Calcium in PDB 2vnv: Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
Protein crystallography data
The structure of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution, PDB code: 2vnv
was solved by
E.Lameignere,
L.Malinovska,
E.P.Mitchell,
A.Imberty,
M.Wimmerova,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
93.66 /
1.70
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.010,
185.702,
187.551,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.9 /
20.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
(pdb code 2vnv). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution, PDB code: 2vnv:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 2vnv
Go back to
Calcium Binding Sites List in 2vnv
Calcium binding site 1 out
of 10 in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:10.8
occ:1.00
|
OD1
|
A:ASP113
|
2.3
|
13.7
|
1.0
|
|
OE1
|
A:GLU109
|
2.4
|
11.7
|
1.0
|
|
OD1
|
A:ASP115
|
2.4
|
8.5
|
1.0
|
|
OD2
|
A:ASP118
|
2.5
|
10.1
|
1.0
|
|
OE2
|
A:GLU109
|
2.5
|
10.1
|
1.0
|
|
O4
|
A:MMA201
|
2.5
|
11.8
|
1.0
|
|
O3
|
A:MMA201
|
2.5
|
7.1
|
1.0
|
|
OD1
|
A:ASP118
|
2.6
|
10.3
|
1.0
|
|
CD
|
A:GLU109
|
2.8
|
10.2
|
1.0
|
|
CG
|
A:ASP118
|
2.9
|
9.7
|
1.0
|
|
C4
|
A:MMA201
|
3.3
|
11.4
|
1.0
|
|
CG
|
A:ASP113
|
3.4
|
13.6
|
1.0
|
|
C3
|
A:MMA201
|
3.4
|
10.4
|
1.0
|
|
CG
|
A:ASP115
|
3.5
|
10.5
|
1.0
|
|
CA
|
A:CA302
|
3.8
|
10.9
|
1.0
|
|
OD2
|
A:ASP113
|
3.8
|
12.7
|
1.0
|
|
OD2
|
A:ASP115
|
4.1
|
14.2
|
1.0
|
|
OD1
|
A:ASP110
|
4.1
|
12.8
|
1.0
|
|
N
|
A:ASP113
|
4.2
|
13.6
|
1.0
|
|
N
|
A:ASP115
|
4.2
|
9.9
|
1.0
|
|
CG
|
A:GLU109
|
4.3
|
10.8
|
1.0
|
|
CB
|
A:ASP118
|
4.4
|
9.7
|
1.0
|
|
N
|
A:TYR116
|
4.4
|
9.6
|
1.0
|
|
C
|
A:ASP113
|
4.4
|
13.1
|
1.0
|
|
N
|
A:ASP110
|
4.5
|
11.8
|
1.0
|
|
O
|
A:ASP113
|
4.6
|
14.2
|
1.0
|
|
CB
|
A:ASP113
|
4.6
|
12.9
|
1.0
|
|
CA
|
A:ASP113
|
4.6
|
12.5
|
1.0
|
|
CA
|
A:GLU109
|
4.7
|
10.0
|
1.0
|
|
CB
|
A:ASP115
|
4.7
|
10.5
|
1.0
|
|
OD1
|
A:ASN117
|
4.7
|
7.1
|
1.0
|
|
CG
|
A:ASP110
|
4.7
|
11.9
|
1.0
|
|
C2
|
A:MMA201
|
4.7
|
11.8
|
1.0
|
|
C5
|
A:MMA201
|
4.8
|
13.7
|
1.0
|
|
CA
|
A:ASP115
|
4.8
|
9.8
|
1.0
|
|
N
|
A:SER114
|
4.8
|
11.7
|
1.0
|
|
N
|
A:HIS112
|
4.9
|
14.8
|
1.0
|
|
CB
|
A:GLU109
|
4.9
|
10.8
|
1.0
|
|
O2
|
A:MMA201
|
4.9
|
10.0
|
1.0
|
|
N
|
A:GLY111
|
4.9
|
13.7
|
1.0
|
|
Calcium binding site 2 out
of 10 in 2vnv
Go back to
Calcium Binding Sites List in 2vnv
Calcium binding site 2 out
of 10 in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:10.9
occ:1.00
|
OD1
|
A:ASN117
|
2.3
|
7.1
|
1.0
|
|
O
|
A:ASN28
|
2.4
|
9.9
|
1.0
|
|
OD1
|
A:ASP118
|
2.4
|
10.3
|
1.0
|
|
O
|
B:GLY128
|
2.4
|
15.6
|
1.0
|
|
O2
|
A:MMA201
|
2.5
|
10.0
|
1.0
|
|
OD2
|
A:ASP115
|
2.5
|
14.2
|
1.0
|
|
O3
|
A:MMA201
|
2.5
|
7.1
|
1.0
|
|
OD1
|
A:ASP115
|
3.0
|
8.5
|
1.0
|
|
CG
|
A:ASP115
|
3.2
|
10.5
|
1.0
|
|
CG
|
A:ASN117
|
3.4
|
11.5
|
1.0
|
|
C3
|
A:MMA201
|
3.4
|
10.4
|
1.0
|
|
C
|
B:GLY128
|
3.4
|
17.7
|
1.0
|
|
C2
|
A:MMA201
|
3.4
|
11.8
|
1.0
|
|
C
|
A:ASN28
|
3.5
|
9.7
|
1.0
|
|
CG
|
A:ASP118
|
3.6
|
9.7
|
1.0
|
|
OXT
|
B:GLY128
|
3.7
|
17.9
|
1.0
|
|
ND2
|
A:ASN117
|
3.7
|
11.5
|
1.0
|
|
CA
|
A:CA301
|
3.8
|
10.8
|
1.0
|
|
C4
|
A:MMA201
|
3.8
|
11.4
|
1.0
|
|
CB
|
A:ASN28
|
4.0
|
9.5
|
1.0
|
|
CA
|
A:ASP118
|
4.2
|
9.2
|
1.0
|
|
N
|
A:ASP118
|
4.3
|
8.4
|
1.0
|
|
N
|
A:ALA29
|
4.4
|
11.2
|
1.0
|
|
CA
|
A:ALA29
|
4.5
|
11.6
|
1.0
|
|
CA
|
A:ASN28
|
4.5
|
9.4
|
1.0
|
|
C
|
A:ASN117
|
4.5
|
8.6
|
1.0
|
|
O
|
A:HOH2205
|
4.5
|
16.7
|
0.5
|
|
OD2
|
A:ASP118
|
4.5
|
10.1
|
1.0
|
|
O4
|
A:MMA201
|
4.5
|
11.8
|
1.0
|
|
CB
|
A:ASP118
|
4.5
|
9.7
|
1.0
|
|
CB
|
A:ASP115
|
4.6
|
10.5
|
1.0
|
|
CB
|
A:ASN117
|
4.7
|
8.9
|
1.0
|
|
O
|
A:HOH2206
|
4.7
|
16.9
|
0.5
|
|
CA
|
B:GLY128
|
4.7
|
17.0
|
1.0
|
|
O
|
A:ASN117
|
4.7
|
8.2
|
1.0
|
|
C1
|
A:MMA201
|
4.8
|
13.2
|
1.0
|
|
OD2
|
A:ASP113
|
4.8
|
12.7
|
1.0
|
|
N
|
A:ASN117
|
4.8
|
7.9
|
1.0
|
|
CB
|
A:ALA29
|
4.9
|
11.8
|
1.0
|
|
CA
|
A:ASN117
|
4.9
|
9.1
|
1.0
|
|
OD1
|
A:ASP113
|
4.9
|
13.7
|
1.0
|
|
O5
|
A:MMA201
|
5.0
|
14.3
|
1.0
|
|
Calcium binding site 3 out
of 10 in 2vnv
Go back to
Calcium Binding Sites List in 2vnv
Calcium binding site 3 out
of 10 in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:11.7
occ:1.00
|
OD1
|
B:ASP113
|
2.3
|
11.9
|
1.0
|
|
OD1
|
B:ASP115
|
2.4
|
10.5
|
1.0
|
|
OD2
|
B:ASP118
|
2.4
|
11.7
|
1.0
|
|
OE1
|
B:GLU109
|
2.4
|
10.4
|
1.0
|
|
O3
|
B:MMA201
|
2.5
|
9.9
|
1.0
|
|
O4
|
B:MMA201
|
2.5
|
12.2
|
1.0
|
|
OE2
|
B:GLU109
|
2.6
|
10.6
|
1.0
|
|
OD1
|
B:ASP118
|
2.6
|
10.2
|
1.0
|
|
CG
|
B:ASP118
|
2.8
|
9.7
|
1.0
|
|
CD
|
B:GLU109
|
2.9
|
12.5
|
1.0
|
|
CG
|
B:ASP113
|
3.3
|
14.5
|
1.0
|
|
C4
|
B:MMA201
|
3.3
|
12.3
|
1.0
|
|
CG
|
B:ASP115
|
3.4
|
10.8
|
1.0
|
|
C3
|
B:MMA201
|
3.4
|
13.0
|
1.0
|
|
OD2
|
B:ASP113
|
3.7
|
14.7
|
1.0
|
|
CA
|
B:CA302
|
3.7
|
11.3
|
1.0
|
|
OD2
|
B:ASP115
|
3.9
|
12.6
|
1.0
|
|
OD1
|
B:ASP110
|
4.1
|
13.6
|
1.0
|
|
N
|
B:ASP115
|
4.2
|
11.7
|
1.0
|
|
N
|
B:ASP113
|
4.2
|
17.5
|
1.0
|
|
CB
|
B:ASP118
|
4.4
|
9.6
|
1.0
|
|
CG
|
B:GLU109
|
4.4
|
10.4
|
1.0
|
|
N
|
B:TYR116
|
4.4
|
9.1
|
1.0
|
|
C
|
B:ASP113
|
4.5
|
15.9
|
1.0
|
|
N
|
B:ASP110
|
4.5
|
10.0
|
1.0
|
|
CB
|
B:ASP115
|
4.5
|
10.3
|
1.0
|
|
CB
|
B:ASP113
|
4.6
|
15.6
|
1.0
|
|
O
|
B:ASP113
|
4.6
|
15.6
|
1.0
|
|
CA
|
B:ASP113
|
4.7
|
15.7
|
1.0
|
|
OD1
|
B:ASN117
|
4.7
|
9.2
|
1.0
|
|
CA
|
B:ASP115
|
4.7
|
10.4
|
1.0
|
|
CG
|
B:ASP110
|
4.7
|
11.4
|
1.0
|
|
C2
|
B:MMA201
|
4.7
|
15.5
|
1.0
|
|
CA
|
B:GLU109
|
4.7
|
9.7
|
1.0
|
|
N
|
B:SER114
|
4.8
|
14.0
|
1.0
|
|
C5
|
B:MMA201
|
4.8
|
16.5
|
1.0
|
|
O2
|
B:MMA201
|
4.8
|
12.4
|
1.0
|
|
N
|
B:HIS112
|
4.9
|
17.6
|
0.5
|
|
N
|
B:HIS112
|
4.9
|
17.6
|
0.5
|
|
C
|
B:ASP115
|
4.9
|
9.9
|
1.0
|
|
N
|
B:GLY111
|
5.0
|
13.6
|
1.0
|
|
OD2
|
B:ASP110
|
5.0
|
14.8
|
1.0
|
|
CB
|
B:GLU109
|
5.0
|
9.7
|
1.0
|
|
Calcium binding site 4 out
of 10 in 2vnv
Go back to
Calcium Binding Sites List in 2vnv
Calcium binding site 4 out
of 10 in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca302
b:11.3
occ:1.00
|
OD1
|
B:ASN117
|
2.3
|
9.2
|
1.0
|
|
O
|
B:ASN28
|
2.4
|
11.7
|
1.0
|
|
OD1
|
B:ASP118
|
2.4
|
10.2
|
1.0
|
|
OD2
|
B:ASP115
|
2.4
|
12.6
|
1.0
|
|
O
|
A:GLY128
|
2.4
|
14.8
|
1.0
|
|
O2
|
B:MMA201
|
2.5
|
12.4
|
1.0
|
|
O3
|
B:MMA201
|
2.5
|
9.9
|
1.0
|
|
OD1
|
B:ASP115
|
3.0
|
10.5
|
1.0
|
|
CG
|
B:ASP115
|
3.1
|
10.8
|
1.0
|
|
C3
|
B:MMA201
|
3.4
|
13.0
|
1.0
|
|
C2
|
B:MMA201
|
3.4
|
15.5
|
1.0
|
|
CG
|
B:ASN117
|
3.4
|
9.9
|
1.0
|
|
C
|
A:GLY128
|
3.4
|
18.7
|
1.0
|
|
C
|
B:ASN28
|
3.6
|
12.5
|
1.0
|
|
CG
|
B:ASP118
|
3.6
|
9.7
|
1.0
|
|
OXT
|
A:GLY128
|
3.6
|
20.4
|
1.0
|
|
CA
|
B:CA301
|
3.7
|
11.7
|
1.0
|
|
ND2
|
B:ASN117
|
3.8
|
12.1
|
1.0
|
|
C4
|
B:MMA201
|
3.9
|
12.3
|
1.0
|
|
CB
|
B:ASN28
|
4.1
|
12.2
|
1.0
|
|
CA
|
B:ASP118
|
4.2
|
8.8
|
1.0
|
|
N
|
B:ASP118
|
4.4
|
9.0
|
1.0
|
|
OD2
|
B:ASP118
|
4.5
|
11.7
|
1.0
|
|
O4
|
B:MMA201
|
4.5
|
12.2
|
1.0
|
|
CB
|
B:ASP118
|
4.5
|
9.6
|
1.0
|
|
N
|
B:ALA29
|
4.5
|
11.8
|
1.0
|
|
C
|
B:ASN117
|
4.5
|
8.2
|
1.0
|
|
CA
|
B:ALA29
|
4.5
|
12.6
|
1.0
|
|
CB
|
B:ASP115
|
4.5
|
10.3
|
1.0
|
|
CA
|
B:ASN28
|
4.5
|
11.5
|
1.0
|
|
O
|
B:HOH2253
|
4.6
|
34.9
|
1.0
|
|
OD2
|
B:ASP113
|
4.7
|
14.7
|
1.0
|
|
O
|
B:ASN117
|
4.7
|
8.1
|
1.0
|
|
C1
|
B:MMA201
|
4.7
|
19.3
|
1.0
|
|
CB
|
B:ASN117
|
4.7
|
8.1
|
1.0
|
|
CA
|
A:GLY128
|
4.8
|
19.1
|
1.0
|
|
O
|
A:HOH2211
|
4.8
|
40.3
|
1.0
|
|
CB
|
B:ALA29
|
4.9
|
12.0
|
1.0
|
|
N
|
B:ASN117
|
4.9
|
7.9
|
1.0
|
|
OD1
|
B:ASP113
|
4.9
|
11.9
|
1.0
|
|
CA
|
B:ASN117
|
4.9
|
8.8
|
1.0
|
|
Calcium binding site 5 out
of 10 in 2vnv
Go back to
Calcium Binding Sites List in 2vnv
Calcium binding site 5 out
of 10 in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca301
b:12.1
occ:1.00
|
OD1
|
C:ASP113
|
2.4
|
13.3
|
1.0
|
|
OE1
|
C:GLU109
|
2.4
|
11.5
|
1.0
|
|
OD2
|
C:ASP118
|
2.4
|
11.7
|
1.0
|
|
OE2
|
C:GLU109
|
2.4
|
11.4
|
1.0
|
|
OD1
|
C:ASP115
|
2.5
|
11.7
|
1.0
|
|
O4
|
C:MMA201
|
2.5
|
12.4
|
1.0
|
|
O3
|
C:MMA201
|
2.5
|
8.5
|
1.0
|
|
OD1
|
C:ASP118
|
2.6
|
11.3
|
1.0
|
|
CD
|
C:GLU109
|
2.7
|
11.1
|
1.0
|
|
CG
|
C:ASP118
|
2.9
|
12.5
|
1.0
|
|
C4
|
C:MMA201
|
3.3
|
13.2
|
1.0
|
|
CG
|
C:ASP113
|
3.4
|
15.0
|
1.0
|
|
C3
|
C:MMA201
|
3.4
|
11.6
|
1.0
|
|
CG
|
C:ASP115
|
3.5
|
11.8
|
1.0
|
|
CA
|
C:CA302
|
3.7
|
11.9
|
1.0
|
|
OD2
|
C:ASP113
|
3.8
|
14.2
|
1.0
|
|
OD2
|
C:ASP115
|
4.1
|
11.9
|
1.0
|
|
OD1
|
C:ASP110
|
4.1
|
13.3
|
1.0
|
|
N
|
C:ASP113
|
4.2
|
14.8
|
1.0
|
|
N
|
C:ASP115
|
4.2
|
10.9
|
1.0
|
|
CG
|
C:GLU109
|
4.3
|
10.9
|
1.0
|
|
CB
|
C:ASP118
|
4.4
|
10.7
|
1.0
|
|
N
|
C:TYR116
|
4.4
|
11.4
|
1.0
|
|
N
|
C:ASP110
|
4.4
|
12.3
|
1.0
|
|
C
|
C:ASP113
|
4.5
|
14.1
|
1.0
|
|
O
|
C:ASP113
|
4.5
|
14.1
|
1.0
|
|
CB
|
C:ASP113
|
4.6
|
13.3
|
1.0
|
|
CA
|
C:GLU109
|
4.7
|
11.2
|
1.0
|
|
CA
|
C:ASP113
|
4.7
|
13.6
|
1.0
|
|
CG
|
C:ASP110
|
4.7
|
14.1
|
1.0
|
|
OD1
|
C:ASN117
|
4.7
|
10.1
|
1.0
|
|
CB
|
C:ASP115
|
4.7
|
10.1
|
1.0
|
|
C2
|
C:MMA201
|
4.8
|
13.9
|
1.0
|
|
C5
|
C:MMA201
|
4.8
|
14.2
|
1.0
|
|
N
|
C:SER114
|
4.8
|
12.8
|
1.0
|
|
CA
|
C:ASP115
|
4.8
|
11.3
|
1.0
|
|
N
|
C:HIS112
|
4.9
|
15.5
|
1.0
|
|
CB
|
C:GLU109
|
4.9
|
11.1
|
1.0
|
|
O2
|
C:MMA201
|
4.9
|
12.6
|
1.0
|
|
OD2
|
C:ASP110
|
5.0
|
13.2
|
1.0
|
|
N
|
C:GLY111
|
5.0
|
14.1
|
1.0
|
|
Calcium binding site 6 out
of 10 in 2vnv
Go back to
Calcium Binding Sites List in 2vnv
Calcium binding site 6 out
of 10 in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca302
b:11.9
occ:1.00
|
OD1
|
C:ASN117
|
2.3
|
10.1
|
1.0
|
|
O
|
C:ASN28
|
2.4
|
9.8
|
1.0
|
|
OD1
|
C:ASP118
|
2.4
|
11.3
|
1.0
|
|
O
|
D:GLY128
|
2.4
|
14.5
|
1.0
|
|
OD2
|
C:ASP115
|
2.5
|
11.9
|
1.0
|
|
O3
|
C:MMA201
|
2.5
|
8.5
|
1.0
|
|
O2
|
C:MMA201
|
2.6
|
12.6
|
1.0
|
|
OD1
|
C:ASP115
|
3.0
|
11.7
|
1.0
|
|
CG
|
C:ASP115
|
3.1
|
11.8
|
1.0
|
|
C3
|
C:MMA201
|
3.4
|
11.6
|
1.0
|
|
CG
|
C:ASN117
|
3.4
|
9.5
|
1.0
|
|
C2
|
C:MMA201
|
3.4
|
13.9
|
1.0
|
|
C
|
D:GLY128
|
3.4
|
17.1
|
1.0
|
|
C
|
C:ASN28
|
3.5
|
10.2
|
1.0
|
|
CG
|
C:ASP118
|
3.7
|
12.5
|
1.0
|
|
OXT
|
D:GLY128
|
3.7
|
18.5
|
1.0
|
|
CA
|
C:CA301
|
3.7
|
12.1
|
1.0
|
|
ND2
|
C:ASN117
|
3.7
|
9.9
|
1.0
|
|
C4
|
C:MMA201
|
3.8
|
13.2
|
1.0
|
|
CB
|
C:ASN28
|
4.1
|
10.8
|
1.0
|
|
CA
|
C:ASP118
|
4.2
|
10.1
|
1.0
|
|
N
|
C:ASP118
|
4.3
|
9.8
|
1.0
|
|
N
|
C:ALA29
|
4.4
|
11.2
|
1.0
|
|
C
|
C:ASN117
|
4.5
|
10.3
|
1.0
|
|
CA
|
C:ALA29
|
4.5
|
11.4
|
1.0
|
|
O4
|
C:MMA201
|
4.5
|
12.4
|
1.0
|
|
OD2
|
C:ASP118
|
4.5
|
11.7
|
1.0
|
|
CA
|
C:ASN28
|
4.5
|
9.8
|
1.0
|
|
CB
|
C:ASP118
|
4.5
|
10.7
|
1.0
|
|
O
|
C:HOH2237
|
4.6
|
16.2
|
0.5
|
|
CB
|
C:ASP115
|
4.6
|
10.1
|
1.0
|
|
O
|
C:HOH2239
|
4.7
|
15.0
|
0.5
|
|
OD2
|
C:ASP113
|
4.7
|
14.2
|
1.0
|
|
CB
|
C:ASN117
|
4.7
|
9.9
|
1.0
|
|
CA
|
D:GLY128
|
4.7
|
16.8
|
1.0
|
|
C1
|
C:MMA201
|
4.7
|
15.9
|
1.0
|
|
O
|
C:ASN117
|
4.8
|
9.8
|
1.0
|
|
N
|
C:ASN117
|
4.8
|
9.6
|
1.0
|
|
CB
|
C:ALA29
|
4.8
|
12.1
|
1.0
|
|
CA
|
C:ASN117
|
4.9
|
10.0
|
1.0
|
|
OD1
|
C:ASP113
|
4.9
|
13.3
|
1.0
|
|
Calcium binding site 7 out
of 10 in 2vnv
Go back to
Calcium Binding Sites List in 2vnv
Calcium binding site 7 out
of 10 in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca301
b:9.3
occ:1.00
|
OD1
|
D:ASP113
|
2.3
|
8.7
|
1.0
|
|
OD2
|
D:ASP118
|
2.3
|
7.8
|
1.0
|
|
OE1
|
D:GLU109
|
2.4
|
9.6
|
1.0
|
|
OD1
|
D:ASP115
|
2.4
|
6.7
|
1.0
|
|
OE2
|
D:GLU109
|
2.5
|
8.4
|
1.0
|
|
O4
|
D:MMA201
|
2.5
|
10.5
|
1.0
|
|
O3
|
D:MMA201
|
2.6
|
5.2
|
1.0
|
|
OD1
|
D:ASP118
|
2.6
|
7.6
|
1.0
|
|
CD
|
D:GLU109
|
2.8
|
9.2
|
1.0
|
|
CG
|
D:ASP118
|
2.8
|
7.3
|
1.0
|
|
C4
|
D:MMA201
|
3.3
|
7.8
|
1.0
|
|
CG
|
D:ASP113
|
3.4
|
12.4
|
1.0
|
|
C3
|
D:MMA201
|
3.4
|
6.8
|
1.0
|
|
CG
|
D:ASP115
|
3.5
|
8.5
|
1.0
|
|
CA
|
D:CA302
|
3.7
|
9.2
|
1.0
|
|
OD2
|
D:ASP113
|
3.8
|
11.7
|
1.0
|
|
OD1
|
D:ASP110
|
4.0
|
10.9
|
1.0
|
|
OD2
|
D:ASP115
|
4.1
|
10.8
|
1.0
|
|
N
|
D:ASP115
|
4.2
|
9.4
|
1.0
|
|
N
|
D:ASP113
|
4.2
|
10.4
|
1.0
|
|
CG
|
D:GLU109
|
4.3
|
9.1
|
1.0
|
|
CB
|
D:ASP118
|
4.3
|
8.1
|
1.0
|
|
N
|
D:TYR116
|
4.4
|
8.9
|
1.0
|
|
C
|
D:ASP113
|
4.4
|
10.9
|
1.0
|
|
N
|
D:ASP110
|
4.5
|
9.6
|
1.0
|
|
CB
|
D:ASP113
|
4.6
|
10.9
|
1.0
|
|
O
|
D:ASP113
|
4.6
|
12.3
|
1.0
|
|
CA
|
D:ASP113
|
4.6
|
11.2
|
1.0
|
|
CB
|
D:ASP115
|
4.6
|
8.7
|
1.0
|
|
OD1
|
D:ASN117
|
4.6
|
8.2
|
1.0
|
|
CA
|
D:GLU109
|
4.7
|
9.2
|
1.0
|
|
CG
|
D:ASP110
|
4.7
|
10.8
|
1.0
|
|
N
|
D:SER114
|
4.7
|
10.6
|
1.0
|
|
CA
|
D:ASP115
|
4.7
|
9.3
|
1.0
|
|
C2
|
D:MMA201
|
4.7
|
8.6
|
1.0
|
|
C5
|
D:MMA201
|
4.8
|
9.2
|
1.0
|
|
O2
|
D:MMA201
|
4.9
|
9.9
|
1.0
|
|
CB
|
D:GLU109
|
4.9
|
10.0
|
1.0
|
|
N
|
D:HIS112
|
4.9
|
12.2
|
0.5
|
|
N
|
D:HIS112
|
4.9
|
11.9
|
0.5
|
|
C
|
D:ASP115
|
5.0
|
8.5
|
1.0
|
|
N
|
D:GLY111
|
5.0
|
11.5
|
1.0
|
|
Calcium binding site 8 out
of 10 in 2vnv
Go back to
Calcium Binding Sites List in 2vnv
Calcium binding site 8 out
of 10 in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca302
b:9.2
occ:1.00
|
OD1
|
D:ASN117
|
2.3
|
8.2
|
1.0
|
|
O
|
D:ASN28
|
2.4
|
9.3
|
1.0
|
|
OD1
|
D:ASP118
|
2.4
|
7.6
|
1.0
|
|
OD2
|
D:ASP115
|
2.5
|
10.8
|
1.0
|
|
O2
|
D:MMA201
|
2.5
|
9.9
|
1.0
|
|
O
|
C:GLY128
|
2.5
|
13.1
|
1.0
|
|
O3
|
D:MMA201
|
2.5
|
5.2
|
1.0
|
|
OD1
|
D:ASP115
|
3.0
|
6.7
|
1.0
|
|
CG
|
D:ASP115
|
3.1
|
8.5
|
1.0
|
|
CG
|
D:ASN117
|
3.3
|
10.0
|
1.0
|
|
C3
|
D:MMA201
|
3.3
|
6.8
|
1.0
|
|
C2
|
D:MMA201
|
3.4
|
8.6
|
1.0
|
|
C
|
C:GLY128
|
3.4
|
17.5
|
1.0
|
|
C
|
D:ASN28
|
3.6
|
8.6
|
1.0
|
|
OXT
|
C:GLY128
|
3.6
|
18.4
|
1.0
|
|
CG
|
D:ASP118
|
3.6
|
7.3
|
1.0
|
|
ND2
|
D:ASN117
|
3.7
|
10.8
|
1.0
|
|
CA
|
D:CA301
|
3.7
|
9.3
|
1.0
|
|
C4
|
D:MMA201
|
3.8
|
7.8
|
1.0
|
|
CB
|
D:ASN28
|
4.1
|
9.2
|
1.0
|
|
CA
|
D:ASP118
|
4.3
|
6.9
|
1.0
|
|
N
|
D:ASP118
|
4.4
|
7.1
|
1.0
|
|
N
|
D:ALA29
|
4.4
|
8.8
|
1.0
|
|
C
|
D:ASN117
|
4.5
|
7.5
|
1.0
|
|
O
|
D:HOH2265
|
4.5
|
15.6
|
0.5
|
|
OD2
|
D:ASP118
|
4.5
|
7.8
|
1.0
|
|
O4
|
D:MMA201
|
4.5
|
10.5
|
1.0
|
|
CA
|
D:ALA29
|
4.5
|
9.3
|
1.0
|
|
CB
|
D:ASP118
|
4.5
|
8.1
|
1.0
|
|
CA
|
D:ASN28
|
4.5
|
8.4
|
1.0
|
|
CB
|
D:ASP115
|
4.6
|
8.7
|
1.0
|
|
O
|
D:HOH2267
|
4.6
|
23.8
|
0.5
|
|
CB
|
D:ASN117
|
4.7
|
8.7
|
1.0
|
|
C1
|
D:MMA201
|
4.7
|
11.7
|
1.0
|
|
O
|
D:HOH2260
|
4.7
|
36.4
|
1.0
|
|
O
|
D:ASN117
|
4.7
|
7.3
|
1.0
|
|
OD2
|
D:ASP113
|
4.8
|
11.7
|
1.0
|
|
N
|
D:ASN117
|
4.8
|
6.9
|
1.0
|
|
CA
|
C:GLY128
|
4.8
|
17.0
|
1.0
|
|
OD1
|
D:ASP113
|
4.9
|
8.7
|
1.0
|
|
CB
|
D:ALA29
|
4.9
|
8.9
|
1.0
|
|
CA
|
D:ASN117
|
4.9
|
8.3
|
1.0
|
|
Calcium binding site 9 out
of 10 in 2vnv
Go back to
Calcium Binding Sites List in 2vnv
Calcium binding site 9 out
of 10 in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca301
b:10.7
occ:1.00
|
OD1
|
E:ASP113
|
2.3
|
11.6
|
1.0
|
|
OD2
|
E:ASP118
|
2.3
|
9.9
|
1.0
|
|
OD1
|
E:ASP115
|
2.4
|
8.8
|
1.0
|
|
OE1
|
E:GLU109
|
2.4
|
12.3
|
1.0
|
|
OE2
|
E:GLU109
|
2.5
|
10.8
|
1.0
|
|
O4
|
E:MMA201
|
2.5
|
11.1
|
1.0
|
|
O3
|
E:MMA201
|
2.6
|
7.9
|
1.0
|
|
OD1
|
E:ASP118
|
2.6
|
8.8
|
1.0
|
|
CD
|
E:GLU109
|
2.8
|
11.1
|
1.0
|
|
CG
|
E:ASP118
|
2.8
|
10.5
|
1.0
|
|
C4
|
E:MMA201
|
3.3
|
11.6
|
1.0
|
|
CG
|
E:ASP113
|
3.4
|
13.4
|
1.0
|
|
C3
|
E:MMA201
|
3.4
|
9.9
|
1.0
|
|
CG
|
E:ASP115
|
3.5
|
8.8
|
1.0
|
|
CA
|
E:CA302
|
3.7
|
10.9
|
1.0
|
|
OD2
|
E:ASP113
|
3.8
|
12.2
|
1.0
|
|
OD1
|
E:ASP110
|
4.0
|
10.9
|
1.0
|
|
OD2
|
E:ASP115
|
4.1
|
11.9
|
1.0
|
|
N
|
E:ASP115
|
4.2
|
10.3
|
1.0
|
|
N
|
E:ASP113
|
4.2
|
12.4
|
1.0
|
|
CG
|
E:GLU109
|
4.3
|
10.8
|
1.0
|
|
CB
|
E:ASP118
|
4.3
|
9.1
|
1.0
|
|
N
|
E:TYR116
|
4.4
|
9.1
|
1.0
|
|
C
|
E:ASP113
|
4.5
|
12.2
|
1.0
|
|
N
|
E:ASP110
|
4.5
|
10.2
|
1.0
|
|
CB
|
E:ASP113
|
4.6
|
11.6
|
1.0
|
|
O
|
E:ASP113
|
4.6
|
11.8
|
1.0
|
|
CA
|
E:ASP113
|
4.6
|
12.4
|
1.0
|
|
CB
|
E:ASP115
|
4.6
|
9.0
|
1.0
|
|
CA
|
E:GLU109
|
4.7
|
10.3
|
1.0
|
|
OD1
|
E:ASN117
|
4.7
|
9.5
|
1.0
|
|
CG
|
E:ASP110
|
4.7
|
9.4
|
1.0
|
|
C2
|
E:MMA201
|
4.7
|
12.6
|
1.0
|
|
N
|
E:SER114
|
4.8
|
11.6
|
1.0
|
|
CA
|
E:ASP115
|
4.8
|
9.3
|
1.0
|
|
C5
|
E:MMA201
|
4.8
|
14.0
|
1.0
|
|
O2
|
E:MMA201
|
4.9
|
11.6
|
1.0
|
|
CB
|
E:GLU109
|
4.9
|
10.7
|
1.0
|
|
N
|
E:HIS112
|
4.9
|
12.9
|
1.0
|
|
C
|
E:ASP115
|
5.0
|
10.1
|
1.0
|
|
N
|
E:GLY111
|
5.0
|
12.2
|
1.0
|
|
Calcium binding site 10 out
of 10 in 2vnv
Go back to
Calcium Binding Sites List in 2vnv
Calcium binding site 10 out
of 10 in the Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Bcla Lectin From Burkholderia Cenocepacia in Complex with Alpha-Methyl-Mannoside at 1.7 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca302
b:10.9
occ:1.00
|
OD1
|
E:ASN117
|
2.3
|
9.5
|
1.0
|
|
OD1
|
E:ASP118
|
2.3
|
8.8
|
1.0
|
|
O
|
E:ASN28
|
2.4
|
11.0
|
1.0
|
|
O2
|
E:MMA201
|
2.5
|
11.6
|
1.0
|
|
O3
|
E:MMA201
|
2.5
|
7.9
|
1.0
|
|
OD2
|
E:ASP115
|
2.6
|
11.9
|
1.0
|
|
OD1
|
E:ASP115
|
3.0
|
8.8
|
1.0
|
|
CG
|
E:ASP115
|
3.1
|
8.8
|
1.0
|
|
C2
|
E:MMA201
|
3.3
|
12.6
|
1.0
|
|
C3
|
E:MMA201
|
3.4
|
9.9
|
1.0
|
|
CG
|
E:ASN117
|
3.4
|
11.0
|
1.0
|
|
C
|
E:ASN28
|
3.5
|
10.7
|
1.0
|
|
CG
|
E:ASP118
|
3.6
|
10.5
|
1.0
|
|
CA
|
E:CA301
|
3.7
|
10.7
|
1.0
|
|
ND2
|
E:ASN117
|
3.8
|
10.9
|
1.0
|
|
C4
|
E:MMA201
|
3.9
|
11.6
|
1.0
|
|
CB
|
E:ASN28
|
4.0
|
11.0
|
1.0
|
|
CA
|
E:ASP118
|
4.2
|
9.0
|
1.0
|
|
N
|
E:ASP118
|
4.3
|
8.6
|
1.0
|
|
OD2
|
E:ASP118
|
4.4
|
9.9
|
1.0
|
|
N
|
E:ALA29
|
4.4
|
11.2
|
1.0
|
|
C
|
E:ASN117
|
4.4
|
8.7
|
1.0
|
|
CB
|
E:ASP118
|
4.4
|
9.1
|
1.0
|
|
CA
|
E:ASN28
|
4.5
|
10.9
|
1.0
|
|
CA
|
E:ALA29
|
4.5
|
11.1
|
1.0
|
|
O4
|
E:MMA201
|
4.5
|
11.1
|
1.0
|
|
O
|
E:HOH2224
|
4.5
|
22.9
|
1.0
|
|
CB
|
E:ASP115
|
4.6
|
9.0
|
1.0
|
|
O
|
E:ASN117
|
4.7
|
7.7
|
1.0
|
|
CB
|
E:ASN117
|
4.7
|
10.5
|
1.0
|
|
C1
|
E:MMA201
|
4.7
|
15.3
|
1.0
|
|
OD2
|
E:ASP113
|
4.8
|
12.2
|
1.0
|
|
N
|
E:ASN117
|
4.8
|
9.2
|
1.0
|
|
OD1
|
E:ASP113
|
4.9
|
11.6
|
1.0
|
|
CA
|
E:ASN117
|
4.9
|
9.2
|
1.0
|
|
CB
|
E:ALA29
|
4.9
|
11.8
|
1.0
|
|
Reference:
E.Lameignere,
L.Malinovska,
M.Slavikova,
E.Duchaud,
E.P.Mitchell,
A.Varrot,
O.Sedo,
A.Imberty,
M.Wimmerova.
Structural Basis For Mannose Recognition By A Lectin From Opportunistic Bacteria Burkholderia Cenocepacia Biochem.J. V. 411 307 2008.
ISSN: ISSN 0264-6021
PubMed: 18215132
DOI: 10.1042/BJ20071276
Page generated: Tue Jul 8 08:42:09 2025
|
