Calcium in PDB 5fre: Characterization of A Novel Cbm From Clostridium Perfringens
Protein crystallography data
The structure of Characterization of A Novel Cbm From Clostridium Perfringens, PDB code: 5fre
was solved by
J.Ribeiro,
W.Pau,
C.Pifferi,
O.Renaudet,
A.Varrot,
L.K.Mahal,
A.Imberty,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.61 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.348,
76.714,
67.254,
90.00,
93.46,
90.00
|
R / Rfree (%)
|
17.291 /
20.874
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Characterization of A Novel Cbm From Clostridium Perfringens
(pdb code 5fre). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Characterization of A Novel Cbm From Clostridium Perfringens, PDB code: 5fre:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 5fre
Go back to
Calcium Binding Sites List in 5fre
Calcium binding site 1 out
of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca210
b:24.5
occ:1.00
|
O
|
A:SER41
|
2.3
|
18.4
|
1.0
|
OD1
|
A:ASN40
|
2.3
|
17.9
|
1.0
|
O
|
A:ASP102
|
2.4
|
23.4
|
1.0
|
O
|
A:HOH2046
|
2.4
|
24.6
|
1.0
|
O
|
A:HOH2045
|
2.4
|
30.0
|
1.0
|
O
|
A:HOH2055
|
2.5
|
25.2
|
0.5
|
O
|
A:HOH2054
|
2.5
|
26.1
|
1.0
|
C
|
A:SER41
|
3.4
|
19.9
|
1.0
|
C
|
A:ASP102
|
3.5
|
25.0
|
1.0
|
CG
|
A:ASN40
|
3.5
|
19.9
|
1.0
|
O
|
A:HOH2019
|
4.0
|
24.6
|
1.0
|
N
|
A:SER41
|
4.0
|
19.4
|
1.0
|
ND2
|
A:ASN40
|
4.2
|
20.7
|
1.0
|
CA
|
A:ASP102
|
4.3
|
27.6
|
1.0
|
O
|
A:HOH2020
|
4.3
|
30.0
|
0.5
|
CA
|
A:SER41
|
4.4
|
19.7
|
1.0
|
O
|
A:HOH2052
|
4.4
|
23.7
|
1.0
|
N
|
A:LYS42
|
4.4
|
20.6
|
1.0
|
O
|
A:GLY103
|
4.4
|
19.8
|
1.0
|
C
|
A:ASN40
|
4.4
|
18.7
|
1.0
|
O
|
A:HOH2048
|
4.5
|
30.0
|
1.0
|
N
|
A:GLY103
|
4.5
|
21.5
|
1.0
|
CA
|
A:LYS42
|
4.5
|
20.7
|
1.0
|
O
|
A:HOH2053
|
4.6
|
25.4
|
1.0
|
O
|
A:ASN101
|
4.6
|
21.4
|
1.0
|
CA
|
A:GLY103
|
4.7
|
21.1
|
1.0
|
CA
|
A:ASN40
|
4.7
|
18.3
|
1.0
|
CB
|
A:ASN40
|
4.7
|
18.0
|
1.0
|
C
|
A:GLY103
|
4.9
|
19.5
|
1.0
|
O
|
A:HOH2018
|
4.9
|
30.0
|
1.0
|
O
|
A:ASN40
|
5.0
|
18.1
|
1.0
|
|
Calcium binding site 2 out
of 8 in 5fre
Go back to
Calcium Binding Sites List in 5fre
Calcium binding site 2 out
of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca211
b:25.6
occ:1.00
|
O
|
A:ASN133
|
2.3
|
19.0
|
1.0
|
O
|
A:HOH2124
|
2.5
|
30.0
|
1.0
|
O
|
A:HOH2157
|
2.5
|
30.0
|
1.0
|
OD1
|
A:ASP131
|
2.6
|
24.1
|
1.0
|
OD2
|
A:ASP131
|
2.6
|
22.3
|
1.0
|
O
|
A:HOH2126
|
2.6
|
30.0
|
1.0
|
O
|
A:HOH2116
|
2.7
|
30.0
|
1.0
|
CG
|
A:ASP131
|
2.9
|
23.1
|
1.0
|
C
|
A:ASN133
|
3.3
|
19.6
|
1.0
|
CA
|
A:ASN133
|
4.0
|
24.1
|
1.0
|
CB
|
A:ASN133
|
4.1
|
27.2
|
1.0
|
N
|
A:THR134
|
4.2
|
19.4
|
1.0
|
N
|
A:ASN133
|
4.3
|
22.7
|
1.0
|
CA
|
A:THR134
|
4.4
|
18.9
|
1.0
|
CB
|
A:ASP131
|
4.4
|
21.1
|
1.0
|
O
|
A:HOH2098
|
4.4
|
30.0
|
1.0
|
O
|
A:HOH2123
|
4.6
|
30.0
|
1.0
|
ND2
|
A:ASN133
|
4.6
|
33.8
|
1.0
|
CG
|
A:ASN133
|
4.8
|
30.7
|
1.0
|
OH
|
A:TYR117
|
4.9
|
22.5
|
1.0
|
C
|
A:THR134
|
4.9
|
19.5
|
1.0
|
|
Calcium binding site 3 out
of 8 in 5fre
Go back to
Calcium Binding Sites List in 5fre
Calcium binding site 3 out
of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca212
b:26.4
occ:1.00
|
O
|
A:HOH2070
|
2.4
|
26.5
|
1.0
|
OD1
|
A:ASN152
|
2.4
|
22.2
|
1.0
|
O
|
A:HOH2134
|
2.4
|
26.2
|
1.0
|
O
|
A:HOH2133
|
2.4
|
23.9
|
1.0
|
O
|
A:ARG153
|
2.4
|
17.3
|
1.0
|
O
|
A:HOH2158
|
2.5
|
30.0
|
1.0
|
OE2
|
A:GLU159
|
3.2
|
34.9
|
1.0
|
C
|
A:ARG153
|
3.5
|
18.4
|
1.0
|
CG
|
A:ASN152
|
3.6
|
20.3
|
1.0
|
N
|
A:ARG153
|
3.7
|
17.2
|
1.0
|
CA
|
A:ARG153
|
4.2
|
17.4
|
1.0
|
C
|
A:ASN152
|
4.2
|
16.4
|
1.0
|
ND2
|
A:ASN152
|
4.3
|
19.9
|
1.0
|
CD
|
A:GLU159
|
4.5
|
30.0
|
1.0
|
CA
|
A:ASN152
|
4.5
|
16.6
|
1.0
|
N
|
A:TYR154
|
4.5
|
18.9
|
1.0
|
O
|
A:HOH2137
|
4.6
|
30.0
|
1.0
|
CB
|
A:ASN152
|
4.6
|
17.5
|
1.0
|
CA
|
A:TYR154
|
4.7
|
22.4
|
1.0
|
N
|
A:GLY155
|
4.8
|
24.2
|
1.0
|
O
|
A:GLY155
|
4.8
|
21.6
|
1.0
|
C
|
A:TYR154
|
4.9
|
21.4
|
1.0
|
O
|
A:SER55
|
4.9
|
20.7
|
1.0
|
O
|
A:HOH2064
|
5.0
|
39.4
|
1.0
|
CB
|
A:SER55
|
5.0
|
19.5
|
1.0
|
|
Calcium binding site 4 out
of 8 in 5fre
Go back to
Calcium Binding Sites List in 5fre
Calcium binding site 4 out
of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca210
b:20.6
occ:1.00
|
OD1
|
B:ASN152
|
2.3
|
14.6
|
1.0
|
O
|
B:ARG153
|
2.4
|
10.8
|
1.0
|
O
|
B:HOH2160
|
2.4
|
30.0
|
1.0
|
OE2
|
B:GLU159
|
2.5
|
16.5
|
1.0
|
O
|
B:HOH2156
|
2.6
|
22.5
|
1.0
|
O
|
B:HOH2158
|
2.6
|
30.0
|
1.0
|
O
|
B:HOH2078
|
2.7
|
30.0
|
1.0
|
C
|
B:ARG153
|
3.5
|
12.2
|
1.0
|
CG
|
B:ASN152
|
3.5
|
13.6
|
1.0
|
N
|
B:ARG153
|
3.6
|
10.6
|
1.0
|
CD
|
B:GLU159
|
3.7
|
19.5
|
1.0
|
OE1
|
B:GLU159
|
4.1
|
19.4
|
1.0
|
C
|
B:ASN152
|
4.2
|
11.2
|
1.0
|
CA
|
B:ARG153
|
4.2
|
11.1
|
1.0
|
ND2
|
B:ASN152
|
4.3
|
13.9
|
1.0
|
O
|
B:HOH2159
|
4.4
|
30.0
|
1.0
|
CA
|
B:ASN152
|
4.4
|
11.3
|
1.0
|
O
|
B:HOH2164
|
4.4
|
40.8
|
1.0
|
O
|
B:HOH2157
|
4.5
|
30.0
|
1.0
|
N
|
B:TYR154
|
4.6
|
11.8
|
1.0
|
CB
|
B:ASN152
|
4.6
|
11.8
|
1.0
|
O
|
B:HOH2163
|
4.6
|
20.4
|
1.0
|
O
|
B:GLY155
|
4.7
|
18.6
|
1.0
|
CA
|
B:TYR154
|
4.8
|
13.6
|
1.0
|
N
|
B:GLY155
|
4.8
|
14.9
|
1.0
|
C
|
B:TYR154
|
4.9
|
14.4
|
1.0
|
CG
|
B:GLU159
|
4.9
|
17.7
|
1.0
|
O
|
B:ASN152
|
5.0
|
11.0
|
1.0
|
O
|
B:SER55
|
5.0
|
12.3
|
1.0
|
|
Calcium binding site 5 out
of 8 in 5fre
Go back to
Calcium Binding Sites List in 5fre
Calcium binding site 5 out
of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca213
b:30.0
occ:1.00
|
O
|
B:ASP102
|
2.3
|
19.9
|
1.0
|
O
|
B:SER41
|
2.5
|
17.4
|
1.0
|
O
|
B:HOH2064
|
2.5
|
30.0
|
1.0
|
O
|
B:HOH2065
|
2.5
|
30.0
|
1.0
|
O
|
B:HOH2067
|
2.6
|
26.5
|
1.0
|
OD1
|
B:ASN40
|
2.7
|
15.0
|
1.0
|
C
|
B:SER41
|
3.5
|
17.4
|
1.0
|
C
|
B:ASP102
|
3.5
|
17.5
|
1.0
|
CG
|
B:ASN40
|
3.9
|
15.4
|
1.0
|
N
|
B:SER41
|
3.9
|
13.2
|
1.0
|
O
|
B:GLY103
|
4.2
|
14.1
|
1.0
|
NZ
|
B:LYS42
|
4.3
|
40.3
|
1.0
|
CA
|
B:SER41
|
4.3
|
15.8
|
1.0
|
C
|
B:ASN40
|
4.4
|
12.9
|
1.0
|
N
|
B:GLY103
|
4.4
|
16.2
|
1.0
|
N
|
B:LYS42
|
4.5
|
19.4
|
1.0
|
CA
|
B:ASP102
|
4.5
|
16.3
|
1.0
|
CA
|
B:GLY103
|
4.5
|
15.3
|
1.0
|
CD
|
B:LYS42
|
4.5
|
30.9
|
1.0
|
O
|
B:HOH2126
|
4.6
|
22.9
|
1.0
|
ND2
|
B:ASN40
|
4.6
|
16.6
|
1.0
|
OD1
|
B:ASP102
|
4.6
|
23.4
|
1.0
|
CA
|
B:LYS42
|
4.6
|
21.8
|
1.0
|
CA
|
B:ASN40
|
4.7
|
12.6
|
1.0
|
C
|
B:GLY103
|
4.8
|
14.5
|
1.0
|
CG
|
B:ASP102
|
4.9
|
21.1
|
1.0
|
O
|
B:ASN101
|
4.9
|
13.2
|
1.0
|
CB
|
B:ASN40
|
4.9
|
13.7
|
1.0
|
|
Calcium binding site 6 out
of 8 in 5fre
Go back to
Calcium Binding Sites List in 5fre
Calcium binding site 6 out
of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca214
b:30.0
occ:1.00
|
O
|
B:ASN133
|
2.1
|
22.3
|
1.0
|
O
|
B:HOH2150
|
2.4
|
30.0
|
1.0
|
O
|
B:HOH2146
|
2.5
|
30.0
|
1.0
|
OD1
|
B:ASP131
|
2.5
|
25.7
|
1.0
|
O
|
B:HOH2132
|
2.6
|
23.1
|
1.0
|
OD2
|
B:ASP131
|
2.6
|
23.4
|
1.0
|
CG
|
B:ASP131
|
2.9
|
25.4
|
1.0
|
O
|
B:HOH2147
|
2.9
|
30.0
|
1.0
|
C
|
B:ASN133
|
3.1
|
21.2
|
1.0
|
CA
|
B:ASN133
|
4.0
|
25.8
|
1.0
|
CB
|
B:ASN133
|
4.0
|
29.6
|
1.0
|
N
|
B:THR134
|
4.1
|
18.6
|
1.0
|
N
|
B:ASN133
|
4.2
|
24.4
|
1.0
|
CA
|
B:THR134
|
4.3
|
17.1
|
1.0
|
ND2
|
B:ASN133
|
4.3
|
37.6
|
1.0
|
CB
|
B:ASP131
|
4.3
|
24.4
|
1.0
|
O
|
B:HOH2113
|
4.5
|
24.4
|
1.0
|
CG
|
B:ASN133
|
4.7
|
33.3
|
1.0
|
OH
|
B:TYR117
|
4.8
|
21.0
|
1.0
|
C
|
B:THR134
|
4.8
|
16.6
|
1.0
|
|
Calcium binding site 7 out
of 8 in 5fre
Go back to
Calcium Binding Sites List in 5fre
Calcium binding site 7 out
of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca210
b:44.2
occ:1.00
|
O
|
C:ASP102
|
2.3
|
28.9
|
1.0
|
O
|
C:SER41
|
2.4
|
22.6
|
1.0
|
O
|
C:HOH2059
|
2.4
|
24.9
|
1.0
|
O
|
C:HOH2062
|
2.5
|
26.9
|
1.0
|
OD1
|
C:ASN40
|
2.6
|
18.3
|
1.0
|
O
|
C:HOH2108
|
2.8
|
30.0
|
1.0
|
C
|
C:SER41
|
3.4
|
19.5
|
1.0
|
C
|
C:ASP102
|
3.5
|
26.5
|
1.0
|
CG
|
C:ASN40
|
3.7
|
20.1
|
1.0
|
N
|
C:SER41
|
3.7
|
18.4
|
1.0
|
O
|
C:GLY103
|
4.2
|
19.0
|
1.0
|
CA
|
C:SER41
|
4.2
|
20.1
|
1.0
|
C
|
C:ASN40
|
4.2
|
18.0
|
1.0
|
CA
|
C:GLY103
|
4.4
|
24.0
|
1.0
|
N
|
C:GLY103
|
4.4
|
23.8
|
1.0
|
CA
|
C:ASP102
|
4.4
|
25.0
|
1.0
|
ND2
|
C:ASN40
|
4.4
|
21.1
|
1.0
|
CA
|
C:ASN40
|
4.6
|
17.2
|
1.0
|
C
|
C:GLY103
|
4.6
|
20.6
|
1.0
|
O
|
C:HOH2061
|
4.7
|
30.0
|
1.0
|
CB
|
C:ASN40
|
4.8
|
18.0
|
1.0
|
O
|
C:ASN101
|
4.9
|
21.9
|
1.0
|
O
|
C:ASN40
|
5.0
|
16.4
|
1.0
|
|
Calcium binding site 8 out
of 8 in 5fre
Go back to
Calcium Binding Sites List in 5fre
Calcium binding site 8 out
of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca211
b:25.7
occ:1.00
|
O
|
C:ARG153
|
2.3
|
15.3
|
1.0
|
OD1
|
C:ASN152
|
2.4
|
14.4
|
1.0
|
O
|
C:HOH2137
|
2.4
|
29.0
|
1.0
|
O
|
C:HOH2139
|
2.5
|
26.6
|
1.0
|
O
|
C:HOH2141
|
2.5
|
30.0
|
1.0
|
OE2
|
C:GLU159
|
2.6
|
18.1
|
1.0
|
O
|
C:HOH2076
|
2.6
|
30.0
|
1.0
|
C
|
C:ARG153
|
3.5
|
16.1
|
1.0
|
N
|
C:ARG153
|
3.6
|
13.6
|
1.0
|
CG
|
C:ASN152
|
3.6
|
13.7
|
1.0
|
CD
|
C:GLU159
|
3.8
|
19.2
|
1.0
|
CA
|
C:ARG153
|
4.2
|
15.1
|
1.0
|
C
|
C:ASN152
|
4.2
|
13.9
|
1.0
|
OE1
|
C:GLU159
|
4.3
|
22.2
|
1.0
|
ND2
|
C:ASN152
|
4.4
|
12.7
|
1.0
|
CA
|
C:ASN152
|
4.4
|
13.9
|
1.0
|
N
|
C:TYR154
|
4.5
|
18.0
|
1.0
|
O
|
C:HOH2145
|
4.5
|
24.5
|
1.0
|
O
|
C:HOH2138
|
4.6
|
30.0
|
1.0
|
CB
|
C:ASN152
|
4.6
|
13.4
|
1.0
|
CA
|
C:TYR154
|
4.7
|
19.9
|
1.0
|
O
|
C:HOH2140
|
4.8
|
32.3
|
1.0
|
O
|
C:GLY155
|
4.9
|
20.2
|
1.0
|
C
|
C:TYR154
|
4.9
|
19.1
|
1.0
|
N
|
C:GLY155
|
4.9
|
19.4
|
1.0
|
CG
|
C:GLU159
|
5.0
|
18.1
|
1.0
|
O
|
C:ASN152
|
5.0
|
14.2
|
1.0
|
|
Reference:
J.P.Ribeiro,
W.Pau,
C.Pifferi,
O.Renaudet,
A.Varrot,
L.K.Mahal,
A.Imberty.
Characterization of A High-Affinity Sialic Acid-Specific CBM40 From Clostridium Perfringens and Engineering of A Divalent Form. Biochem.J. V. 473 2109 2016.
ISSN: ISSN 0264-6021
PubMed: 27208171
DOI: 10.1042/BCJ20160340
Page generated: Sun Jul 14 19:19:22 2024
|