Calcium in PDB 8x39: Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum
Protein crystallography data
The structure of Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum, PDB code: 8x39
was solved by
C.Chen,
S.Dong,
Y.Feng,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
45.73 /
1.70
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.16,
68.95,
74,
90,
90,
90
|
|
R / Rfree (%)
|
16.6 /
20.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum
(pdb code 8x39). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum, PDB code: 8x39:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 8x39
Go back to
Calcium Binding Sites List in 8x39
Calcium binding site 1 out
of 8 in the Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum
 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 Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca201
b:19.1
occ:1.00
|
O
|
A:GLU13
|
2.2
|
19.9
|
1.0
|
|
OD1
|
A:ASP7
|
2.3
|
20.1
|
1.0
|
|
OD1
|
A:ASP9
|
2.3
|
21.3
|
1.0
|
|
O
|
A:HOH322
|
2.4
|
19.4
|
1.0
|
|
OD1
|
A:ASN11
|
2.4
|
21.0
|
1.0
|
|
OD2
|
A:ASP18
|
2.4
|
16.9
|
1.0
|
|
OD1
|
A:ASP18
|
2.5
|
19.0
|
1.0
|
|
CG
|
A:ASP18
|
2.8
|
16.8
|
1.0
|
|
CG
|
A:ASP9
|
3.2
|
22.7
|
1.0
|
|
H
|
A:ASN11
|
3.3
|
27.2
|
1.0
|
|
CG
|
A:ASN11
|
3.4
|
25.0
|
1.0
|
|
H
|
A:GLU13
|
3.4
|
24.7
|
1.0
|
|
C
|
A:GLU13
|
3.4
|
18.5
|
1.0
|
|
HA
|
A:ASP7
|
3.5
|
22.8
|
1.0
|
|
CG
|
A:ASP7
|
3.5
|
22.7
|
1.0
|
|
OD2
|
A:ASP9
|
3.6
|
23.6
|
1.0
|
|
H
|
A:ASP9
|
3.6
|
22.0
|
1.0
|
|
HA
|
A:ILE14
|
3.7
|
19.1
|
1.0
|
|
HG
|
A:SER15
|
3.9
|
28.4
|
1.0
|
|
HD22
|
A:ASN11
|
4.0
|
32.7
|
1.0
|
|
H
|
A:SER15
|
4.1
|
21.2
|
1.0
|
|
N
|
A:GLU13
|
4.1
|
20.6
|
1.0
|
|
ND2
|
A:ASN11
|
4.1
|
27.2
|
1.0
|
|
N
|
A:ASN11
|
4.1
|
22.7
|
1.0
|
|
H
|
A:GLY10
|
4.1
|
27.6
|
1.0
|
|
CA
|
A:ASP7
|
4.2
|
19.0
|
1.0
|
|
H
|
A:GLY12
|
4.2
|
27.6
|
1.0
|
|
N
|
A:ASP9
|
4.3
|
18.4
|
1.0
|
|
CB
|
A:ASP18
|
4.3
|
17.8
|
1.0
|
|
N
|
A:ILE14
|
4.3
|
18.0
|
1.0
|
|
CA
|
A:GLU13
|
4.4
|
20.6
|
1.0
|
|
CB
|
A:ASN11
|
4.4
|
24.6
|
1.0
|
|
CB
|
A:ASP7
|
4.4
|
20.6
|
1.0
|
|
HD13
|
A:ILE14
|
4.4
|
22.5
|
1.0
|
|
OD2
|
A:ASP7
|
4.4
|
20.2
|
1.0
|
|
CA
|
A:ILE14
|
4.4
|
15.9
|
1.0
|
|
HB3
|
A:ASN11
|
4.4
|
29.6
|
1.0
|
|
CB
|
A:ASP9
|
4.4
|
22.2
|
1.0
|
|
C
|
A:ASP7
|
4.5
|
19.1
|
1.0
|
|
N
|
A:GLY10
|
4.5
|
23.0
|
1.0
|
|
H
|
A:ILE8
|
4.5
|
22.3
|
1.0
|
|
N
|
A:SER15
|
4.5
|
17.6
|
1.0
|
|
HB2
|
A:GLU13
|
4.6
|
25.4
|
1.0
|
|
OG
|
A:SER15
|
4.6
|
23.7
|
1.0
|
|
N
|
A:GLY12
|
4.6
|
23.0
|
1.0
|
|
HB2
|
A:ASP7
|
4.6
|
24.7
|
1.0
|
|
CA
|
A:ASN11
|
4.6
|
23.8
|
1.0
|
|
O
|
A:HOH374
|
4.6
|
25.3
|
1.0
|
|
H
|
A:ASP18
|
4.6
|
18.4
|
1.0
|
|
N
|
A:ILE8
|
4.7
|
18.6
|
1.0
|
|
HB2
|
A:ASP18
|
4.7
|
21.4
|
1.0
|
|
HB3
|
A:SER15
|
4.7
|
25.7
|
1.0
|
|
CA
|
A:ASP9
|
4.7
|
22.3
|
1.0
|
|
HB3
|
A:ASP18
|
4.7
|
21.4
|
1.0
|
|
HB3
|
A:ASP9
|
4.8
|
26.6
|
1.0
|
|
C
|
A:ASP9
|
4.8
|
25.8
|
1.0
|
|
C
|
A:ASN11
|
4.8
|
24.0
|
1.0
|
|
C
|
A:ILE14
|
4.9
|
16.7
|
1.0
|
|
HD21
|
A:ASN11
|
4.9
|
32.7
|
1.0
|
|
Calcium binding site 2 out
of 8 in 8x39
Go back to
Calcium Binding Sites List in 8x39
Calcium binding site 2 out
of 8 in the Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum
 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 Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:17.8
occ:1.00
|
O
|
A:TYR46
|
2.3
|
23.4
|
1.0
|
|
OD1
|
A:ASP42
|
2.3
|
21.3
|
1.0
|
|
OD1
|
A:ASP40
|
2.4
|
20.7
|
1.0
|
|
OD1
|
A:ASN44
|
2.4
|
23.3
|
1.0
|
|
O
|
A:HOH317
|
2.4
|
20.1
|
1.0
|
|
OD2
|
A:ASP51
|
2.4
|
19.9
|
1.0
|
|
OD1
|
A:ASP51
|
2.5
|
18.9
|
1.0
|
|
CG
|
A:ASP51
|
2.8
|
17.0
|
1.0
|
|
CG
|
A:ASP42
|
3.2
|
23.8
|
1.0
|
|
CG
|
A:ASN44
|
3.3
|
24.3
|
1.0
|
|
H
|
A:ASN44
|
3.4
|
25.9
|
1.0
|
|
C
|
A:TYR46
|
3.5
|
23.2
|
1.0
|
|
HA
|
A:ASP40
|
3.5
|
21.1
|
1.0
|
|
HD22
|
A:ASN44
|
3.5
|
29.6
|
1.0
|
|
CG
|
A:ASP40
|
3.6
|
20.2
|
1.0
|
|
H
|
A:ASP42
|
3.6
|
23.1
|
1.0
|
|
H
|
A:TYR46
|
3.6
|
26.8
|
1.0
|
|
OD2
|
A:ASP42
|
3.6
|
21.5
|
1.0
|
|
HA
|
A:VAL47
|
3.7
|
25.2
|
1.0
|
|
ND2
|
A:ASN44
|
3.8
|
24.6
|
1.0
|
|
N
|
A:TYR46
|
4.2
|
22.4
|
1.0
|
|
H
|
A:GLY43
|
4.2
|
25.0
|
1.0
|
|
H
|
A:GLY45
|
4.2
|
26.4
|
1.0
|
|
H
|
A:ASN48
|
4.2
|
22.4
|
1.0
|
|
N
|
A:ASN44
|
4.2
|
21.6
|
1.0
|
|
CA
|
A:ASP40
|
4.2
|
17.6
|
1.0
|
|
N
|
A:ASP42
|
4.3
|
19.2
|
1.0
|
|
CB
|
A:ASP51
|
4.3
|
16.6
|
1.0
|
|
CB
|
A:ASP40
|
4.4
|
19.1
|
1.0
|
|
OD1
|
A:ASN48
|
4.4
|
20.8
|
1.0
|
|
N
|
A:VAL47
|
4.4
|
20.5
|
1.0
|
|
CA
|
A:TYR46
|
4.4
|
22.6
|
1.0
|
|
OD2
|
A:ASP40
|
4.4
|
21.9
|
1.0
|
|
CA
|
A:VAL47
|
4.5
|
21.0
|
1.0
|
|
C
|
A:ASP40
|
4.5
|
17.9
|
1.0
|
|
CB
|
A:ASP42
|
4.5
|
21.0
|
1.0
|
|
CB
|
A:ASN44
|
4.5
|
23.9
|
1.0
|
|
H
|
A:VAL41
|
4.5
|
24.2
|
1.0
|
|
N
|
A:GLY43
|
4.5
|
20.8
|
1.0
|
|
HB2
|
A:ASP40
|
4.6
|
22.9
|
1.0
|
|
HD21
|
A:ASN44
|
4.6
|
29.6
|
1.0
|
|
N
|
A:GLY45
|
4.6
|
22.0
|
1.0
|
|
H
|
A:ASP51
|
4.6
|
20.7
|
1.0
|
|
HB2
|
A:TYR46
|
4.7
|
37.3
|
1.0
|
|
N
|
A:VAL41
|
4.7
|
20.2
|
1.0
|
|
HB2
|
A:ASP51
|
4.7
|
19.9
|
1.0
|
|
CA
|
A:ASN44
|
4.7
|
22.9
|
1.0
|
|
CA
|
A:ASP42
|
4.8
|
20.4
|
1.0
|
|
HB3
|
A:ASP51
|
4.8
|
19.9
|
1.0
|
|
N
|
A:ASN48
|
4.8
|
18.7
|
1.0
|
|
HD22
|
A:ASN48
|
4.8
|
31.8
|
1.0
|
|
HB3
|
A:ASN44
|
4.8
|
28.6
|
1.0
|
|
CG
|
A:ASN48
|
4.8
|
22.5
|
1.0
|
|
C
|
A:ASP42
|
4.9
|
19.2
|
1.0
|
|
C
|
A:ASN44
|
4.9
|
22.2
|
1.0
|
|
HB3
|
A:ASP42
|
4.9
|
25.2
|
1.0
|
|
O
|
A:ASP40
|
5.0
|
20.1
|
1.0
|
|
ND2
|
A:ASN48
|
5.0
|
26.5
|
1.0
|
|
Calcium binding site 3 out
of 8 in 8x39
Go back to
Calcium Binding Sites List in 8x39
Calcium binding site 3 out
of 8 in the Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum
 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 Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:24.5
occ:1.00
|
OD1
|
A:ASP80
|
2.2
|
26.7
|
1.0
|
|
OD1
|
A:ASN82
|
2.3
|
25.9
|
1.0
|
|
O
|
A:ILE84
|
2.3
|
27.2
|
1.0
|
|
O
|
A:HOH338
|
2.3
|
25.1
|
1.0
|
|
OD1
|
A:ASP78
|
2.4
|
26.2
|
1.0
|
|
OD2
|
A:ASP89
|
2.5
|
21.1
|
1.0
|
|
OD1
|
A:ASP89
|
2.5
|
22.9
|
1.0
|
|
CG
|
A:ASP89
|
2.8
|
20.9
|
1.0
|
|
CG
|
A:ASP80
|
3.2
|
30.8
|
1.0
|
|
CG
|
A:ASN82
|
3.3
|
30.4
|
1.0
|
|
HA
|
A:ASP78
|
3.3
|
30.0
|
1.0
|
|
HG23
|
A:ILE84
|
3.3
|
43.5
|
1.0
|
|
H
|
A:ASN82
|
3.4
|
33.5
|
1.0
|
|
CG
|
A:ASP78
|
3.4
|
29.1
|
1.0
|
|
C
|
A:ILE84
|
3.5
|
27.5
|
1.0
|
|
H
|
A:ILE84
|
3.5
|
37.4
|
1.0
|
|
OD2
|
A:ASP80
|
3.5
|
30.7
|
1.0
|
|
HD22
|
A:ASN82
|
3.6
|
36.5
|
1.0
|
|
H
|
A:ASP80
|
3.6
|
30.8
|
1.0
|
|
HA
|
A:VAL85
|
3.7
|
31.6
|
1.0
|
|
ND2
|
A:ASN82
|
3.8
|
30.4
|
1.0
|
|
HG22
|
A:ILE84
|
4.0
|
43.5
|
1.0
|
|
CA
|
A:ASP78
|
4.0
|
25.0
|
1.0
|
|
CG2
|
A:ILE84
|
4.1
|
36.3
|
1.0
|
|
H
|
A:ASP86
|
4.2
|
27.9
|
1.0
|
|
H
|
A:ASN81
|
4.2
|
33.7
|
1.0
|
|
H
|
A:ILE79
|
4.2
|
28.4
|
1.0
|
|
N
|
A:ASN82
|
4.2
|
27.9
|
1.0
|
|
CB
|
A:ASP78
|
4.2
|
27.2
|
1.0
|
|
N
|
A:ILE84
|
4.2
|
31.2
|
1.0
|
|
OD2
|
A:ASP78
|
4.3
|
31.2
|
1.0
|
|
CB
|
A:ASP89
|
4.3
|
19.9
|
1.0
|
|
N
|
A:ASP80
|
4.4
|
25.7
|
1.0
|
|
OD1
|
A:ASP86
|
4.4
|
25.9
|
1.0
|
|
HB2
|
A:ASP78
|
4.4
|
32.7
|
1.0
|
|
C
|
A:ASP78
|
4.4
|
24.9
|
1.0
|
|
CA
|
A:ILE84
|
4.4
|
32.8
|
1.0
|
|
CB
|
A:ASN82
|
4.4
|
34.1
|
1.0
|
|
N
|
A:VAL85
|
4.4
|
26.8
|
1.0
|
|
N
|
A:ILE79
|
4.5
|
23.7
|
1.0
|
|
CA
|
A:VAL85
|
4.5
|
26.3
|
1.0
|
|
H
|
A:GLY83
|
4.5
|
38.9
|
1.0
|
|
N
|
A:ASN81
|
4.5
|
28.1
|
1.0
|
|
CB
|
A:ASP80
|
4.5
|
30.2
|
1.0
|
|
H
|
A:ASP89
|
4.6
|
23.3
|
1.0
|
|
HB3
|
A:ASN82
|
4.6
|
40.9
|
1.0
|
|
HD21
|
A:ASN82
|
4.6
|
36.5
|
1.0
|
|
HB2
|
A:ASP89
|
4.7
|
23.9
|
1.0
|
|
CA
|
A:ASN82
|
4.7
|
30.2
|
1.0
|
|
N
|
A:ASP86
|
4.8
|
23.2
|
1.0
|
|
HG21
|
A:ILE84
|
4.8
|
43.5
|
1.0
|
|
HB3
|
A:ASP89
|
4.8
|
23.9
|
1.0
|
|
CA
|
A:ASP80
|
4.8
|
26.9
|
1.0
|
|
C
|
A:ASP80
|
4.8
|
26.6
|
1.0
|
|
N
|
A:GLY83
|
4.8
|
32.4
|
1.0
|
|
CB
|
A:ILE84
|
4.9
|
36.1
|
1.0
|
|
N
|
A:ASP89
|
4.9
|
19.4
|
1.0
|
|
CG
|
A:ASP86
|
5.0
|
25.9
|
1.0
|
|
C
|
A:ASN82
|
5.0
|
31.0
|
1.0
|
|
HB2
|
A:ASN88
|
5.0
|
26.7
|
1.0
|
|
HA
|
A:ASP89
|
5.0
|
24.6
|
1.0
|
|
Calcium binding site 4 out
of 8 in 8x39
Go back to
Calcium Binding Sites List in 8x39
Calcium binding site 4 out
of 8 in the Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum
 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 Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca204
b:18.8
occ:1.00
|
O
|
A:VAL118
|
2.3
|
20.5
|
1.0
|
|
OD1
|
A:ASP114
|
2.3
|
24.0
|
1.0
|
|
O
|
A:HOH345
|
2.3
|
22.5
|
1.0
|
|
OD1
|
A:ASP112
|
2.3
|
20.6
|
1.0
|
|
OD1
|
A:ASN116
|
2.4
|
23.1
|
1.0
|
|
OD2
|
A:ASP123
|
2.4
|
18.4
|
1.0
|
|
OD1
|
A:ASP123
|
2.5
|
20.1
|
1.0
|
|
CG
|
A:ASP123
|
2.8
|
21.1
|
1.0
|
|
CG
|
A:ASP114
|
3.3
|
24.6
|
1.0
|
|
CG
|
A:ASN116
|
3.3
|
25.0
|
1.0
|
|
H
|
A:ASN116
|
3.4
|
29.2
|
1.0
|
|
H
|
A:VAL118
|
3.4
|
26.1
|
1.0
|
|
C
|
A:VAL118
|
3.5
|
22.0
|
1.0
|
|
H
|
A:ASP114
|
3.5
|
27.6
|
1.0
|
|
CG
|
A:ASP112
|
3.6
|
22.6
|
1.0
|
|
HD22
|
A:ASN116
|
3.6
|
30.4
|
1.0
|
|
HA
|
A:ASP112
|
3.6
|
21.0
|
1.0
|
|
OD2
|
A:ASP114
|
3.7
|
27.2
|
1.0
|
|
HA
|
A:ILE119
|
3.8
|
23.6
|
1.0
|
|
ND2
|
A:ASN116
|
3.8
|
25.4
|
1.0
|
|
HB
|
A:VAL118
|
4.1
|
26.7
|
1.0
|
|
H
|
A:ASP120
|
4.1
|
22.8
|
1.0
|
|
N
|
A:VAL118
|
4.2
|
21.7
|
1.0
|
|
HD13
|
A:ILE119
|
4.2
|
22.6
|
1.0
|
|
N
|
A:ASN116
|
4.2
|
24.3
|
1.0
|
|
H
|
A:GLY115
|
4.3
|
27.1
|
1.0
|
|
CA
|
A:ASP112
|
4.3
|
17.5
|
1.0
|
|
CA
|
A:VAL118
|
4.3
|
22.9
|
1.0
|
|
CB
|
A:ASP123
|
4.3
|
20.4
|
1.0
|
|
N
|
A:ASP114
|
4.3
|
23.0
|
1.0
|
|
OD2
|
A:ASP112
|
4.4
|
21.2
|
1.0
|
|
OD1
|
A:ASP120
|
4.4
|
23.7
|
1.0
|
|
N
|
A:ILE119
|
4.4
|
19.7
|
1.0
|
|
CB
|
A:ASP112
|
4.5
|
21.2
|
1.0
|
|
H
|
A:ALA113
|
4.5
|
24.1
|
1.0
|
|
H
|
A:ASP123
|
4.5
|
25.1
|
1.0
|
|
H
|
A:ASN117
|
4.5
|
28.1
|
1.0
|
|
CA
|
A:ILE119
|
4.5
|
19.6
|
1.0
|
|
CB
|
A:ASN116
|
4.5
|
27.2
|
1.0
|
|
C
|
A:ASP112
|
4.6
|
20.6
|
1.0
|
|
CB
|
A:ASP114
|
4.6
|
26.5
|
1.0
|
|
N
|
A:GLY115
|
4.6
|
22.6
|
1.0
|
|
HD21
|
A:ASN116
|
4.6
|
30.4
|
1.0
|
|
N
|
A:ALA113
|
4.7
|
20.1
|
1.0
|
|
CB
|
A:VAL118
|
4.7
|
22.3
|
1.0
|
|
HB3
|
A:ASN116
|
4.7
|
32.6
|
1.0
|
|
N
|
A:ASP120
|
4.7
|
19.0
|
1.0
|
|
HB2
|
A:ASP123
|
4.7
|
24.5
|
1.0
|
|
HB3
|
A:ASP123
|
4.8
|
24.5
|
1.0
|
|
HB2
|
A:ASP112
|
4.8
|
25.4
|
1.0
|
|
CA
|
A:ASN116
|
4.8
|
26.3
|
1.0
|
|
HG12
|
A:VAL118
|
4.8
|
31.1
|
1.0
|
|
N
|
A:ASN117
|
4.8
|
23.4
|
1.0
|
|
CA
|
A:ASP114
|
4.8
|
23.3
|
1.0
|
|
HB
|
A:THR122
|
4.8
|
35.2
|
1.0
|
|
C
|
A:ASP114
|
4.8
|
26.9
|
1.0
|
|
HE2
|
A:PHE33
|
4.9
|
26.5
|
1.0
|
|
C
|
A:ASN116
|
4.9
|
22.6
|
1.0
|
|
N
|
A:ASP123
|
5.0
|
21.0
|
1.0
|
|
HB3
|
A:ASP114
|
5.0
|
31.9
|
1.0
|
|
CG
|
A:ASP120
|
5.0
|
26.0
|
1.0
|
|
Calcium binding site 5 out
of 8 in 8x39
Go back to
Calcium Binding Sites List in 8x39
Calcium binding site 5 out
of 8 in the Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum
 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 Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca201
b:19.3
occ:1.00
|
OD1
|
B:ASP9
|
2.3
|
21.3
|
1.0
|
|
O
|
B:GLU13
|
2.3
|
19.6
|
1.0
|
|
O
|
B:HOH343
|
2.3
|
19.9
|
1.0
|
|
OD1
|
B:ASP7
|
2.3
|
18.5
|
1.0
|
|
OD1
|
B:ASN11
|
2.4
|
18.9
|
1.0
|
|
OD1
|
B:ASP18
|
2.4
|
17.7
|
1.0
|
|
OD2
|
B:ASP18
|
2.5
|
19.0
|
1.0
|
|
CG
|
B:ASP18
|
2.8
|
16.0
|
1.0
|
|
CG
|
B:ASP9
|
3.2
|
23.2
|
1.0
|
|
H
|
B:ASN11
|
3.3
|
24.5
|
1.0
|
|
CG
|
B:ASN11
|
3.3
|
22.1
|
1.0
|
|
HA
|
B:ASP7
|
3.4
|
21.9
|
1.0
|
|
H
|
B:GLU13
|
3.4
|
22.6
|
1.0
|
|
C
|
B:GLU13
|
3.5
|
20.1
|
1.0
|
|
CG
|
B:ASP7
|
3.5
|
18.3
|
1.0
|
|
H
|
B:ASP9
|
3.6
|
23.6
|
1.0
|
|
OD2
|
B:ASP9
|
3.7
|
23.6
|
1.0
|
|
HA
|
B:ILE14
|
3.8
|
20.5
|
1.0
|
|
HD22
|
B:ASN11
|
3.9
|
27.7
|
1.0
|
|
HG
|
B:SER15
|
3.9
|
28.6
|
1.0
|
|
H
|
B:SER15
|
4.0
|
21.8
|
1.0
|
|
ND2
|
B:ASN11
|
4.0
|
23.1
|
1.0
|
|
H
|
B:GLY10
|
4.1
|
27.2
|
1.0
|
|
N
|
B:ASN11
|
4.1
|
20.4
|
1.0
|
|
N
|
B:GLU13
|
4.1
|
18.8
|
1.0
|
|
CA
|
B:ASP7
|
4.1
|
18.2
|
1.0
|
|
H
|
B:GLY12
|
4.3
|
28.0
|
1.0
|
|
N
|
B:ASP9
|
4.3
|
19.6
|
1.0
|
|
CB
|
B:ASP18
|
4.3
|
17.5
|
1.0
|
|
CB
|
B:ASP7
|
4.3
|
19.9
|
1.0
|
|
CB
|
B:ASN11
|
4.4
|
23.4
|
1.0
|
|
OD2
|
B:ASP7
|
4.4
|
19.5
|
1.0
|
|
N
|
B:ILE14
|
4.4
|
16.5
|
1.0
|
|
HD13
|
B:ILE14
|
4.4
|
22.0
|
1.0
|
|
CA
|
B:GLU13
|
4.4
|
22.1
|
1.0
|
|
HB3
|
B:ASN11
|
4.4
|
28.1
|
1.0
|
|
CB
|
B:ASP9
|
4.4
|
23.5
|
1.0
|
|
H
|
B:ILE8
|
4.5
|
23.2
|
1.0
|
|
N
|
B:GLY10
|
4.5
|
22.6
|
1.0
|
|
CA
|
B:ILE14
|
4.5
|
17.1
|
1.0
|
|
C
|
B:ASP7
|
4.5
|
18.7
|
1.0
|
|
N
|
B:SER15
|
4.5
|
18.1
|
1.0
|
|
HB2
|
B:ASP7
|
4.6
|
23.9
|
1.0
|
|
N
|
B:ILE8
|
4.6
|
19.4
|
1.0
|
|
H
|
B:ASP18
|
4.6
|
21.7
|
1.0
|
|
CA
|
B:ASN11
|
4.6
|
24.1
|
1.0
|
|
N
|
B:GLY12
|
4.7
|
23.3
|
1.0
|
|
OG
|
B:SER15
|
4.7
|
23.8
|
1.0
|
|
HB2
|
B:GLU13
|
4.7
|
29.9
|
1.0
|
|
HB2
|
B:ASP18
|
4.7
|
21.0
|
1.0
|
|
CA
|
B:ASP9
|
4.7
|
20.7
|
1.0
|
|
HB3
|
B:ASP9
|
4.7
|
28.2
|
1.0
|
|
HB3
|
B:ASP18
|
4.7
|
21.0
|
1.0
|
|
HD21
|
B:ASN11
|
4.8
|
27.7
|
1.0
|
|
C
|
B:ASP9
|
4.8
|
22.5
|
1.0
|
|
O
|
B:HOH381
|
4.8
|
35.8
|
1.0
|
|
C
|
B:ASN11
|
4.8
|
24.9
|
1.0
|
|
C
|
B:ILE14
|
4.9
|
18.6
|
1.0
|
|
HB3
|
B:SER15
|
4.9
|
28.4
|
1.0
|
|
HA
|
B:ASP18
|
5.0
|
19.6
|
1.0
|
|
Calcium binding site 6 out
of 8 in 8x39
Go back to
Calcium Binding Sites List in 8x39
Calcium binding site 6 out
of 8 in the Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum
 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 Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca202
b:17.0
occ:1.00
|
OD1
|
B:ASP40
|
2.3
|
17.5
|
1.0
|
|
O
|
B:TYR46
|
2.3
|
20.6
|
1.0
|
|
OD1
|
B:ASP42
|
2.3
|
18.4
|
1.0
|
|
O
|
B:HOH351
|
2.4
|
19.1
|
1.0
|
|
OD2
|
B:ASP51
|
2.4
|
16.7
|
1.0
|
|
OD1
|
B:ASN44
|
2.4
|
17.8
|
1.0
|
|
OD1
|
B:ASP51
|
2.5
|
18.0
|
1.0
|
|
CG
|
B:ASP51
|
2.8
|
17.6
|
1.0
|
|
CG
|
B:ASN44
|
3.3
|
21.0
|
1.0
|
|
CG
|
B:ASP42
|
3.3
|
19.1
|
1.0
|
|
H
|
B:ASN44
|
3.3
|
21.2
|
1.0
|
|
HA
|
B:ASP40
|
3.4
|
22.6
|
1.0
|
|
HD22
|
B:ASN44
|
3.5
|
29.7
|
1.0
|
|
CG
|
B:ASP40
|
3.5
|
20.1
|
1.0
|
|
C
|
B:TYR46
|
3.5
|
20.1
|
1.0
|
|
H
|
B:ASP42
|
3.5
|
22.1
|
1.0
|
|
H
|
B:TYR46
|
3.5
|
21.6
|
1.0
|
|
ND2
|
B:ASN44
|
3.7
|
24.7
|
1.0
|
|
OD2
|
B:ASP42
|
3.7
|
19.6
|
1.0
|
|
HA
|
B:VAL47
|
3.7
|
21.3
|
1.0
|
|
N
|
B:TYR46
|
4.1
|
18.0
|
1.0
|
|
H
|
B:GLY43
|
4.1
|
23.0
|
1.0
|
|
N
|
B:ASN44
|
4.1
|
17.7
|
1.0
|
|
CA
|
B:ASP40
|
4.2
|
18.9
|
1.0
|
|
H
|
B:ASN48
|
4.2
|
19.9
|
1.0
|
|
N
|
B:ASP42
|
4.3
|
18.4
|
1.0
|
|
CB
|
B:ASP51
|
4.3
|
16.7
|
1.0
|
|
CB
|
B:ASP40
|
4.3
|
18.6
|
1.0
|
|
OD2
|
B:ASP40
|
4.3
|
18.9
|
1.0
|
|
H
|
B:GLY45
|
4.4
|
25.2
|
1.0
|
|
CA
|
B:TYR46
|
4.4
|
19.4
|
1.0
|
|
C
|
B:ASP40
|
4.4
|
17.6
|
1.0
|
|
H
|
B:VAL41
|
4.4
|
20.8
|
1.0
|
|
CB
|
B:ASN44
|
4.4
|
20.6
|
1.0
|
|
N
|
B:VAL47
|
4.4
|
18.4
|
1.0
|
|
OD1
|
B:ASN48
|
4.4
|
18.5
|
1.0
|
|
HD21
|
B:ASN44
|
4.5
|
29.7
|
1.0
|
|
CA
|
B:VAL47
|
4.5
|
17.8
|
1.0
|
|
HD22
|
B:ASN48
|
4.5
|
27.2
|
1.0
|
|
N
|
B:GLY43
|
4.5
|
19.1
|
1.0
|
|
CB
|
B:ASP42
|
4.5
|
19.0
|
1.0
|
|
HB2
|
B:ASP40
|
4.5
|
22.3
|
1.0
|
|
N
|
B:VAL41
|
4.6
|
17.3
|
1.0
|
|
HB2
|
B:TYR46
|
4.6
|
27.6
|
1.0
|
|
H
|
B:ASP51
|
4.6
|
19.5
|
1.0
|
|
HB3
|
B:ASN44
|
4.6
|
24.7
|
1.0
|
|
CA
|
B:ASN44
|
4.7
|
18.9
|
1.0
|
|
N
|
B:GLY45
|
4.7
|
21.0
|
1.0
|
|
HB2
|
B:ASP51
|
4.7
|
20.1
|
1.0
|
|
HB3
|
B:ASP51
|
4.7
|
20.1
|
1.0
|
|
CA
|
B:ASP42
|
4.7
|
17.8
|
1.0
|
|
N
|
B:ASN48
|
4.8
|
16.6
|
1.0
|
|
ND2
|
B:ASN48
|
4.8
|
22.7
|
1.0
|
|
CG
|
B:ASN48
|
4.8
|
19.8
|
1.0
|
|
C
|
B:ASP42
|
4.8
|
18.9
|
1.0
|
|
C
|
B:ASN44
|
4.9
|
19.8
|
1.0
|
|
O
|
B:ASP40
|
4.9
|
18.0
|
1.0
|
|
HB3
|
B:ASP42
|
4.9
|
22.8
|
1.0
|
|
HA
|
B:ASP51
|
5.0
|
18.9
|
1.0
|
|
HG22
|
B:VAL47
|
5.0
|
21.1
|
1.0
|
|
Calcium binding site 7 out
of 8 in 8x39
Go back to
Calcium Binding Sites List in 8x39
Calcium binding site 7 out
of 8 in the Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum
 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 Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca203
b:24.3
occ:1.00
|
OD1
|
B:ASP80
|
2.1
|
29.1
|
1.0
|
|
OD1
|
B:ASP78
|
2.3
|
25.3
|
1.0
|
|
OD1
|
B:ASN82
|
2.3
|
29.2
|
1.0
|
|
O
|
B:ILE84
|
2.3
|
26.1
|
1.0
|
|
O
|
B:HOH314
|
2.4
|
24.6
|
1.0
|
|
OD2
|
B:ASP89
|
2.5
|
22.0
|
1.0
|
|
OD1
|
B:ASP89
|
2.5
|
21.9
|
1.0
|
|
CG
|
B:ASP89
|
2.8
|
21.0
|
1.0
|
|
CG
|
B:ASP80
|
3.1
|
30.7
|
1.0
|
|
CG
|
B:ASN82
|
3.2
|
29.4
|
1.0
|
|
HA
|
B:ASP78
|
3.2
|
28.0
|
1.0
|
|
H
|
B:ASN82
|
3.3
|
35.7
|
1.0
|
|
CG
|
B:ASP78
|
3.4
|
28.4
|
1.0
|
|
OD2
|
B:ASP80
|
3.5
|
31.9
|
1.0
|
|
HD22
|
B:ASN82
|
3.5
|
37.3
|
1.0
|
|
H
|
B:ASP80
|
3.5
|
34.4
|
1.0
|
|
H
|
B:ILE84
|
3.5
|
36.3
|
1.0
|
|
C
|
B:ILE84
|
3.5
|
27.8
|
1.0
|
|
HA
|
B:VAL85
|
3.7
|
26.6
|
1.0
|
|
ND2
|
B:ASN82
|
3.7
|
31.1
|
1.0
|
|
HG13
|
B:ILE84
|
3.8
|
43.3
|
1.0
|
|
H
|
B:ILE79
|
4.0
|
28.8
|
1.0
|
|
CA
|
B:ASP78
|
4.0
|
23.3
|
1.0
|
|
H
|
B:ASP86
|
4.1
|
25.9
|
1.0
|
|
N
|
B:ASN82
|
4.1
|
29.7
|
1.0
|
|
H
|
B:ASN81
|
4.2
|
37.1
|
1.0
|
|
CB
|
B:ASP78
|
4.2
|
23.5
|
1.0
|
|
N
|
B:ILE84
|
4.2
|
30.2
|
1.0
|
|
N
|
B:ASP80
|
4.3
|
28.7
|
1.0
|
|
OD2
|
B:ASP78
|
4.3
|
29.1
|
1.0
|
|
HG12
|
B:ILE84
|
4.3
|
43.3
|
1.0
|
|
CB
|
B:ASP89
|
4.3
|
20.1
|
1.0
|
|
CB
|
B:ASN82
|
4.3
|
34.9
|
1.0
|
|
N
|
B:ILE79
|
4.4
|
24.0
|
1.0
|
|
H
|
B:GLY83
|
4.4
|
36.0
|
1.0
|
|
HB2
|
B:ASP78
|
4.4
|
28.2
|
1.0
|
|
OD1
|
B:ASP86
|
4.4
|
23.7
|
1.0
|
|
C
|
B:ASP78
|
4.4
|
26.8
|
1.0
|
|
N
|
B:VAL85
|
4.4
|
27.8
|
1.0
|
|
CB
|
B:ASP80
|
4.4
|
32.6
|
1.0
|
|
CA
|
B:VAL85
|
4.5
|
22.1
|
1.0
|
|
CG1
|
B:ILE84
|
4.5
|
36.1
|
1.0
|
|
HD21
|
B:ASN82
|
4.5
|
37.3
|
1.0
|
|
HB3
|
B:ASN82
|
4.5
|
41.9
|
1.0
|
|
CA
|
B:ILE84
|
4.5
|
29.8
|
1.0
|
|
N
|
B:ASN81
|
4.5
|
30.9
|
1.0
|
|
H
|
B:ASP89
|
4.5
|
24.3
|
1.0
|
|
CA
|
B:ASN82
|
4.7
|
32.0
|
1.0
|
|
HB2
|
B:ASP89
|
4.7
|
24.1
|
1.0
|
|
CA
|
B:ASP80
|
4.7
|
29.6
|
1.0
|
|
HB3
|
B:ASP89
|
4.7
|
24.1
|
1.0
|
|
N
|
B:GLY83
|
4.7
|
30.0
|
1.0
|
|
C
|
B:ASP80
|
4.8
|
32.6
|
1.0
|
|
N
|
B:ASP86
|
4.8
|
21.6
|
1.0
|
|
C
|
B:ASN82
|
4.9
|
31.6
|
1.0
|
|
O
|
B:GLY77
|
4.9
|
25.7
|
1.0
|
|
HG22
|
B:VAL85
|
4.9
|
31.3
|
1.0
|
|
HB3
|
B:ASP80
|
4.9
|
39.2
|
1.0
|
|
N
|
B:ASP89
|
4.9
|
20.2
|
1.0
|
|
HA
|
B:ASP89
|
5.0
|
24.8
|
1.0
|
|
Calcium binding site 8 out
of 8 in 8x39
Go back to
Calcium Binding Sites List in 8x39
Calcium binding site 8 out
of 8 in the Crystal Structure of Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum
 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 Cellulosomal Double-Dockerin Module of CLO1313_0689 From Clostridium Thermocellum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca204
b:20.8
occ:1.00
|
OD1
|
B:ASP114
|
2.3
|
27.6
|
1.0
|
|
O
|
B:VAL118
|
2.3
|
22.8
|
1.0
|
|
O
|
B:HOH342
|
2.3
|
22.6
|
1.0
|
|
OD1
|
B:ASP112
|
2.4
|
21.6
|
1.0
|
|
OD2
|
B:ASP123
|
2.4
|
19.9
|
1.0
|
|
OD1
|
B:ASN116
|
2.4
|
23.4
|
1.0
|
|
OD1
|
B:ASP123
|
2.5
|
19.0
|
1.0
|
|
CG
|
B:ASP123
|
2.8
|
19.8
|
1.0
|
|
CG
|
B:ASP114
|
3.3
|
27.7
|
1.0
|
|
CG
|
B:ASN116
|
3.4
|
27.1
|
1.0
|
|
H
|
B:VAL118
|
3.5
|
29.5
|
1.0
|
|
C
|
B:VAL118
|
3.5
|
22.6
|
1.0
|
|
H
|
B:ASP114
|
3.5
|
33.2
|
1.0
|
|
H
|
B:ASN116
|
3.5
|
32.6
|
1.0
|
|
CG
|
B:ASP112
|
3.6
|
21.7
|
1.0
|
|
HD22
|
B:ASN116
|
3.6
|
39.4
|
1.0
|
|
HA
|
B:ASP112
|
3.6
|
24.7
|
1.0
|
|
HA
|
B:ILE119
|
3.6
|
26.0
|
1.0
|
|
OD2
|
B:ASP114
|
3.8
|
28.2
|
1.0
|
|
HD13
|
B:ILE119
|
3.9
|
22.7
|
1.0
|
|
ND2
|
B:ASN116
|
3.9
|
32.8
|
1.0
|
|
HB
|
B:VAL118
|
4.1
|
34.5
|
1.0
|
|
H
|
B:ASP120
|
4.1
|
28.6
|
1.0
|
|
H
|
B:ALA113
|
4.2
|
28.2
|
1.0
|
|
N
|
B:VAL118
|
4.2
|
24.6
|
1.0
|
|
OD2
|
B:ASP112
|
4.3
|
21.1
|
1.0
|
|
CB
|
B:ASP123
|
4.3
|
18.8
|
1.0
|
|
CA
|
B:ASP112
|
4.3
|
20.6
|
1.0
|
|
N
|
B:ASP114
|
4.4
|
27.6
|
1.0
|
|
H
|
B:GLY115
|
4.4
|
32.2
|
1.0
|
|
N
|
B:ASN116
|
4.4
|
27.1
|
1.0
|
|
CA
|
B:VAL118
|
4.4
|
24.2
|
1.0
|
|
N
|
B:ILE119
|
4.4
|
21.9
|
1.0
|
|
CA
|
B:ILE119
|
4.4
|
21.7
|
1.0
|
|
OD1
|
B:ASP120
|
4.4
|
25.7
|
1.0
|
|
H
|
B:ASP123
|
4.4
|
24.3
|
1.0
|
|
CB
|
B:ASP112
|
4.5
|
18.9
|
1.0
|
|
N
|
B:ALA113
|
4.5
|
23.5
|
1.0
|
|
HB
|
B:THR122
|
4.6
|
28.4
|
1.0
|
|
H
|
B:ASN117
|
4.6
|
27.0
|
1.0
|
|
CB
|
B:ASP114
|
4.6
|
30.6
|
1.0
|
|
CB
|
B:ASN116
|
4.7
|
25.2
|
1.0
|
|
C
|
B:ASP112
|
4.7
|
22.3
|
1.0
|
|
N
|
B:GLY115
|
4.7
|
26.9
|
1.0
|
|
N
|
B:ASP120
|
4.7
|
23.8
|
1.0
|
|
HD21
|
B:ASN116
|
4.7
|
39.4
|
1.0
|
|
CB
|
B:VAL118
|
4.7
|
28.8
|
1.0
|
|
HB2
|
B:ASP123
|
4.7
|
22.6
|
1.0
|
|
HB3
|
B:ASP123
|
4.8
|
22.6
|
1.0
|
|
HE2
|
B:PHE33
|
4.8
|
27.8
|
1.0
|
|
CD1
|
B:ILE119
|
4.8
|
18.9
|
1.0
|
|
HB2
|
B:ASP112
|
4.8
|
22.7
|
1.0
|
|
CA
|
B:ASP114
|
4.9
|
27.1
|
1.0
|
|
N
|
B:ASN117
|
4.9
|
22.5
|
1.0
|
|
N
|
B:ASP123
|
4.9
|
20.2
|
1.0
|
|
CA
|
B:ASN116
|
4.9
|
25.9
|
1.0
|
|
CG
|
B:ASP120
|
4.9
|
26.0
|
1.0
|
|
C
|
B:ASP114
|
4.9
|
28.1
|
1.0
|
|
HB3
|
B:ASN116
|
4.9
|
30.3
|
1.0
|
|
HD12
|
B:ILE119
|
5.0
|
22.7
|
1.0
|
|
HG12
|
B:VAL118
|
5.0
|
37.6
|
1.0
|
|
Reference:
C.Chen,
H.Yang,
S.Dong,
C.You,
S.Morais,
E.A.Bayer,
Y.J.Liu,
J.Xuan,
Q.Cui,
I.Mizrahi,
Y.Feng.
A Cellulosomal Double-Dockerin Module From Clostridium Thermocellum Shows Distinct Structural and Cohesin-Binding Features. Protein Sci. V. 33 E4937 2024.
ISSN: ESSN 1469-896X
PubMed: 38501488
DOI: 10.1002/PRO.4937
Page generated: Fri Jul 19 12:41:24 2024
|
