Calcium in PDB 7psy: X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose
Protein crystallography data
The structure of X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose, PDB code: 7psy
was solved by
L.Gajdos,
M.P.Blakeley,
M.Haertlein,
T.V.Forsyth,
J.M.Devos,
A.Imberty,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.53 /
0.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.6,
72.989,
55.19,
90,
94.58,
90
|
R / Rfree (%)
|
11.6 /
13.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose
(pdb code 7psy). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose, PDB code: 7psy:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 7psy
Go back to
Calcium Binding Sites List in 7psy
Calcium binding site 1 out
of 8 in the X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:8.4
occ:1.00
|
OD1
|
A:ASP99
|
2.3
|
10.4
|
1.0
|
OD1
|
A:ASP101
|
2.4
|
9.3
|
1.0
|
OD2
|
A:ASP104
|
2.4
|
8.7
|
1.0
|
OE2
|
A:GLU95
|
2.4
|
9.1
|
1.0
|
OE1
|
A:GLU95
|
2.5
|
9.0
|
1.0
|
O3
|
A:FUC201
|
2.5
|
8.9
|
1.0
|
O2
|
A:FUC201
|
2.5
|
8.7
|
1.0
|
OD1
|
A:ASP104
|
2.7
|
8.3
|
1.0
|
CD
|
A:GLU95
|
2.8
|
9.1
|
1.0
|
CG
|
A:ASP104
|
2.9
|
7.9
|
1.0
|
C2
|
A:FUC201
|
3.3
|
8.8
|
1.0
|
C3
|
A:FUC201
|
3.4
|
8.9
|
1.0
|
H
|
A:ASP101
|
3.4
|
12.3
|
1.0
|
CG
|
A:ASP99
|
3.4
|
10.1
|
1.0
|
CG
|
A:ASP101
|
3.4
|
8.8
|
1.0
|
OD2
|
A:ASP99
|
3.7
|
11.3
|
1.0
|
H
|
A:TYR102
|
3.7
|
11.1
|
1.0
|
H
|
A:ASP96
|
3.7
|
10.0
|
1.0
|
CA
|
A:CA203
|
3.8
|
8.1
|
1.0
|
HA
|
A:GLU95
|
3.9
|
10.2
|
1.0
|
OD2
|
A:ASP101
|
4.0
|
9.2
|
1.0
|
H
|
A:ASP99
|
4.1
|
13.9
|
1.0
|
O
|
A:HOH416
|
4.1
|
12.8
|
1.0
|
H
|
A:ASN100
|
4.1
|
13.4
|
1.0
|
H
|
A:GLY97
|
4.1
|
12.1
|
1.0
|
N
|
A:ASP101
|
4.1
|
10.3
|
1.0
|
OD1
|
A:ASP96
|
4.2
|
9.3
|
1.0
|
CG
|
A:GLU95
|
4.3
|
9.0
|
1.0
|
CB
|
A:ASP104
|
4.4
|
8.6
|
1.0
|
N
|
A:TYR102
|
4.4
|
9.2
|
1.0
|
H
|
A:ASN103
|
4.4
|
9.8
|
1.0
|
N
|
A:ASN100
|
4.5
|
11.2
|
1.0
|
N
|
A:ASP96
|
4.5
|
8.3
|
1.0
|
CB
|
A:ASP101
|
4.5
|
9.6
|
1.0
|
HG3
|
A:GLU95
|
4.6
|
10.8
|
1.0
|
HA3
|
A:GLY97
|
4.6
|
13.2
|
1.0
|
N
|
A:GLY97
|
4.7
|
10.1
|
1.0
|
C4
|
A:FUC201
|
4.7
|
9.3
|
1.0
|
CA
|
A:ASP101
|
4.7
|
9.9
|
1.0
|
CA
|
A:GLU95
|
4.7
|
8.5
|
1.0
|
HB2
|
A:ASP104
|
4.7
|
10.3
|
1.0
|
H
|
A:ASP104
|
4.7
|
9.6
|
1.0
|
CB
|
A:ASP99
|
4.7
|
11.5
|
1.0
|
N
|
A:ASP99
|
4.7
|
11.6
|
1.0
|
C1
|
A:FUC201
|
4.8
|
9.0
|
1.0
|
OD1
|
A:ASN103
|
4.8
|
8.2
|
1.0
|
HG2
|
A:GLU95
|
4.8
|
10.8
|
1.0
|
O4
|
A:FUC201
|
4.8
|
8.7
|
1.0
|
HB3
|
A:ASP101
|
4.8
|
11.6
|
1.0
|
HB3
|
A:ASP104
|
4.8
|
10.3
|
1.0
|
HA
|
A:ASN100
|
4.9
|
13.8
|
1.0
|
CG
|
A:ASP96
|
4.9
|
9.0
|
1.0
|
CB
|
A:GLU95
|
4.9
|
9.1
|
1.0
|
HB2
|
A:GLU95
|
4.9
|
10.9
|
1.0
|
C
|
A:ASP101
|
5.0
|
9.1
|
1.0
|
C
|
A:ASP99
|
5.0
|
11.1
|
1.0
|
H
|
A:THR98
|
5.0
|
13.6
|
1.0
|
|
Calcium binding site 2 out
of 8 in 7psy
Go back to
Calcium Binding Sites List in 7psy
Calcium binding site 2 out
of 8 in the X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:8.1
occ:1.00
|
OD1
|
A:ASN103
|
2.3
|
8.2
|
1.0
|
OD1
|
A:ASP104
|
2.4
|
8.3
|
1.0
|
O
|
A:ASN21
|
2.4
|
8.4
|
1.0
|
O
|
B:GLY114
|
2.4
|
8.9
|
1.0
|
OD2
|
A:ASP101
|
2.4
|
9.2
|
1.0
|
O4
|
A:FUC201
|
2.5
|
8.7
|
1.0
|
O3
|
A:FUC201
|
2.5
|
8.9
|
1.0
|
OD1
|
A:ASP101
|
3.1
|
9.3
|
1.0
|
CG
|
A:ASP101
|
3.1
|
8.8
|
1.0
|
HD21
|
A:ASN103
|
3.4
|
11.1
|
1.0
|
CG
|
A:ASN103
|
3.4
|
8.1
|
1.0
|
C3
|
A:FUC201
|
3.4
|
8.9
|
1.0
|
C
|
B:GLY114
|
3.4
|
8.9
|
1.0
|
C4
|
A:FUC201
|
3.4
|
9.3
|
1.0
|
HA
|
A:ASP104
|
3.5
|
9.1
|
1.0
|
C
|
A:ASN21
|
3.6
|
8.3
|
1.0
|
CG
|
A:ASP104
|
3.6
|
7.9
|
1.0
|
HB3
|
A:ASN21
|
3.6
|
9.8
|
1.0
|
OXT
|
B:GLY114
|
3.7
|
10.3
|
1.0
|
ND2
|
A:ASN103
|
3.8
|
9.2
|
1.0
|
CA
|
A:CA202
|
3.8
|
8.4
|
1.0
|
HA
|
A:SER22
|
3.8
|
10.0
|
1.0
|
HB2
|
A:ASN21
|
3.8
|
9.8
|
1.0
|
C2
|
A:FUC201
|
3.8
|
8.8
|
1.0
|
HB2
|
A:SER22
|
4.0
|
9.8
|
1.0
|
CB
|
A:ASN21
|
4.1
|
8.2
|
1.0
|
H
|
A:ASN103
|
4.2
|
9.8
|
1.0
|
CA
|
A:ASP104
|
4.2
|
7.6
|
1.0
|
N
|
A:ASP104
|
4.3
|
8.0
|
1.0
|
O
|
A:HOH350
|
4.4
|
15.4
|
1.0
|
CA
|
A:SER22
|
4.4
|
8.3
|
1.0
|
N
|
A:SER22
|
4.4
|
7.9
|
1.0
|
OD2
|
A:ASP104
|
4.4
|
8.7
|
1.0
|
O2
|
A:FUC201
|
4.5
|
8.7
|
1.0
|
CB
|
A:ASP104
|
4.5
|
8.6
|
1.0
|
C
|
A:ASN103
|
4.5
|
8.2
|
1.0
|
CA
|
A:ASN21
|
4.5
|
7.8
|
1.0
|
CB
|
A:ASP101
|
4.6
|
9.6
|
1.0
|
OD2
|
A:ASP99
|
4.6
|
11.3
|
1.0
|
H
|
A:ASP104
|
4.6
|
9.6
|
1.0
|
HD22
|
A:ASN103
|
4.6
|
11.1
|
1.0
|
CB
|
A:SER22
|
4.7
|
8.2
|
1.0
|
CB
|
A:ASN103
|
4.7
|
8.3
|
1.0
|
HB2
|
A:ASP101
|
4.7
|
11.6
|
1.0
|
C5
|
A:FUC201
|
4.7
|
9.1
|
1.0
|
CA
|
B:GLY114
|
4.8
|
9.4
|
1.0
|
O
|
A:ASN103
|
4.8
|
8.2
|
1.0
|
HB3
|
A:ASP104
|
4.8
|
10.3
|
1.0
|
O
|
A:HOH464
|
4.8
|
37.1
|
1.0
|
N
|
A:ASN103
|
4.9
|
8.1
|
1.0
|
CA
|
A:ASN103
|
4.9
|
8.0
|
1.0
|
HB3
|
A:ASP101
|
4.9
|
11.6
|
1.0
|
OD1
|
A:ASP99
|
5.0
|
10.4
|
1.0
|
|
Calcium binding site 3 out
of 8 in 7psy
Go back to
Calcium Binding Sites List in 7psy
Calcium binding site 3 out
of 8 in the X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca203
b:8.1
occ:1.00
|
OD1
|
B:ASN103
|
2.3
|
8.7
|
1.0
|
OD1
|
B:ASP104
|
2.4
|
8.2
|
1.0
|
O
|
B:ASN21
|
2.4
|
8.3
|
1.0
|
OD2
|
B:ASP101
|
2.4
|
8.8
|
1.0
|
O
|
A:GLY114
|
2.4
|
8.9
|
1.0
|
O3
|
B:FUC201
|
2.5
|
8.5
|
1.0
|
O4
|
B:FUC201
|
2.5
|
9.2
|
1.0
|
OD1
|
B:ASP101
|
3.0
|
8.7
|
1.0
|
CG
|
B:ASP101
|
3.1
|
8.8
|
1.0
|
HD21
|
B:ASN103
|
3.3
|
10.8
|
1.0
|
CG
|
B:ASN103
|
3.4
|
8.1
|
1.0
|
C3
|
B:FUC201
|
3.4
|
9.3
|
1.0
|
C4
|
B:FUC201
|
3.4
|
9.6
|
1.0
|
C
|
A:GLY114
|
3.4
|
9.5
|
1.0
|
HA
|
B:ASP104
|
3.5
|
9.4
|
1.0
|
C
|
B:ASN21
|
3.5
|
8.2
|
1.0
|
CG
|
B:ASP104
|
3.6
|
7.8
|
1.0
|
HB3
|
B:ASN21
|
3.7
|
9.9
|
1.0
|
OXT
|
A:GLY114
|
3.7
|
11.1
|
1.0
|
HA
|
B:SER22
|
3.7
|
10.8
|
1.0
|
ND2
|
B:ASN103
|
3.7
|
9.0
|
1.0
|
CA
|
B:CA204
|
3.7
|
8.2
|
1.0
|
C2
|
B:FUC201
|
3.8
|
9.4
|
1.0
|
HB2
|
B:ASN21
|
3.9
|
9.9
|
1.0
|
HB2
|
B:SER22
|
3.9
|
10.6
|
1.0
|
H
|
B:ASN103
|
4.2
|
9.6
|
1.0
|
CB
|
B:ASN21
|
4.2
|
8.2
|
1.0
|
CA
|
B:ASP104
|
4.2
|
7.8
|
1.0
|
N
|
B:ASP104
|
4.3
|
7.8
|
1.0
|
CA
|
B:SER22
|
4.3
|
9.0
|
1.0
|
N
|
B:SER22
|
4.4
|
8.5
|
1.0
|
O
|
B:HOH354
|
4.4
|
15.9
|
1.0
|
O2
|
B:FUC201
|
4.5
|
9.0
|
1.0
|
C
|
B:ASN103
|
4.5
|
7.5
|
1.0
|
OD2
|
B:ASP104
|
4.5
|
8.7
|
1.0
|
CB
|
B:ASP104
|
4.5
|
8.4
|
1.0
|
CB
|
B:ASP101
|
4.5
|
8.9
|
1.0
|
CA
|
B:ASN21
|
4.5
|
8.3
|
1.0
|
OD2
|
B:ASP99
|
4.6
|
10.5
|
1.0
|
H
|
B:ASP104
|
4.6
|
9.3
|
1.0
|
HD22
|
B:ASN103
|
4.6
|
10.8
|
1.0
|
CB
|
B:SER22
|
4.6
|
8.8
|
1.0
|
HB2
|
B:ASP101
|
4.7
|
10.7
|
1.0
|
CB
|
B:ASN103
|
4.7
|
8.1
|
1.0
|
O
|
B:ASN103
|
4.8
|
8.0
|
1.0
|
CA
|
A:GLY114
|
4.8
|
9.4
|
1.0
|
C5
|
B:FUC201
|
4.8
|
10.2
|
1.0
|
HB3
|
B:ASP104
|
4.8
|
10.1
|
1.0
|
N
|
B:ASN103
|
4.9
|
8.0
|
1.0
|
HB3
|
B:ASP101
|
4.9
|
10.7
|
1.0
|
CA
|
B:ASN103
|
4.9
|
8.3
|
1.0
|
|
Calcium binding site 4 out
of 8 in 7psy
Go back to
Calcium Binding Sites List in 7psy
Calcium binding site 4 out
of 8 in the X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca204
b:8.2
occ:1.00
|
OD1
|
B:ASP99
|
2.4
|
10.0
|
1.0
|
OD1
|
B:ASP101
|
2.4
|
8.7
|
1.0
|
OD2
|
B:ASP104
|
2.4
|
8.7
|
1.0
|
OE2
|
B:GLU95
|
2.4
|
8.6
|
1.0
|
O3
|
B:FUC201
|
2.5
|
8.5
|
1.0
|
OE1
|
B:GLU95
|
2.5
|
8.6
|
1.0
|
O2
|
B:FUC201
|
2.5
|
9.0
|
1.0
|
OD1
|
B:ASP104
|
2.6
|
8.2
|
1.0
|
CD
|
B:GLU95
|
2.8
|
8.2
|
1.0
|
CG
|
B:ASP104
|
2.9
|
7.8
|
1.0
|
C2
|
B:FUC201
|
3.3
|
9.4
|
1.0
|
C3
|
B:FUC201
|
3.3
|
9.3
|
1.0
|
H
|
B:ASP101
|
3.4
|
10.3
|
1.0
|
CG
|
B:ASP99
|
3.4
|
9.6
|
1.0
|
CG
|
B:ASP101
|
3.4
|
8.8
|
1.0
|
OD2
|
B:ASP99
|
3.7
|
10.5
|
1.0
|
CA
|
B:CA203
|
3.7
|
8.1
|
1.0
|
H
|
B:TYR102
|
3.7
|
10.0
|
1.0
|
H
|
B:ASP96
|
3.8
|
10.8
|
1.0
|
HA
|
B:GLU95
|
3.9
|
9.8
|
1.0
|
OD2
|
B:ASP101
|
4.0
|
8.8
|
1.0
|
H
|
B:ASN100
|
4.0
|
11.0
|
1.0
|
H
|
B:GLY97
|
4.1
|
11.7
|
1.0
|
H
|
B:ASP99
|
4.1
|
11.9
|
1.0
|
O
|
B:HOH399
|
4.1
|
13.3
|
1.0
|
N
|
B:ASP101
|
4.1
|
8.6
|
1.0
|
OD1
|
B:ASP96
|
4.2
|
10.4
|
1.0
|
CG
|
B:GLU95
|
4.3
|
8.7
|
1.0
|
CB
|
B:ASP104
|
4.4
|
8.4
|
1.0
|
N
|
B:TYR102
|
4.4
|
8.3
|
1.0
|
H
|
B:ASN103
|
4.4
|
9.6
|
1.0
|
N
|
B:ASN100
|
4.5
|
9.2
|
1.0
|
N
|
B:ASP96
|
4.5
|
9.0
|
1.0
|
CB
|
B:ASP101
|
4.6
|
8.9
|
1.0
|
HG3
|
B:GLU95
|
4.6
|
10.4
|
1.0
|
N
|
B:GLY97
|
4.6
|
9.7
|
1.0
|
HA3
|
B:GLY97
|
4.7
|
13.0
|
1.0
|
C4
|
B:FUC201
|
4.7
|
9.6
|
1.0
|
HB2
|
B:ASP104
|
4.7
|
10.1
|
1.0
|
CA
|
B:ASP101
|
4.7
|
9.0
|
1.0
|
CA
|
B:GLU95
|
4.7
|
8.2
|
1.0
|
H
|
B:ASP104
|
4.7
|
9.3
|
1.0
|
CB
|
B:ASP99
|
4.7
|
10.6
|
1.0
|
OD1
|
B:ASN103
|
4.7
|
8.7
|
1.0
|
N
|
B:ASP99
|
4.8
|
9.9
|
1.0
|
C1
|
B:FUC201
|
4.8
|
10.0
|
1.0
|
HG2
|
B:GLU95
|
4.8
|
10.4
|
1.0
|
HA
|
B:ASN100
|
4.8
|
10.7
|
1.0
|
O4
|
B:FUC201
|
4.8
|
9.2
|
1.0
|
HB3
|
B:ASP104
|
4.8
|
10.1
|
1.0
|
HB3
|
B:ASP101
|
4.9
|
10.7
|
1.0
|
CB
|
B:GLU95
|
4.9
|
8.5
|
1.0
|
HB2
|
B:GLU95
|
4.9
|
10.2
|
1.0
|
CG
|
B:ASP96
|
5.0
|
9.3
|
1.0
|
C
|
B:ASP101
|
5.0
|
8.6
|
1.0
|
C
|
B:ASP99
|
5.0
|
9.8
|
1.0
|
HA
|
B:TYR102
|
5.0
|
9.9
|
1.0
|
|
Calcium binding site 5 out
of 8 in 7psy
Go back to
Calcium Binding Sites List in 7psy
Calcium binding site 5 out
of 8 in the X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca202
b:8.5
occ:1.00
|
OD1
|
C:ASN103
|
2.3
|
8.5
|
1.0
|
O
|
C:ASN21
|
2.4
|
8.4
|
1.0
|
OD1
|
C:ASP104
|
2.4
|
8.7
|
1.0
|
O
|
D:GLY114
|
2.4
|
9.2
|
1.0
|
OD2
|
C:ASP101
|
2.4
|
10.0
|
1.0
|
O4
|
C:FUC201
|
2.5
|
9.2
|
1.0
|
O3
|
C:FUC201
|
2.5
|
9.3
|
1.0
|
OD1
|
C:ASP101
|
3.0
|
10.7
|
1.0
|
CG
|
C:ASP101
|
3.1
|
10.1
|
1.0
|
C3
|
C:FUC201
|
3.4
|
9.4
|
1.0
|
CG
|
C:ASN103
|
3.4
|
8.7
|
1.0
|
HD21
|
C:ASN103
|
3.4
|
11.1
|
1.0
|
C
|
D:GLY114
|
3.4
|
9.1
|
1.0
|
C4
|
C:FUC201
|
3.4
|
10.0
|
1.0
|
HA
|
C:ASP104
|
3.5
|
9.6
|
1.0
|
C
|
C:ASN21
|
3.6
|
8.2
|
1.0
|
CG
|
C:ASP104
|
3.6
|
8.8
|
1.0
|
HB3
|
C:ASN21
|
3.6
|
10.0
|
1.0
|
OXT
|
D:GLY114
|
3.7
|
10.9
|
1.0
|
CA
|
C:CA203
|
3.8
|
9.2
|
1.0
|
ND2
|
C:ASN103
|
3.8
|
9.2
|
1.0
|
HA
|
C:SER22
|
3.8
|
10.4
|
1.0
|
C2
|
C:FUC201
|
3.8
|
9.3
|
1.0
|
HB2
|
C:ASN21
|
3.9
|
10.0
|
1.0
|
HB2
|
C:SER22
|
4.0
|
10.5
|
1.0
|
H
|
C:ASN103
|
4.2
|
10.1
|
1.0
|
CB
|
C:ASN21
|
4.2
|
8.4
|
1.0
|
CA
|
C:ASP104
|
4.2
|
8.0
|
1.0
|
N
|
C:ASP104
|
4.3
|
8.0
|
1.0
|
CA
|
C:SER22
|
4.4
|
8.7
|
1.0
|
N
|
C:SER22
|
4.4
|
8.2
|
1.0
|
O
|
C:HOH351
|
4.4
|
17.4
|
1.0
|
C
|
C:ASN103
|
4.4
|
8.1
|
1.0
|
OD2
|
C:ASP104
|
4.5
|
9.3
|
1.0
|
O2
|
C:FUC201
|
4.5
|
10.0
|
1.0
|
CB
|
C:ASP104
|
4.5
|
8.6
|
1.0
|
CA
|
C:ASN21
|
4.5
|
7.9
|
1.0
|
H
|
C:ASP104
|
4.5
|
9.6
|
1.0
|
OD2
|
C:ASP99
|
4.5
|
11.5
|
1.0
|
CB
|
C:ASP101
|
4.6
|
11.0
|
1.0
|
HD22
|
C:ASN103
|
4.6
|
11.1
|
1.0
|
CB
|
C:SER22
|
4.6
|
8.7
|
1.0
|
CB
|
C:ASN103
|
4.7
|
8.4
|
1.0
|
HB2
|
C:ASP101
|
4.7
|
13.2
|
1.0
|
C5
|
C:FUC201
|
4.8
|
10.4
|
1.0
|
O
|
C:ASN103
|
4.8
|
8.1
|
1.0
|
CA
|
D:GLY114
|
4.8
|
9.8
|
1.0
|
HB3
|
C:ASP104
|
4.8
|
10.3
|
1.0
|
N
|
C:ASN103
|
4.8
|
8.4
|
1.0
|
CA
|
C:ASN103
|
4.9
|
8.0
|
1.0
|
HB3
|
C:ASP101
|
4.9
|
13.2
|
1.0
|
OD1
|
C:ASP99
|
5.0
|
11.9
|
1.0
|
|
Calcium binding site 6 out
of 8 in 7psy
Go back to
Calcium Binding Sites List in 7psy
Calcium binding site 6 out
of 8 in the X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca203
b:9.2
occ:1.00
|
OD1
|
C:ASP101
|
2.4
|
10.7
|
1.0
|
OD1
|
C:ASP99
|
2.4
|
11.9
|
1.0
|
OE2
|
C:GLU95
|
2.4
|
9.8
|
1.0
|
OD2
|
C:ASP104
|
2.4
|
9.3
|
1.0
|
OE1
|
C:GLU95
|
2.4
|
9.6
|
1.0
|
O3
|
C:FUC201
|
2.5
|
9.3
|
1.0
|
O2
|
C:FUC201
|
2.5
|
10.0
|
1.0
|
OD1
|
C:ASP104
|
2.6
|
8.7
|
1.0
|
CD
|
C:GLU95
|
2.8
|
10.0
|
1.0
|
CG
|
C:ASP104
|
2.9
|
8.8
|
1.0
|
C2
|
C:FUC201
|
3.3
|
9.3
|
1.0
|
C3
|
C:FUC201
|
3.4
|
9.4
|
1.0
|
H
|
C:ASP101
|
3.4
|
13.6
|
1.0
|
CG
|
C:ASP99
|
3.4
|
11.2
|
1.0
|
CG
|
C:ASP101
|
3.4
|
10.1
|
1.0
|
H
|
C:TYR102
|
3.7
|
11.8
|
1.0
|
OD2
|
C:ASP99
|
3.7
|
11.5
|
1.0
|
CA
|
C:CA202
|
3.8
|
8.5
|
1.0
|
H
|
C:ASP96
|
3.8
|
10.9
|
1.0
|
HA
|
C:GLU95
|
3.9
|
11.0
|
1.0
|
OD2
|
C:ASP101
|
4.0
|
10.0
|
1.0
|
H
|
C:ASP99
|
4.0
|
15.4
|
1.0
|
H
|
C:GLY97
|
4.1
|
12.8
|
1.0
|
O
|
C:HOH393
|
4.1
|
17.0
|
1.0
|
N
|
C:ASP101
|
4.1
|
11.3
|
1.0
|
H
|
C:ASN100
|
4.2
|
14.7
|
1.0
|
CG
|
C:GLU95
|
4.2
|
10.0
|
1.0
|
OD1
|
C:ASP96
|
4.3
|
10.5
|
1.0
|
CB
|
C:ASP104
|
4.4
|
8.6
|
1.0
|
N
|
C:TYR102
|
4.4
|
9.9
|
1.0
|
H
|
C:ASN103
|
4.4
|
10.1
|
1.0
|
N
|
C:ASP96
|
4.5
|
9.1
|
1.0
|
CB
|
C:ASP101
|
4.5
|
11.0
|
1.0
|
N
|
C:ASN100
|
4.5
|
12.2
|
1.0
|
HG3
|
C:GLU95
|
4.6
|
12.0
|
1.0
|
HA3
|
C:GLY97
|
4.6
|
14.4
|
1.0
|
N
|
C:GLY97
|
4.6
|
10.7
|
1.0
|
H
|
C:ASP104
|
4.7
|
9.6
|
1.0
|
CA
|
C:ASP101
|
4.7
|
10.8
|
1.0
|
C4
|
C:FUC201
|
4.7
|
10.0
|
1.0
|
CA
|
C:GLU95
|
4.7
|
9.2
|
1.0
|
HB2
|
C:ASP104
|
4.7
|
10.3
|
1.0
|
N
|
C:ASP99
|
4.7
|
12.8
|
1.0
|
CB
|
C:ASP99
|
4.7
|
12.4
|
1.0
|
HG2
|
C:GLU95
|
4.8
|
12.0
|
1.0
|
OD1
|
C:ASN103
|
4.8
|
8.5
|
1.0
|
C1
|
C:FUC201
|
4.8
|
10.5
|
1.0
|
O4
|
C:FUC201
|
4.8
|
9.2
|
1.0
|
HB3
|
C:ASP101
|
4.8
|
13.2
|
1.0
|
HB3
|
C:ASP104
|
4.9
|
10.3
|
1.0
|
CB
|
C:GLU95
|
4.9
|
9.6
|
1.0
|
HB2
|
C:GLU95
|
4.9
|
11.5
|
1.0
|
HA
|
C:ASN100
|
4.9
|
14.8
|
1.0
|
CG
|
C:ASP96
|
4.9
|
9.5
|
1.0
|
C
|
C:ASP101
|
5.0
|
10.0
|
1.0
|
C
|
C:ASP99
|
5.0
|
12.3
|
1.0
|
|
Calcium binding site 7 out
of 8 in 7psy
Go back to
Calcium Binding Sites List in 7psy
Calcium binding site 7 out
of 8 in the X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca202
b:8.1
occ:1.00
|
OD1
|
D:ASP101
|
2.4
|
8.8
|
1.0
|
OD1
|
D:ASP99
|
2.4
|
10.3
|
1.0
|
OD2
|
D:ASP104
|
2.4
|
8.7
|
1.0
|
OE2
|
D:GLU95
|
2.4
|
8.7
|
1.0
|
O3
|
D:FUC201
|
2.5
|
8.8
|
1.0
|
OE1
|
D:GLU95
|
2.5
|
8.8
|
1.0
|
O2
|
D:FUC201
|
2.5
|
9.0
|
1.0
|
OD1
|
D:ASP104
|
2.6
|
8.6
|
1.0
|
CD
|
D:GLU95
|
2.8
|
8.1
|
1.0
|
CG
|
D:ASP104
|
2.9
|
8.3
|
1.0
|
C2
|
D:FUC201
|
3.3
|
8.5
|
1.0
|
C3
|
D:FUC201
|
3.3
|
8.7
|
1.0
|
H
|
D:ASP101
|
3.3
|
11.0
|
1.0
|
CG
|
D:ASP99
|
3.4
|
9.7
|
1.0
|
CG
|
D:ASP101
|
3.4
|
8.6
|
1.0
|
H
|
D:TYR102
|
3.7
|
10.0
|
1.0
|
CA
|
D:CA203
|
3.7
|
7.9
|
1.0
|
OD2
|
D:ASP99
|
3.7
|
10.0
|
1.0
|
H
|
D:ASP96
|
3.8
|
10.3
|
1.0
|
HA
|
D:GLU95
|
3.9
|
10.4
|
1.0
|
OD2
|
D:ASP101
|
4.0
|
8.7
|
1.0
|
H
|
D:ASN100
|
4.0
|
11.6
|
1.0
|
H
|
D:ASP99
|
4.1
|
12.2
|
1.0
|
H
|
D:GLY97
|
4.1
|
11.4
|
1.0
|
N
|
D:ASP101
|
4.1
|
9.1
|
1.0
|
O
|
D:HOH398
|
4.1
|
13.2
|
1.0
|
CG
|
D:GLU95
|
4.2
|
9.2
|
1.0
|
OD1
|
D:ASP96
|
4.3
|
10.2
|
1.0
|
N
|
D:TYR102
|
4.4
|
8.3
|
1.0
|
CB
|
D:ASP104
|
4.4
|
8.1
|
1.0
|
H
|
D:ASN103
|
4.4
|
9.3
|
1.0
|
N
|
D:ASN100
|
4.5
|
9.7
|
1.0
|
CB
|
D:ASP101
|
4.5
|
9.0
|
1.0
|
N
|
D:ASP96
|
4.5
|
8.6
|
1.0
|
HG3
|
D:GLU95
|
4.6
|
11.1
|
1.0
|
HA3
|
D:GLY97
|
4.6
|
12.6
|
1.0
|
N
|
D:GLY97
|
4.6
|
9.5
|
1.0
|
CA
|
D:ASP101
|
4.7
|
8.7
|
1.0
|
H
|
D:ASP104
|
4.7
|
9.5
|
1.0
|
C4
|
D:FUC201
|
4.7
|
9.6
|
1.0
|
CA
|
D:GLU95
|
4.7
|
8.7
|
1.0
|
HB2
|
D:ASP104
|
4.7
|
9.8
|
1.0
|
CB
|
D:ASP99
|
4.7
|
10.3
|
1.0
|
N
|
D:ASP99
|
4.7
|
10.2
|
1.0
|
C1
|
D:FUC201
|
4.8
|
9.9
|
1.0
|
OD1
|
D:ASN103
|
4.8
|
8.1
|
1.0
|
HG2
|
D:GLU95
|
4.8
|
11.1
|
1.0
|
O4
|
D:FUC201
|
4.8
|
8.8
|
1.0
|
HB3
|
D:ASP101
|
4.8
|
10.8
|
1.0
|
HA
|
D:ASN100
|
4.8
|
11.6
|
1.0
|
HB3
|
D:ASP104
|
4.8
|
9.8
|
1.0
|
CB
|
D:GLU95
|
4.9
|
8.6
|
1.0
|
C
|
D:ASP101
|
4.9
|
8.4
|
1.0
|
HB2
|
D:GLU95
|
4.9
|
10.3
|
1.0
|
CG
|
D:ASP96
|
5.0
|
9.4
|
1.0
|
C
|
D:ASP99
|
5.0
|
9.9
|
1.0
|
HA
|
D:TYR102
|
5.0
|
10.3
|
1.0
|
|
Calcium binding site 8 out
of 8 in 7psy
Go back to
Calcium Binding Sites List in 7psy
Calcium binding site 8 out
of 8 in the X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of X-Ray Crystal Structure of Perdeuterated Lecb Lectin in Complex with Perdeuterated Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca203
b:7.9
occ:1.00
|
OD1
|
D:ASN103
|
2.3
|
8.1
|
1.0
|
O
|
D:ASN21
|
2.4
|
8.2
|
1.0
|
OD1
|
D:ASP104
|
2.4
|
8.6
|
1.0
|
O
|
C:GLY114
|
2.4
|
8.9
|
1.0
|
OD2
|
D:ASP101
|
2.4
|
8.7
|
1.0
|
O3
|
D:FUC201
|
2.5
|
8.8
|
1.0
|
O4
|
D:FUC201
|
2.5
|
8.8
|
1.0
|
OD1
|
D:ASP101
|
3.0
|
8.8
|
1.0
|
CG
|
D:ASP101
|
3.1
|
8.6
|
1.0
|
HD21
|
D:ASN103
|
3.4
|
10.4
|
1.0
|
C3
|
D:FUC201
|
3.4
|
8.7
|
1.0
|
C
|
C:GLY114
|
3.4
|
9.0
|
1.0
|
CG
|
D:ASN103
|
3.4
|
7.6
|
1.0
|
C4
|
D:FUC201
|
3.4
|
9.6
|
1.0
|
HA
|
D:ASP104
|
3.5
|
9.3
|
1.0
|
C
|
D:ASN21
|
3.6
|
8.2
|
1.0
|
CG
|
D:ASP104
|
3.6
|
8.3
|
1.0
|
HB3
|
D:ASN21
|
3.6
|
9.4
|
1.0
|
OXT
|
C:GLY114
|
3.7
|
10.2
|
1.0
|
CA
|
D:CA202
|
3.7
|
8.1
|
1.0
|
ND2
|
D:ASN103
|
3.7
|
8.6
|
1.0
|
HA
|
D:SER22
|
3.8
|
10.2
|
1.0
|
C2
|
D:FUC201
|
3.8
|
8.5
|
1.0
|
HB2
|
D:ASN21
|
3.9
|
9.4
|
1.0
|
HB2
|
D:SER22
|
3.9
|
10.9
|
1.0
|
CB
|
D:ASN21
|
4.1
|
7.8
|
1.0
|
H
|
D:ASN103
|
4.1
|
9.3
|
1.0
|
CA
|
D:ASP104
|
4.2
|
7.8
|
1.0
|
N
|
D:ASP104
|
4.3
|
7.9
|
1.0
|
CA
|
D:SER22
|
4.4
|
8.5
|
1.0
|
N
|
D:SER22
|
4.4
|
8.4
|
1.0
|
O2
|
D:FUC201
|
4.4
|
9.0
|
1.0
|
OD2
|
D:ASP104
|
4.4
|
8.7
|
1.0
|
C
|
D:ASN103
|
4.5
|
7.7
|
1.0
|
CB
|
D:ASP104
|
4.5
|
8.1
|
1.0
|
OD2
|
D:ASP99
|
4.5
|
10.0
|
1.0
|
CA
|
D:ASN21
|
4.5
|
7.9
|
1.0
|
CB
|
D:ASP101
|
4.5
|
9.0
|
1.0
|
H
|
D:ASP104
|
4.6
|
9.5
|
1.0
|
HD22
|
D:ASN103
|
4.6
|
10.4
|
1.0
|
CB
|
D:SER22
|
4.6
|
9.1
|
1.0
|
O
|
D:HOH372
|
4.7
|
11.9
|
1.0
|
CB
|
D:ASN103
|
4.7
|
8.0
|
1.0
|
HB2
|
D:ASP101
|
4.7
|
10.8
|
1.0
|
CA
|
C:GLY114
|
4.8
|
8.9
|
1.0
|
C5
|
D:FUC201
|
4.8
|
9.7
|
1.0
|
O
|
D:ASN103
|
4.8
|
8.0
|
1.0
|
HB3
|
D:ASP104
|
4.8
|
9.8
|
1.0
|
N
|
D:ASN103
|
4.8
|
7.8
|
1.0
|
CA
|
D:ASN103
|
4.9
|
7.4
|
1.0
|
HB3
|
D:ASP101
|
4.9
|
10.8
|
1.0
|
OD1
|
D:ASP99
|
4.9
|
10.3
|
1.0
|
|
Reference:
L.Gajdos,
M.P.Blakeley,
M.Haertlein,
V.T.Forsyth,
J.M.Devos,
A.Imberty.
Neutron Crystallography Reveals Mechanisms Used By Pseudomonas Aeruginosa For Host-Cell Binding. Nat Commun V. 13 194 2022.
ISSN: ESSN 2041-1723
PubMed: 35017516
DOI: 10.1038/S41467-021-27871-8
Page generated: Fri Jul 19 03:14:50 2024
|