Calcium in PDB 6d5b: Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
Protein crystallography data
The structure of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321, PDB code: 6d5b
was solved by
P.M.Alahuhta,
V.V.Lunin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
85.91 /
2.00
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.167,
86.199,
86.567,
83.87,
83.93,
60.55
|
|
R / Rfree (%)
|
17.8 /
24.3
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
(pdb code 6d5b). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321, PDB code: 6d5b:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 6d5b
Go back to
Calcium Binding Sites List in 6d5b
Calcium binding site 1 out
of 12 in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca201
b:31.1
occ:1.00
|
O
|
A:ASN133
|
2.3
|
29.5
|
1.0
|
|
O
|
A:THR61
|
2.4
|
23.1
|
1.0
|
|
OD1
|
A:ASN136
|
2.4
|
34.8
|
1.0
|
|
OD2
|
A:ASP63
|
2.5
|
30.4
|
1.0
|
|
O
|
A:HOH365
|
2.5
|
27.8
|
1.0
|
|
OG1
|
A:THR61
|
2.5
|
27.4
|
1.0
|
|
OD1
|
A:ASP137
|
2.6
|
31.1
|
1.0
|
|
OD1
|
A:ASP63
|
2.7
|
35.0
|
1.0
|
|
CG
|
A:ASP63
|
2.9
|
29.9
|
1.0
|
|
C
|
A:THR61
|
3.4
|
24.4
|
1.0
|
|
C
|
A:ASN133
|
3.4
|
27.2
|
1.0
|
|
CG
|
A:ASP137
|
3.4
|
27.4
|
1.0
|
|
CG
|
A:ASN136
|
3.5
|
35.6
|
1.0
|
|
CB
|
A:THR61
|
3.5
|
25.8
|
1.0
|
|
OD2
|
A:ASP137
|
3.7
|
27.2
|
1.0
|
|
CA
|
A:THR61
|
3.8
|
23.5
|
1.0
|
|
N
|
A:THR61
|
3.9
|
23.5
|
1.0
|
|
ND2
|
A:ASN136
|
3.9
|
32.8
|
1.0
|
|
N
|
A:ASN133
|
4.0
|
33.1
|
1.0
|
|
CA
|
A:ASN133
|
4.1
|
32.4
|
1.0
|
|
CB
|
A:ASN133
|
4.3
|
32.9
|
1.0
|
|
CB
|
A:ASP63
|
4.3
|
30.3
|
1.0
|
|
O
|
A:ASN136
|
4.4
|
23.5
|
1.0
|
|
N
|
A:GLN134
|
4.4
|
24.6
|
1.0
|
|
C
|
A:ASN136
|
4.4
|
26.4
|
1.0
|
|
N
|
A:VAL62
|
4.5
|
23.5
|
1.0
|
|
CA
|
A:GLN134
|
4.5
|
26.7
|
1.0
|
|
N
|
A:ASP137
|
4.6
|
24.2
|
1.0
|
|
N
|
A:ASP63
|
4.6
|
27.4
|
1.0
|
|
CB
|
A:ASP137
|
4.7
|
27.6
|
1.0
|
|
CB
|
A:ASN136
|
4.8
|
30.5
|
1.0
|
|
N
|
A:ASN136
|
4.8
|
28.7
|
1.0
|
|
C
|
A:VAL62
|
4.8
|
28.1
|
1.0
|
|
CG2
|
A:THR61
|
4.8
|
28.2
|
1.0
|
|
CG
|
A:ASN133
|
4.9
|
37.5
|
1.0
|
|
C
|
A:GLN134
|
4.9
|
27.1
|
1.0
|
|
CA
|
A:ASP137
|
4.9
|
26.9
|
1.0
|
|
CA
|
A:ASN136
|
4.9
|
29.8
|
1.0
|
|
Calcium binding site 2 out
of 12 in 6d5b
Go back to
Calcium Binding Sites List in 6d5b
Calcium binding site 2 out
of 12 in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca201
b:29.4
occ:1.00
|
O
|
B:ASN133
|
2.3
|
29.9
|
1.0
|
|
OD1
|
B:ASN136
|
2.3
|
33.5
|
1.0
|
|
OD1
|
B:ASP137
|
2.4
|
27.0
|
1.0
|
|
O
|
B:THR61
|
2.4
|
25.9
|
1.0
|
|
OD2
|
B:ASP63
|
2.5
|
30.6
|
1.0
|
|
O
|
B:HOH307
|
2.5
|
24.5
|
1.0
|
|
OG1
|
B:THR61
|
2.6
|
24.1
|
1.0
|
|
OD1
|
B:ASP63
|
2.8
|
27.7
|
1.0
|
|
CG
|
B:ASP63
|
3.0
|
27.8
|
1.0
|
|
CG
|
B:ASP137
|
3.3
|
27.0
|
1.0
|
|
C
|
B:THR61
|
3.3
|
23.3
|
1.0
|
|
CG
|
B:ASN136
|
3.4
|
32.1
|
1.0
|
|
C
|
B:ASN133
|
3.5
|
27.8
|
1.0
|
|
CB
|
B:THR61
|
3.5
|
26.9
|
1.0
|
|
OD2
|
B:ASP137
|
3.5
|
27.5
|
1.0
|
|
CA
|
B:THR61
|
3.7
|
24.9
|
1.0
|
|
N
|
B:THR61
|
3.7
|
23.1
|
1.0
|
|
ND2
|
B:ASN136
|
3.8
|
30.5
|
1.0
|
|
N
|
B:ASN133
|
4.0
|
26.4
|
1.0
|
|
CA
|
B:ASN133
|
4.2
|
31.7
|
1.0
|
|
CB
|
B:ASN133
|
4.3
|
29.7
|
1.0
|
|
C
|
B:ASN136
|
4.4
|
29.7
|
1.0
|
|
CB
|
B:ASP63
|
4.4
|
26.6
|
1.0
|
|
O
|
B:ASN136
|
4.4
|
27.4
|
1.0
|
|
N
|
B:GLN134
|
4.5
|
28.1
|
1.0
|
|
N
|
B:VAL62
|
4.5
|
23.3
|
1.0
|
|
N
|
B:ASP137
|
4.5
|
27.9
|
1.0
|
|
CB
|
B:ASP137
|
4.6
|
26.4
|
1.0
|
|
N
|
B:ASP63
|
4.6
|
26.0
|
1.0
|
|
CA
|
B:GLN134
|
4.6
|
26.3
|
1.0
|
|
CB
|
B:ASN136
|
4.6
|
29.0
|
1.0
|
|
CA
|
B:ASP137
|
4.8
|
27.3
|
1.0
|
|
C
|
B:VAL62
|
4.8
|
25.1
|
1.0
|
|
CG2
|
B:THR61
|
4.8
|
27.7
|
1.0
|
|
CA
|
B:ASN136
|
4.8
|
27.9
|
1.0
|
|
N
|
B:ASN136
|
4.8
|
27.4
|
1.0
|
|
O
|
B:HOH305
|
4.9
|
38.1
|
0.9
|
|
C
|
B:TYR60
|
5.0
|
23.2
|
1.0
|
|
Calcium binding site 3 out
of 12 in 6d5b
Go back to
Calcium Binding Sites List in 6d5b
Calcium binding site 3 out
of 12 in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca201
b:33.6
occ:1.00
|
OG1
|
C:THR61
|
2.2
|
27.1
|
1.0
|
|
OD1
|
C:ASP137
|
2.4
|
27.1
|
1.0
|
|
O
|
C:ASN133
|
2.4
|
27.1
|
1.0
|
|
O
|
C:THR61
|
2.4
|
28.2
|
1.0
|
|
O
|
C:HOH308
|
2.5
|
23.9
|
1.0
|
|
OD1
|
C:ASN136
|
2.5
|
45.4
|
1.0
|
|
OD2
|
C:ASP63
|
2.6
|
40.8
|
1.0
|
|
OD1
|
C:ASP63
|
2.6
|
32.8
|
1.0
|
|
CG
|
C:ASP63
|
2.9
|
37.0
|
1.0
|
|
CG
|
C:ASP137
|
3.3
|
28.3
|
1.0
|
|
C
|
C:THR61
|
3.3
|
28.4
|
1.0
|
|
CB
|
C:THR61
|
3.4
|
27.1
|
1.0
|
|
C
|
C:ASN133
|
3.6
|
29.3
|
1.0
|
|
CG
|
C:ASN136
|
3.6
|
43.8
|
1.0
|
|
OD2
|
C:ASP137
|
3.7
|
27.5
|
1.0
|
|
CA
|
C:THR61
|
3.7
|
28.0
|
1.0
|
|
N
|
C:THR61
|
3.8
|
29.7
|
1.0
|
|
ND2
|
C:ASN136
|
4.1
|
46.5
|
1.0
|
|
N
|
C:ASN133
|
4.2
|
35.7
|
1.0
|
|
CA
|
C:ASN133
|
4.3
|
33.4
|
1.0
|
|
CB
|
C:ASN133
|
4.4
|
34.3
|
1.0
|
|
CB
|
C:ASP63
|
4.4
|
35.4
|
1.0
|
|
C
|
C:ASN136
|
4.5
|
35.2
|
1.0
|
|
O
|
C:ASN136
|
4.5
|
34.0
|
1.0
|
|
N
|
C:VAL62
|
4.5
|
30.6
|
1.0
|
|
CG2
|
C:THR61
|
4.6
|
26.0
|
1.0
|
|
N
|
C:ASP137
|
4.6
|
30.5
|
1.0
|
|
N
|
C:GLN134
|
4.6
|
30.1
|
1.0
|
|
CB
|
C:ASP137
|
4.6
|
28.2
|
1.0
|
|
N
|
C:ASP63
|
4.7
|
35.0
|
1.0
|
|
CA
|
C:GLN134
|
4.8
|
33.1
|
1.0
|
|
CA
|
C:ASP137
|
4.8
|
30.1
|
1.0
|
|
N
|
C:ASN136
|
4.8
|
35.1
|
1.0
|
|
CB
|
C:ASN136
|
4.8
|
44.7
|
1.0
|
|
C
|
C:VAL62
|
4.9
|
29.8
|
1.0
|
|
CA
|
C:ASN136
|
4.9
|
38.0
|
1.0
|
|
Calcium binding site 4 out
of 12 in 6d5b
Go back to
Calcium Binding Sites List in 6d5b
Calcium binding site 4 out
of 12 in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca201
b:25.5
occ:1.00
|
OD1
|
D:ASP137
|
2.3
|
24.8
|
1.0
|
|
O
|
D:ASN133
|
2.4
|
21.2
|
1.0
|
|
OD1
|
D:ASN136
|
2.4
|
30.6
|
1.0
|
|
O
|
D:THR61
|
2.4
|
22.6
|
1.0
|
|
OD2
|
D:ASP63
|
2.4
|
26.7
|
1.0
|
|
O
|
D:HOH346
|
2.4
|
25.9
|
1.0
|
|
OG1
|
D:THR61
|
2.5
|
20.7
|
1.0
|
|
OD1
|
D:ASP63
|
2.6
|
26.7
|
1.0
|
|
CG
|
D:ASP63
|
2.8
|
27.4
|
1.0
|
|
CG
|
D:ASP137
|
3.3
|
26.1
|
1.0
|
|
C
|
D:THR61
|
3.3
|
22.3
|
1.0
|
|
C
|
D:ASN133
|
3.5
|
25.1
|
1.0
|
|
CG
|
D:ASN136
|
3.5
|
28.6
|
1.0
|
|
CB
|
D:THR61
|
3.6
|
22.6
|
1.0
|
|
OD2
|
D:ASP137
|
3.6
|
26.6
|
1.0
|
|
CA
|
D:THR61
|
3.7
|
20.9
|
1.0
|
|
N
|
D:THR61
|
3.8
|
20.9
|
1.0
|
|
ND2
|
D:ASN136
|
4.0
|
26.5
|
1.0
|
|
N
|
D:ASN133
|
4.0
|
29.4
|
1.0
|
|
CA
|
D:ASN133
|
4.2
|
26.2
|
1.0
|
|
CB
|
D:ASN133
|
4.3
|
27.8
|
1.0
|
|
CB
|
D:ASP63
|
4.3
|
26.6
|
1.0
|
|
C
|
D:ASN136
|
4.4
|
27.5
|
1.0
|
|
O
|
D:ASN136
|
4.5
|
30.3
|
1.0
|
|
N
|
D:GLN134
|
4.5
|
23.1
|
1.0
|
|
N
|
D:VAL62
|
4.5
|
21.1
|
1.0
|
|
CB
|
D:ASP137
|
4.6
|
24.3
|
1.0
|
|
CA
|
D:GLN134
|
4.6
|
22.9
|
1.0
|
|
N
|
D:ASP63
|
4.6
|
23.9
|
1.0
|
|
N
|
D:ASP137
|
4.7
|
26.4
|
1.0
|
|
CB
|
D:ASN136
|
4.7
|
28.1
|
1.0
|
|
N
|
D:ASN136
|
4.8
|
25.8
|
1.0
|
|
C
|
D:VAL62
|
4.8
|
24.4
|
1.0
|
|
CG2
|
D:THR61
|
4.8
|
21.2
|
1.0
|
|
CA
|
D:ASP137
|
4.8
|
25.1
|
1.0
|
|
CG
|
D:ASN133
|
4.9
|
29.6
|
1.0
|
|
CA
|
D:ASN136
|
4.9
|
27.9
|
1.0
|
|
C
|
D:GLN134
|
4.9
|
25.2
|
1.0
|
|
CB
|
D:TYR132
|
5.0
|
23.9
|
1.0
|
|
Calcium binding site 5 out
of 12 in 6d5b
Go back to
Calcium Binding Sites List in 6d5b
Calcium binding site 5 out
of 12 in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca201
b:21.8
occ:1.00
|
OG1
|
E:THR61
|
2.2
|
17.3
|
1.0
|
|
OD1
|
E:ASP137
|
2.3
|
15.7
|
1.0
|
|
O
|
E:ASN133
|
2.4
|
19.0
|
1.0
|
|
O
|
E:THR61
|
2.4
|
18.2
|
1.0
|
|
OD2
|
E:ASP63
|
2.5
|
25.3
|
1.0
|
|
OD1
|
E:ASN136
|
2.5
|
24.9
|
1.0
|
|
O
|
E:HOH376
|
2.6
|
20.0
|
1.0
|
|
OD1
|
E:ASP63
|
2.7
|
23.1
|
1.0
|
|
CG
|
E:ASP63
|
2.9
|
23.4
|
1.0
|
|
C
|
E:THR61
|
3.3
|
20.0
|
1.0
|
|
CB
|
E:THR61
|
3.3
|
20.1
|
1.0
|
|
CG
|
E:ASP137
|
3.4
|
16.9
|
1.0
|
|
C
|
E:ASN133
|
3.5
|
19.4
|
1.0
|
|
CG
|
E:ASN136
|
3.5
|
22.3
|
1.0
|
|
CA
|
E:THR61
|
3.6
|
17.6
|
1.0
|
|
N
|
E:THR61
|
3.7
|
18.3
|
1.0
|
|
OD2
|
E:ASP137
|
3.8
|
17.1
|
1.0
|
|
ND2
|
E:ASN136
|
4.0
|
20.6
|
1.0
|
|
N
|
E:ASN133
|
4.1
|
21.0
|
1.0
|
|
CA
|
E:ASN133
|
4.2
|
21.7
|
1.0
|
|
O
|
E:ASN136
|
4.3
|
18.0
|
1.0
|
|
C
|
E:ASN136
|
4.4
|
18.8
|
1.0
|
|
CB
|
E:ASP63
|
4.4
|
23.9
|
1.0
|
|
CB
|
E:ASN133
|
4.4
|
22.4
|
1.0
|
|
N
|
E:GLN134
|
4.4
|
20.0
|
1.0
|
|
N
|
E:ASP137
|
4.5
|
18.4
|
1.0
|
|
CG2
|
E:THR61
|
4.5
|
19.4
|
1.0
|
|
N
|
E:VAL62
|
4.5
|
20.9
|
1.0
|
|
CA
|
E:GLN134
|
4.6
|
20.9
|
1.0
|
|
CB
|
E:ASP137
|
4.6
|
18.7
|
1.0
|
|
N
|
E:ASP63
|
4.7
|
23.4
|
1.0
|
|
CA
|
E:ASP137
|
4.8
|
19.3
|
1.0
|
|
CB
|
E:ASN136
|
4.8
|
22.2
|
1.0
|
|
O
|
E:HOH378
|
4.8
|
33.1
|
1.0
|
|
C
|
E:VAL62
|
4.9
|
22.1
|
1.0
|
|
N
|
E:ASN136
|
4.9
|
20.0
|
1.0
|
|
CA
|
E:ASN136
|
4.9
|
19.0
|
1.0
|
|
C
|
E:TYR60
|
5.0
|
17.8
|
1.0
|
|
Calcium binding site 6 out
of 12 in 6d5b
Go back to
Calcium Binding Sites List in 6d5b
Calcium binding site 6 out
of 12 in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca201
b:22.3
occ:1.00
|
OD1
|
F:ASN136
|
2.3
|
31.8
|
1.0
|
|
O
|
F:THR61
|
2.3
|
21.8
|
1.0
|
|
O
|
F:ASN133
|
2.3
|
19.2
|
1.0
|
|
O
|
F:HOH393
|
2.4
|
22.8
|
1.0
|
|
OD2
|
F:ASP63
|
2.4
|
23.3
|
1.0
|
|
OD1
|
F:ASP137
|
2.4
|
19.1
|
1.0
|
|
OG1
|
F:THR61
|
2.5
|
21.2
|
1.0
|
|
OD1
|
F:ASP63
|
3.0
|
27.0
|
1.0
|
|
CG
|
F:ASP63
|
3.0
|
22.6
|
1.0
|
|
C
|
F:THR61
|
3.3
|
21.5
|
1.0
|
|
CG
|
F:ASP137
|
3.4
|
20.6
|
1.0
|
|
CG
|
F:ASN136
|
3.4
|
26.8
|
1.0
|
|
C
|
F:ASN133
|
3.4
|
22.1
|
1.0
|
|
CB
|
F:THR61
|
3.5
|
22.6
|
1.0
|
|
CA
|
F:THR61
|
3.7
|
21.7
|
1.0
|
|
N
|
F:THR61
|
3.8
|
23.3
|
1.0
|
|
OD2
|
F:ASP137
|
3.9
|
23.7
|
1.0
|
|
ND2
|
F:ASN136
|
4.0
|
27.6
|
1.0
|
|
N
|
F:ASN133
|
4.1
|
24.9
|
1.0
|
|
CA
|
F:ASN133
|
4.2
|
23.2
|
1.0
|
|
CB
|
F:ASN133
|
4.3
|
23.6
|
1.0
|
|
O
|
F:ASN136
|
4.4
|
23.2
|
1.0
|
|
C
|
F:ASN136
|
4.4
|
22.6
|
1.0
|
|
N
|
F:GLN134
|
4.4
|
20.9
|
1.0
|
|
CB
|
F:ASP63
|
4.5
|
23.0
|
1.0
|
|
CA
|
F:GLN134
|
4.5
|
20.1
|
1.0
|
|
N
|
F:VAL62
|
4.5
|
19.5
|
1.0
|
|
N
|
F:ASP137
|
4.6
|
21.1
|
1.0
|
|
CB
|
F:ASP137
|
4.7
|
21.9
|
1.0
|
|
N
|
F:ASP63
|
4.7
|
18.8
|
1.0
|
|
CB
|
F:ASN136
|
4.7
|
24.9
|
1.0
|
|
N
|
F:ASN136
|
4.8
|
23.0
|
1.0
|
|
O
|
F:HOH301
|
4.8
|
48.5
|
1.0
|
|
CG2
|
F:THR61
|
4.8
|
24.1
|
1.0
|
|
CA
|
F:ASN136
|
4.8
|
22.5
|
1.0
|
|
C
|
F:GLN134
|
4.8
|
21.7
|
1.0
|
|
CA
|
F:ASP137
|
4.8
|
22.0
|
1.0
|
|
CG
|
F:ASN133
|
4.9
|
25.8
|
1.0
|
|
C
|
F:VAL62
|
4.9
|
19.1
|
1.0
|
|
Calcium binding site 7 out
of 12 in 6d5b
Go back to
Calcium Binding Sites List in 6d5b
Calcium binding site 7 out
of 12 in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca201
b:32.5
occ:1.00
|
O
|
G:ASN133
|
2.1
|
24.8
|
1.0
|
|
O
|
G:THR61
|
2.2
|
26.2
|
1.0
|
|
OD1
|
G:ASN136
|
2.3
|
35.8
|
1.0
|
|
OG1
|
G:THR61
|
2.4
|
27.4
|
1.0
|
|
OD1
|
G:ASP137
|
2.4
|
27.6
|
1.0
|
|
O
|
G:HOH330
|
2.4
|
26.4
|
1.0
|
|
OD2
|
G:ASP63
|
2.5
|
37.4
|
1.0
|
|
OD1
|
G:ASP63
|
2.6
|
33.5
|
1.0
|
|
CG
|
G:ASP63
|
2.8
|
33.7
|
1.0
|
|
C
|
G:THR61
|
3.2
|
30.1
|
1.0
|
|
CG
|
G:ASN136
|
3.3
|
34.4
|
1.0
|
|
C
|
G:ASN133
|
3.4
|
29.9
|
1.0
|
|
CG
|
G:ASP137
|
3.4
|
28.1
|
1.0
|
|
CB
|
G:THR61
|
3.5
|
29.2
|
1.0
|
|
OD2
|
G:ASP137
|
3.6
|
24.5
|
1.0
|
|
CA
|
G:THR61
|
3.7
|
30.1
|
1.0
|
|
ND2
|
G:ASN136
|
3.8
|
34.8
|
1.0
|
|
N
|
G:THR61
|
3.9
|
28.8
|
1.0
|
|
N
|
G:ASN133
|
4.1
|
30.8
|
1.0
|
|
CA
|
G:ASN133
|
4.2
|
29.7
|
1.0
|
|
O
|
G:ASN136
|
4.3
|
33.4
|
1.0
|
|
CB
|
G:ASP63
|
4.3
|
35.9
|
1.0
|
|
C
|
G:ASN136
|
4.3
|
29.4
|
1.0
|
|
N
|
G:GLN134
|
4.3
|
28.3
|
1.0
|
|
CB
|
G:ASN133
|
4.4
|
32.2
|
1.0
|
|
N
|
G:VAL62
|
4.4
|
31.8
|
1.0
|
|
CA
|
G:GLN134
|
4.5
|
30.3
|
1.0
|
|
CB
|
G:ASN136
|
4.6
|
32.0
|
1.0
|
|
N
|
G:ASP137
|
4.6
|
26.6
|
1.0
|
|
N
|
G:ASP63
|
4.6
|
35.0
|
1.0
|
|
C
|
G:VAL62
|
4.7
|
34.9
|
1.0
|
|
CB
|
G:ASP137
|
4.7
|
25.3
|
1.0
|
|
N
|
G:ASN136
|
4.7
|
29.3
|
1.0
|
|
CG2
|
G:THR61
|
4.7
|
29.8
|
1.0
|
|
CA
|
G:ASN136
|
4.8
|
30.5
|
1.0
|
|
CA
|
G:VAL62
|
4.9
|
35.5
|
1.0
|
|
CA
|
G:ASP137
|
4.9
|
25.1
|
1.0
|
|
C
|
G:GLN134
|
4.9
|
30.1
|
1.0
|
|
CA
|
G:ASP63
|
5.0
|
35.1
|
1.0
|
|
CG
|
G:ASN133
|
5.0
|
36.1
|
1.0
|
|
CB
|
G:TYR132
|
5.0
|
29.5
|
1.0
|
|
Calcium binding site 8 out
of 12 in 6d5b
Go back to
Calcium Binding Sites List in 6d5b
Calcium binding site 8 out
of 12 in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca201
b:23.9
occ:1.00
|
O
|
H:ASN133
|
2.3
|
20.7
|
1.0
|
|
O
|
H:THR61
|
2.3
|
14.3
|
1.0
|
|
OD1
|
H:ASP137
|
2.3
|
21.4
|
1.0
|
|
OD1
|
H:ASN136
|
2.4
|
25.5
|
1.0
|
|
O
|
H:HOH318
|
2.4
|
23.7
|
1.0
|
|
OG1
|
H:THR61
|
2.4
|
17.4
|
1.0
|
|
OD2
|
H:ASP63
|
2.5
|
21.6
|
1.0
|
|
OD1
|
H:ASP63
|
2.7
|
21.8
|
1.0
|
|
CG
|
H:ASP63
|
2.9
|
19.6
|
1.0
|
|
CG
|
H:ASP137
|
3.3
|
21.2
|
1.0
|
|
C
|
H:THR61
|
3.3
|
15.8
|
1.0
|
|
CG
|
H:ASN136
|
3.4
|
25.0
|
1.0
|
|
C
|
H:ASN133
|
3.4
|
21.0
|
1.0
|
|
OD2
|
H:ASP137
|
3.6
|
19.9
|
1.0
|
|
CB
|
H:THR61
|
3.6
|
18.4
|
1.0
|
|
CA
|
H:THR61
|
3.8
|
16.8
|
1.0
|
|
ND2
|
H:ASN136
|
3.8
|
23.2
|
1.0
|
|
N
|
H:THR61
|
3.8
|
16.5
|
1.0
|
|
N
|
H:ASN133
|
4.1
|
22.5
|
1.0
|
|
CA
|
H:ASN133
|
4.2
|
21.0
|
1.0
|
|
CB
|
H:ASN133
|
4.3
|
22.2
|
1.0
|
|
CB
|
H:ASP63
|
4.4
|
21.4
|
1.0
|
|
O
|
H:ASN136
|
4.4
|
24.9
|
1.0
|
|
C
|
H:ASN136
|
4.4
|
21.0
|
1.0
|
|
N
|
H:VAL62
|
4.4
|
16.6
|
1.0
|
|
N
|
H:GLN134
|
4.4
|
20.4
|
1.0
|
|
CA
|
H:GLN134
|
4.5
|
20.3
|
1.0
|
|
CB
|
H:ASP137
|
4.6
|
19.9
|
1.0
|
|
N
|
H:ASP137
|
4.6
|
21.4
|
1.0
|
|
N
|
H:ASP63
|
4.7
|
18.7
|
1.0
|
|
CB
|
H:ASN136
|
4.7
|
22.7
|
1.0
|
|
N
|
H:ASN136
|
4.8
|
20.2
|
1.0
|
|
C
|
H:VAL62
|
4.8
|
17.4
|
1.0
|
|
CG
|
H:ASN133
|
4.8
|
24.2
|
1.0
|
|
CG2
|
H:THR61
|
4.9
|
19.8
|
1.0
|
|
CA
|
H:ASP137
|
4.9
|
20.7
|
1.0
|
|
CA
|
H:ASN136
|
4.9
|
23.0
|
1.0
|
|
C
|
H:GLN134
|
4.9
|
22.4
|
1.0
|
|
CA
|
H:VAL62
|
5.0
|
17.5
|
1.0
|
|
Calcium binding site 9 out
of 12 in 6d5b
Go back to
Calcium Binding Sites List in 6d5b
Calcium binding site 9 out
of 12 in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca201
b:33.1
occ:1.00
|
OG1
|
I:THR61
|
2.3
|
25.2
|
1.0
|
|
OD1
|
I:ASP137
|
2.3
|
26.3
|
1.0
|
|
OD1
|
I:ASN136
|
2.3
|
33.9
|
1.0
|
|
O
|
I:ASN133
|
2.4
|
25.0
|
1.0
|
|
O
|
I:THR61
|
2.4
|
27.3
|
1.0
|
|
OD2
|
I:ASP63
|
2.5
|
33.2
|
1.0
|
|
O
|
I:HOH317
|
2.7
|
24.5
|
1.0
|
|
OD1
|
I:ASP63
|
2.7
|
30.6
|
1.0
|
|
CG
|
I:ASP63
|
3.0
|
31.2
|
1.0
|
|
CG
|
I:ASP137
|
3.3
|
29.0
|
1.0
|
|
C
|
I:THR61
|
3.4
|
27.5
|
1.0
|
|
CG
|
I:ASN136
|
3.4
|
34.9
|
1.0
|
|
CB
|
I:THR61
|
3.4
|
28.0
|
1.0
|
|
C
|
I:ASN133
|
3.5
|
26.7
|
1.0
|
|
OD2
|
I:ASP137
|
3.6
|
29.8
|
1.0
|
|
CA
|
I:THR61
|
3.7
|
26.4
|
1.0
|
|
N
|
I:THR61
|
3.8
|
25.4
|
1.0
|
|
ND2
|
I:ASN136
|
3.9
|
33.1
|
1.0
|
|
N
|
I:ASN133
|
4.2
|
27.8
|
1.0
|
|
CA
|
I:ASN133
|
4.3
|
30.0
|
1.0
|
|
C
|
I:ASN136
|
4.3
|
28.3
|
1.0
|
|
CB
|
I:ASN133
|
4.4
|
30.5
|
1.0
|
|
N
|
I:ASP137
|
4.4
|
27.3
|
1.0
|
|
O
|
I:ASN136
|
4.4
|
31.6
|
1.0
|
|
CB
|
I:ASP63
|
4.4
|
33.9
|
1.0
|
|
N
|
I:GLN134
|
4.5
|
26.0
|
1.0
|
|
CA
|
I:GLN134
|
4.6
|
26.4
|
1.0
|
|
N
|
I:VAL62
|
4.6
|
27.8
|
1.0
|
|
CB
|
I:ASP137
|
4.6
|
27.9
|
1.0
|
|
N
|
I:ASN136
|
4.6
|
27.6
|
1.0
|
|
CG2
|
I:THR61
|
4.6
|
29.1
|
1.0
|
|
CB
|
I:ASN136
|
4.6
|
30.9
|
1.0
|
|
CA
|
I:ASP137
|
4.7
|
25.2
|
1.0
|
|
CA
|
I:ASN136
|
4.7
|
29.0
|
1.0
|
|
ND2
|
I:ASN133
|
4.8
|
31.8
|
1.0
|
|
CG
|
I:ASN133
|
4.8
|
28.5
|
1.0
|
|
N
|
I:ASP63
|
4.9
|
32.7
|
1.0
|
|
C
|
I:GLN134
|
4.9
|
27.9
|
1.0
|
|
O
|
I:HOH412
|
4.9
|
29.3
|
0.9
|
|
Calcium binding site 10 out
of 12 in 6d5b
Go back to
Calcium Binding Sites List in 6d5b
Calcium binding site 10 out
of 12 in the Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Structure of Caldicellulosiruptor Danielii CBM3 Module of Glycoside Hydrolase WP_045175321 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Ca201
b:36.3
occ:1.00
|
O
|
J:ASN133
|
2.3
|
26.7
|
1.0
|
|
OG1
|
J:THR61
|
2.3
|
29.0
|
1.0
|
|
O
|
J:THR61
|
2.4
|
29.1
|
1.0
|
|
OD1
|
J:ASP137
|
2.5
|
28.2
|
1.0
|
|
OD2
|
J:ASP63
|
2.6
|
39.9
|
1.0
|
|
OD1
|
J:ASN136
|
2.6
|
40.6
|
1.0
|
|
OD1
|
J:ASP63
|
2.6
|
38.9
|
1.0
|
|
O
|
J:HOH315
|
2.7
|
23.9
|
1.0
|
|
CG
|
J:ASP63
|
2.9
|
39.3
|
1.0
|
|
C
|
J:THR61
|
3.3
|
26.0
|
1.0
|
|
CG
|
J:ASP137
|
3.4
|
27.4
|
1.0
|
|
CB
|
J:THR61
|
3.4
|
28.3
|
1.0
|
|
CG
|
J:ASN136
|
3.4
|
43.3
|
1.0
|
|
C
|
J:ASN133
|
3.5
|
31.1
|
1.0
|
|
CA
|
J:THR61
|
3.7
|
27.8
|
1.0
|
|
ND2
|
J:ASN136
|
3.7
|
37.4
|
1.0
|
|
OD2
|
J:ASP137
|
3.7
|
27.2
|
1.0
|
|
N
|
J:THR61
|
3.8
|
28.0
|
1.0
|
|
N
|
J:ASN133
|
4.1
|
30.9
|
1.0
|
|
CA
|
J:ASN133
|
4.2
|
33.5
|
1.0
|
|
O
|
J:ASN136
|
4.3
|
30.0
|
1.0
|
|
CB
|
J:ASP63
|
4.3
|
38.7
|
1.0
|
|
CB
|
J:ASN133
|
4.4
|
32.0
|
1.0
|
|
C
|
J:ASN136
|
4.4
|
32.5
|
1.0
|
|
N
|
J:GLN134
|
4.5
|
33.1
|
1.0
|
|
N
|
J:VAL62
|
4.5
|
27.1
|
1.0
|
|
N
|
J:ASP137
|
4.6
|
29.3
|
1.0
|
|
CG2
|
J:THR61
|
4.6
|
31.5
|
1.0
|
|
CB
|
J:ASP137
|
4.7
|
25.9
|
1.0
|
|
CA
|
J:GLN134
|
4.7
|
30.1
|
1.0
|
|
CB
|
J:ASN136
|
4.7
|
37.4
|
1.0
|
|
N
|
J:ASP63
|
4.8
|
38.1
|
1.0
|
|
N
|
J:ASN136
|
4.8
|
30.0
|
1.0
|
|
CA
|
J:ASP137
|
4.9
|
28.3
|
1.0
|
|
C
|
J:VAL62
|
4.9
|
33.4
|
1.0
|
|
CA
|
J:ASN136
|
4.9
|
33.2
|
1.0
|
|
CG
|
J:ASN133
|
4.9
|
34.2
|
1.0
|
|
Reference:
J.M.Conway,
J.R.Crosby,
A.P.Hren,
R.T.Southerland,
L.L.Lee,
V.V.Lunin,
P.M.Alahuhta,
M.E.Himmel,
Y.J.Bomble,
M.W.W.Adams,
R.M.Kelly.
Novel Multidomain, Multifunctional Glycoside Hydrolases From Highly Lignocellulolytic Caldicellulosiruptor Species Aiche J. 2019.
DOI: 10.1002/AIC.16354
Page generated: Mon Jul 15 17:36:28 2024
|
