Calcium in PDB 1vam: Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside
Protein crystallography data
The structure of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside, PDB code: 1vam
was solved by
P.N.Kanellopoulos,
P.A.Tucker,
S.J.Hamodrakas,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
6.00 /
2.75
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.190,
155.380,
71.250,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.5 /
26
|
Other elements in 1vam:
The structure of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside
(pdb code 1vam). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside, PDB code: 1vam:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1vam
Go back to
Calcium Binding Sites List in 1vam
Calcium binding site 1 out
of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca239
b:34.3
occ:1.00
|
O
|
A:TYR12
|
2.2
|
30.4
|
1.0
|
O
|
A:HOH242
|
2.2
|
35.0
|
1.0
|
OD2
|
A:ASP19
|
2.3
|
45.1
|
1.0
|
OD1
|
A:ASN14
|
2.3
|
49.4
|
1.0
|
OD1
|
A:ASP10
|
2.4
|
24.8
|
1.0
|
O
|
A:HOH249
|
2.4
|
26.0
|
1.0
|
OD2
|
A:ASP10
|
2.5
|
24.1
|
1.0
|
CG
|
A:ASP10
|
2.8
|
25.2
|
1.0
|
CG
|
A:ASN14
|
3.2
|
44.3
|
1.0
|
C
|
A:TYR12
|
3.4
|
33.5
|
1.0
|
CG
|
A:ASP19
|
3.5
|
43.6
|
1.0
|
N
|
A:ASN14
|
3.8
|
38.5
|
1.0
|
CB
|
A:ASN14
|
3.9
|
42.2
|
1.0
|
OD1
|
A:ASP19
|
4.0
|
45.4
|
1.0
|
ND2
|
A:ASN14
|
4.1
|
44.8
|
1.0
|
N
|
A:PRO13
|
4.3
|
35.6
|
1.0
|
OD2
|
A:ASP208
|
4.3
|
46.3
|
1.0
|
CA
|
A:TYR12
|
4.3
|
31.3
|
1.0
|
CB
|
A:ASP10
|
4.3
|
21.6
|
1.0
|
N
|
A:TYR12
|
4.3
|
31.4
|
1.0
|
MN
|
A:MN238
|
4.4
|
33.1
|
1.0
|
CA
|
A:PRO13
|
4.4
|
34.6
|
1.0
|
CA
|
A:ASN14
|
4.5
|
40.8
|
1.0
|
C
|
A:PRO13
|
4.5
|
36.4
|
1.0
|
CB
|
A:ASP19
|
4.6
|
42.2
|
1.0
|
O
|
A:HOH247
|
4.6
|
31.4
|
1.0
|
CE1
|
A:HIS24
|
4.6
|
29.6
|
1.0
|
O
|
A:ASP208
|
4.7
|
32.9
|
1.0
|
CB
|
A:TYR12
|
4.7
|
30.7
|
1.0
|
NE2
|
A:HIS24
|
4.9
|
28.8
|
1.0
|
CD1
|
A:TYR12
|
4.9
|
34.4
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1vam
Go back to
Calcium Binding Sites List in 1vam
Calcium binding site 2 out
of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca239
b:30.1
occ:1.00
|
O
|
B:HOH247
|
2.1
|
21.7
|
1.0
|
O
|
B:HOH248
|
2.1
|
30.3
|
1.0
|
OD2
|
B:ASP19
|
2.2
|
31.0
|
1.0
|
OD1
|
B:ASN14
|
2.3
|
32.2
|
1.0
|
OD2
|
B:ASP10
|
2.4
|
18.6
|
1.0
|
O
|
B:TYR12
|
2.5
|
24.3
|
1.0
|
OD1
|
B:ASP10
|
2.5
|
21.4
|
1.0
|
CG
|
B:ASP10
|
2.8
|
20.3
|
1.0
|
CG
|
B:ASP19
|
3.2
|
34.1
|
1.0
|
CG
|
B:ASN14
|
3.5
|
26.6
|
1.0
|
OD1
|
B:ASP19
|
3.6
|
36.9
|
1.0
|
C
|
B:TYR12
|
3.7
|
28.1
|
1.0
|
O
|
B:HOH246
|
4.0
|
44.2
|
1.0
|
MN
|
B:MN238
|
4.1
|
34.6
|
1.0
|
N
|
B:ASN14
|
4.1
|
39.2
|
1.0
|
CB
|
B:ASN14
|
4.2
|
31.1
|
1.0
|
CB
|
B:ASP10
|
4.3
|
20.0
|
1.0
|
CA
|
B:TYR12
|
4.5
|
27.7
|
1.0
|
ND2
|
B:ASN14
|
4.5
|
25.5
|
1.0
|
N
|
B:TYR12
|
4.5
|
29.5
|
1.0
|
CB
|
B:ASP19
|
4.5
|
31.1
|
1.0
|
O
|
B:ASP208
|
4.6
|
27.4
|
1.0
|
N
|
B:PRO13
|
4.7
|
28.7
|
1.0
|
CA
|
B:PRO13
|
4.7
|
32.4
|
1.0
|
CB
|
B:TYR12
|
4.7
|
26.9
|
1.0
|
OD2
|
B:ASP208
|
4.7
|
29.8
|
1.0
|
O
|
B:ARG228
|
4.8
|
35.0
|
1.0
|
C
|
B:PRO13
|
4.8
|
38.3
|
1.0
|
CA
|
B:ASN14
|
4.8
|
35.1
|
1.0
|
CE1
|
B:HIS24
|
4.9
|
26.3
|
1.0
|
CA
|
B:ARG228
|
4.9
|
27.6
|
1.0
|
CD1
|
B:TYR12
|
4.9
|
34.0
|
1.0
|
CB
|
B:ARG228
|
4.9
|
27.4
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1vam
Go back to
Calcium Binding Sites List in 1vam
Calcium binding site 3 out
of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca239
b:24.3
occ:1.00
|
O
|
C:TYR12
|
2.1
|
24.6
|
1.0
|
O
|
C:HOH247
|
2.2
|
23.1
|
1.0
|
OD1
|
C:ASN14
|
2.5
|
39.9
|
1.0
|
O
|
C:HOH248
|
2.5
|
23.3
|
1.0
|
OD2
|
C:ASP10
|
2.5
|
36.8
|
1.0
|
OD1
|
C:ASP10
|
2.6
|
36.1
|
1.0
|
OD2
|
C:ASP19
|
2.7
|
28.7
|
1.0
|
CG
|
C:ASP10
|
2.9
|
37.1
|
1.0
|
C
|
C:TYR12
|
3.4
|
26.1
|
1.0
|
CG
|
C:ASN14
|
3.6
|
33.0
|
1.0
|
N
|
C:ASN14
|
3.8
|
29.5
|
1.0
|
CG
|
C:ASP19
|
3.9
|
27.9
|
1.0
|
MN
|
C:MN238
|
4.2
|
27.9
|
1.0
|
CB
|
C:ASN14
|
4.2
|
29.5
|
1.0
|
N
|
C:PRO13
|
4.3
|
26.9
|
1.0
|
CA
|
C:TYR12
|
4.3
|
26.1
|
1.0
|
CA
|
C:PRO13
|
4.3
|
29.4
|
1.0
|
OD1
|
C:ASP19
|
4.3
|
31.7
|
1.0
|
CB
|
C:ASP10
|
4.4
|
30.1
|
1.0
|
N
|
C:TYR12
|
4.4
|
30.2
|
1.0
|
O
|
C:HOH246
|
4.4
|
25.8
|
1.0
|
C
|
C:PRO13
|
4.5
|
30.7
|
1.0
|
CB
|
C:TYR12
|
4.5
|
26.4
|
1.0
|
CA
|
C:ASN14
|
4.6
|
28.3
|
1.0
|
ND2
|
C:ASN14
|
4.7
|
34.4
|
1.0
|
CE1
|
C:HIS24
|
4.7
|
21.2
|
1.0
|
CD2
|
C:TYR12
|
4.9
|
30.2
|
1.0
|
O
|
C:ARG228
|
4.9
|
25.9
|
1.0
|
CA
|
C:ARG228
|
4.9
|
22.6
|
1.0
|
O
|
C:ASP208
|
5.0
|
27.1
|
1.0
|
OD2
|
C:ASP208
|
5.0
|
31.5
|
1.0
|
CB
|
C:ARG228
|
5.0
|
20.8
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1vam
Go back to
Calcium Binding Sites List in 1vam
Calcium binding site 4 out
of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca239
b:36.4
occ:1.00
|
O
|
D:TYR12
|
2.1
|
43.6
|
1.0
|
OD2
|
D:ASP19
|
2.1
|
35.1
|
1.0
|
OD1
|
D:ASP10
|
2.3
|
31.9
|
1.0
|
O
|
D:HOH245
|
2.5
|
31.9
|
1.0
|
OD2
|
D:ASP10
|
2.5
|
32.9
|
1.0
|
OD1
|
D:ASN14
|
2.5
|
48.0
|
1.0
|
O
|
D:HOH246
|
2.6
|
34.9
|
1.0
|
CG
|
D:ASP10
|
2.7
|
31.1
|
1.0
|
CG
|
D:ASP19
|
3.3
|
42.3
|
1.0
|
C
|
D:TYR12
|
3.3
|
43.3
|
1.0
|
CG
|
D:ASN14
|
3.7
|
46.9
|
1.0
|
OD1
|
D:ASP19
|
3.8
|
41.6
|
1.0
|
N
|
D:ASN14
|
4.0
|
47.4
|
1.0
|
CA
|
D:TYR12
|
4.1
|
41.2
|
1.0
|
N
|
D:TYR12
|
4.2
|
40.0
|
1.0
|
CB
|
D:ASP10
|
4.2
|
31.5
|
1.0
|
MN
|
D:MN238
|
4.2
|
42.6
|
1.0
|
CB
|
D:TYR12
|
4.3
|
43.0
|
1.0
|
N
|
D:PRO13
|
4.3
|
44.1
|
1.0
|
CB
|
D:ASN14
|
4.3
|
45.0
|
1.0
|
CB
|
D:ASP19
|
4.4
|
41.9
|
1.0
|
O
|
D:HOH247
|
4.5
|
34.2
|
1.0
|
O
|
D:ASP208
|
4.5
|
42.0
|
1.0
|
CA
|
D:PRO13
|
4.5
|
43.7
|
1.0
|
ND2
|
D:ASN14
|
4.7
|
49.3
|
1.0
|
C
|
D:PRO13
|
4.7
|
44.7
|
1.0
|
CE1
|
D:HIS24
|
4.8
|
32.8
|
1.0
|
OD1
|
D:ASP208
|
4.8
|
50.7
|
1.0
|
CD1
|
D:TYR12
|
4.8
|
40.0
|
1.0
|
CA
|
D:ASN14
|
4.9
|
48.0
|
1.0
|
O
|
D:ARG228
|
5.0
|
36.2
|
1.0
|
|
Reference:
P.N.Kanellopoulos,
K.Pavlou,
A.Perrakis,
B.Agianian,
C.E.Vorgias,
C.Mavrommatis,
M.Soufi,
P.A.Tucker,
S.J.Hamodrakas.
The Crystal Structure of the Complexes of Concanavalin A with 4'-Nitrophenyl-Alpha-D-Mannopyranoside and 4'-Nitrophenyl-Alpha-D-Glucopyranoside. J.Struct.Biol. V. 116 345 1996.
ISSN: ISSN 1047-8477
PubMed: 8812993
DOI: 10.1006/JSBI.1996.0052
Page generated: Fri Jul 12 00:02:05 2024
|