PRO13
|
4.5
|
27.7
|
1.0
|
CA
|
C:PRO13
|
4.6
|
28.5
|
1.0
|
O
|
C:ASP208
|
4.6
|
16.7
|
1.0
|
C
|
C:PRO13
|
4.6
|
27.9
|
1.0
|
CA
|
C:ASN14
|
4.7
|
29.6
|
1.0
|
ND2
|
C:ASN14
|
4.7
|
25.0
|
1.0
|
OD1
|
C:ASP208
|
4.7
|
26.4
|
1.0
|
CE1
|
C:HIS24
|
4.8
|
17.3
|
1.0
|
O
|
C:ARG228
|
4.8
|
20.6
|
1.0
|
CB
|
C:ASP19
|
4.9
|
25.1
|
1.0
|
CA
|
C:ARG228
|
4.9
|
22.3
|
1.0
|
CD2
|
C:TYR12
|
5.0
|
28.3
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1qdc
Go back to
Calcium Binding Sites List in 1qdc
Calcium 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 Calcium with other atoms in the Ca 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:Ca248
b:17.6
occ:1.00
|
O
|
D:TYR12
|
2.4
|
21.3
|
1.0
|
OD2
|
D:ASP10
|
2.4
|
14.4
|
1.0
|
O
|
D:HOH3245
|
2.5
|
18.2
|
1.0
|
OD1
|
D:ASN14
|
2.5
|
21.1
|
1.0
|
OD2
|
D:ASP19
|
2.5
|
18.9
|
1.0
|
O
|
D:HOH3242
|
2.5
|
15.9
|
1.0
|
OD1
|
D:ASP10
|
2.6
|
19.1
|
1.0
|
CG
|
D:ASP10
|
2.9
|
18.9
|
1.0
|
CG
|
D:ASN14
|
3.6
|
22.6
|
1.0
|
C
|
D:TYR12
|
3.6
|
20.0
|
1.0
|
CG
|
D:ASP19
|
3.6
|
20.7
|
1.0
|
N
|
D:ASN14
|
4.0
|
20.7
|
1.0
|
OD1
|
D:ASP19
|
4.1
|
17.6
|
1.0
|
CB
|
D:ASN14
|
4.1
|
19.6
|
1.0
|
MN
|
D:MN247
|
4.3
|
38.4
|
1.0
|
CB
|
D:ASP10
|
4.3
|
14.4
|
1.0
|
CA
|
D:TYR12
|
4.5
|
19.1
|
1.0
|
CB
|
D:TYR12
|
4.6
|
16.5
|
1.0
|
N
|
D:PRO13
|
4.6
|
22.4
|
1.0
|
CA
|
D:PRO13
|
4.6
|
22.4
|
1.0
|
N
|
D:TYR12
|
4.6
|
19.4
|
1.0
|
O
|
D:ASP208
|
4.6
|
11.7
|
1.0
|
OD1
|
D:ASP208
|
4.7
|
12.0
|
1.0
|
C
|
D:PRO13
|
4.7
|
23.5
|
1.0
|
CA
|
D:ARG228
|
4.7
|
17.3
|
1.0
|
O
|
D:HOH3252
|
4.7
|
23.6
|
1.0
|
CA
|
D:ASN14
|
4.7
|
22.2
|
1.0
|
ND2
|
D:ASN14
|
4.7
|
18.9
|
1.0
|
O
|
D:ARG228
|
4.8
|
16.1
|
1.0
|
CB
|
D:ARG228
|
4.8
|
22.0
|
1.0
|
CB
|
D:ASP19
|
4.8
|
21.2
|
1.0
|
CE1
|
D:HIS24
|
4.9
|
10.9
|
1.0
|
CD2
|
D:TYR12
|
5.0
|
19.5
|
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: Thu Jul 11 21:42:24 2024
|