Calcium in PDB 6sus: Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
Enzymatic activity of Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
All present enzymatic activity of Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis:
4.6.1.1;
Protein crystallography data
The structure of Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis, PDB code: 6sus
was solved by
L.Motlova,
C.Barinka,
L.Bumba,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
45.89 /
1.76
|
|
Space group
|
P 43 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.771,
91.771,
104.465,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18.4 /
20.1
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
15;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
(pdb code 6sus). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 15 binding sites of Calcium where determined in the
Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis, PDB code: 6sus:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 15 in 6sus
Go back to
Calcium Binding Sites List in 6sus
Calcium binding site 1 out
of 15 in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
 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 Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1701
b:32.1
occ:1.00
|
O
|
A:GLU1432
|
2.3
|
34.0
|
1.0
|
|
O
|
A:ASP1413
|
2.3
|
34.1
|
1.0
|
|
OD1
|
A:ASP1435
|
2.4
|
29.8
|
1.0
|
|
O
|
A:GLY1430
|
2.4
|
32.4
|
1.0
|
|
O
|
A:GLN1415
|
2.4
|
35.9
|
0.6
|
|
O
|
A:GLN1415
|
2.4
|
34.2
|
0.4
|
|
OD1
|
A:ASN1417
|
2.5
|
34.4
|
1.0
|
|
OD2
|
A:ASP1435
|
3.0
|
30.5
|
1.0
|
|
CG
|
A:ASP1435
|
3.0
|
31.0
|
1.0
|
|
C
|
A:GLU1432
|
3.5
|
32.6
|
1.0
|
|
CG
|
A:ASN1417
|
3.5
|
34.6
|
1.0
|
|
C
|
A:GLY1430
|
3.5
|
32.5
|
1.0
|
|
C
|
A:ASP1413
|
3.5
|
39.4
|
1.0
|
|
C
|
A:GLN1415
|
3.6
|
34.4
|
0.4
|
|
C
|
A:GLN1415
|
3.6
|
36.5
|
0.6
|
|
C
|
A:GLY1431
|
3.8
|
34.1
|
1.0
|
|
O
|
A:GLY1431
|
3.9
|
32.0
|
1.0
|
|
N
|
A:ASP1413
|
3.9
|
38.9
|
1.0
|
|
N
|
A:GLU1432
|
4.0
|
30.5
|
1.0
|
|
N
|
A:GLN1415
|
4.1
|
35.5
|
0.4
|
|
N
|
A:ASN1417
|
4.1
|
32.1
|
1.0
|
|
N
|
A:GLN1415
|
4.1
|
37.2
|
0.6
|
|
C
|
A:ALA1414
|
4.1
|
36.9
|
1.0
|
|
CB
|
A:ASN1417
|
4.2
|
30.7
|
1.0
|
|
CA
|
A:GLY1431
|
4.2
|
33.5
|
1.0
|
|
N
|
A:GLY1431
|
4.3
|
32.3
|
1.0
|
|
N
|
A:GLY1433
|
4.4
|
30.6
|
1.0
|
|
CA
|
A:ASP1413
|
4.4
|
40.0
|
1.0
|
|
CA
|
A:ALA1414
|
4.4
|
37.5
|
1.0
|
|
N
|
A:ALA1414
|
4.4
|
36.2
|
1.0
|
|
CA
|
A:GLU1432
|
4.4
|
32.9
|
1.0
|
|
CA
|
A:GLY1433
|
4.4
|
32.2
|
1.0
|
|
CB
|
A:ASP1435
|
4.4
|
27.2
|
1.0
|
|
O
|
A:GLY1433
|
4.5
|
32.8
|
1.0
|
|
CA
|
A:GLY1430
|
4.5
|
30.4
|
1.0
|
|
CA
|
A:GLN1415
|
4.5
|
34.3
|
0.4
|
|
ND2
|
A:ASN1417
|
4.5
|
32.5
|
1.0
|
|
CA
|
A:GLN1415
|
4.5
|
37.0
|
0.6
|
|
N
|
A:ALA1416
|
4.5
|
31.9
|
1.0
|
|
OD1
|
A:ASP1413
|
4.5
|
38.9
|
1.0
|
|
C
|
A:GLY1412
|
4.5
|
39.4
|
1.0
|
|
C
|
A:GLY1433
|
4.6
|
33.3
|
1.0
|
|
O
|
A:ALA1414
|
4.6
|
39.6
|
1.0
|
|
CA
|
A:ALA1416
|
4.6
|
33.5
|
1.0
|
|
CA
|
A:GLY1412
|
4.7
|
39.0
|
1.0
|
|
CA
|
A:CA1702
|
4.7
|
29.7
|
1.0
|
|
CA
|
A:ASN1417
|
4.8
|
31.0
|
1.0
|
|
C
|
A:ALA1416
|
4.8
|
34.1
|
1.0
|
|
Calcium binding site 2 out
of 15 in 6sus
Go back to
Calcium Binding Sites List in 6sus
Calcium binding site 2 out
of 15 in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
 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 Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1702
b:29.7
occ:1.00
|
O
|
A:ALA1450
|
2.3
|
31.1
|
1.0
|
|
O
|
A:GLY1448
|
2.3
|
28.4
|
1.0
|
|
OD2
|
A:ASP1435
|
2.4
|
30.5
|
1.0
|
|
O
|
A:GLY1433
|
2.4
|
32.8
|
1.0
|
|
OD1
|
A:ASP1453
|
2.4
|
29.5
|
1.0
|
|
O
|
A:GLY1431
|
2.4
|
32.0
|
1.0
|
|
OD2
|
A:ASP1453
|
2.7
|
30.1
|
1.0
|
|
CG
|
A:ASP1453
|
2.9
|
29.7
|
1.0
|
|
C
|
A:GLY1448
|
3.5
|
28.5
|
1.0
|
|
CG
|
A:ASP1435
|
3.5
|
31.0
|
1.0
|
|
C
|
A:ALA1450
|
3.5
|
30.8
|
1.0
|
|
C
|
A:GLY1433
|
3.6
|
33.3
|
1.0
|
|
C
|
A:GLY1431
|
3.6
|
34.1
|
1.0
|
|
C
|
A:GLU1432
|
3.9
|
32.6
|
1.0
|
|
O
|
A:GLU1432
|
4.0
|
34.0
|
1.0
|
|
C
|
A:ASP1449
|
4.1
|
30.7
|
1.0
|
|
N
|
A:GLY1433
|
4.1
|
30.6
|
1.0
|
|
O
|
A:ASP1449
|
4.1
|
29.6
|
1.0
|
|
CB
|
A:ASP1435
|
4.2
|
27.2
|
1.0
|
|
N
|
A:ASP1435
|
4.2
|
27.7
|
1.0
|
|
N
|
A:ALA1450
|
4.3
|
30.1
|
1.0
|
|
C
|
A:GLY1430
|
4.3
|
32.5
|
1.0
|
|
CA
|
A:GLY1448
|
4.3
|
26.6
|
1.0
|
|
CA
|
A:GLY1451
|
4.3
|
31.4
|
1.0
|
|
CB
|
A:ASP1453
|
4.4
|
26.6
|
1.0
|
|
CA
|
A:GLU1432
|
4.4
|
32.9
|
1.0
|
|
N
|
A:GLY1451
|
4.4
|
30.2
|
1.0
|
|
N
|
A:GLY1431
|
4.4
|
32.3
|
1.0
|
|
N
|
A:ASP1449
|
4.4
|
27.3
|
1.0
|
|
OD1
|
A:ASP1435
|
4.5
|
29.8
|
1.0
|
|
N
|
A:GLU1432
|
4.5
|
30.5
|
1.0
|
|
CA
|
A:GLY1433
|
4.5
|
32.2
|
1.0
|
|
O
|
A:GLY1430
|
4.5
|
32.4
|
1.0
|
|
CA
|
A:GLY1430
|
4.5
|
30.4
|
1.0
|
|
CA
|
A:CA1703
|
4.5
|
31.9
|
0.7
|
|
CA
|
A:ALA1450
|
4.5
|
31.9
|
1.0
|
|
CA
|
A:ASP1449
|
4.6
|
29.9
|
1.0
|
|
N
|
A:ASP1434
|
4.6
|
31.4
|
1.0
|
|
CB
|
A:ASP1449
|
4.6
|
32.0
|
1.0
|
|
CA
|
A:GLY1431
|
4.7
|
33.5
|
1.0
|
|
C
|
A:GLY1451
|
4.7
|
32.2
|
1.0
|
|
CA
|
A:CA1701
|
4.7
|
32.1
|
1.0
|
|
CA
|
A:ASP1434
|
4.7
|
32.1
|
1.0
|
|
CA
|
A:ASP1435
|
4.9
|
28.2
|
1.0
|
|
C
|
A:ASP1434
|
4.9
|
32.2
|
1.0
|
|
O
|
A:GLY1451
|
5.0
|
30.8
|
1.0
|
|
Calcium binding site 3 out
of 15 in 6sus
Go back to
Calcium Binding Sites List in 6sus
Calcium binding site 3 out
of 15 in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
 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 Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1703
b:31.9
occ:0.70
|
OD2
|
A:ASP1453
|
2.3
|
30.1
|
1.0
|
|
OD1
|
A:ASN1470
|
2.4
|
28.7
|
1.0
|
|
OD1
|
A:ASN1473
|
2.4
|
27.7
|
1.0
|
|
O
|
A:ASP1449
|
2.4
|
29.6
|
1.0
|
|
O
|
A:HOH1840
|
2.4
|
28.0
|
1.0
|
|
O
|
A:GLY1451
|
2.5
|
30.8
|
1.0
|
|
CG
|
A:ASN1473
|
3.2
|
29.3
|
1.0
|
|
CG
|
A:ASN1470
|
3.3
|
30.6
|
1.0
|
|
CG
|
A:ASP1453
|
3.4
|
29.7
|
1.0
|
|
C
|
A:GLY1451
|
3.4
|
32.2
|
1.0
|
|
ND2
|
A:ASN1473
|
3.5
|
27.5
|
1.0
|
|
C
|
A:ASP1449
|
3.6
|
30.7
|
1.0
|
|
ND2
|
A:ASN1470
|
3.7
|
29.5
|
1.0
|
|
C
|
A:ALA1450
|
3.8
|
30.8
|
1.0
|
|
O
|
A:ALA1450
|
3.9
|
31.1
|
1.0
|
|
CB
|
A:ASP1453
|
3.9
|
26.6
|
1.0
|
|
C
|
A:GLY1448
|
4.0
|
28.5
|
1.0
|
|
N
|
A:GLY1451
|
4.0
|
30.2
|
1.0
|
|
N
|
A:ASP1453
|
4.1
|
27.8
|
1.0
|
|
O
|
A:GLY1448
|
4.2
|
28.4
|
1.0
|
|
CA
|
A:GLY1448
|
4.2
|
26.6
|
1.0
|
|
N
|
A:ASP1449
|
4.2
|
27.3
|
1.0
|
|
CA
|
A:GLY1451
|
4.3
|
31.4
|
1.0
|
|
N
|
A:ARG1452
|
4.3
|
29.6
|
0.7
|
|
N
|
A:ARG1452
|
4.3
|
30.2
|
0.3
|
|
CA
|
A:ALA1450
|
4.3
|
31.9
|
1.0
|
|
N
|
A:ALA1450
|
4.4
|
30.1
|
1.0
|
|
O
|
A:HOH1952
|
4.4
|
32.1
|
1.0
|
|
CA
|
A:ARG1452
|
4.5
|
31.2
|
0.7
|
|
OD1
|
A:ASP1453
|
4.5
|
29.5
|
1.0
|
|
CA
|
A:ARG1452
|
4.5
|
30.2
|
0.3
|
|
CA
|
A:CA1702
|
4.5
|
29.7
|
1.0
|
|
NE2
|
A:GLN1466
|
4.5
|
26.2
|
1.0
|
|
CA
|
A:ASP1449
|
4.6
|
29.9
|
1.0
|
|
CB
|
A:ASN1473
|
4.6
|
27.1
|
1.0
|
|
OE1
|
A:GLN1466
|
4.6
|
28.7
|
1.0
|
|
C
|
A:ARG1452
|
4.7
|
29.3
|
0.3
|
|
CA
|
A:ASP1453
|
4.7
|
27.3
|
1.0
|
|
CB
|
A:ASN1470
|
4.7
|
28.6
|
1.0
|
|
C
|
A:ARG1452
|
4.7
|
30.1
|
0.7
|
|
O
|
A:HOH1957
|
4.9
|
49.7
|
1.0
|
|
Calcium binding site 4 out
of 15 in 6sus
Go back to
Calcium Binding Sites List in 6sus
Calcium binding site 4 out
of 15 in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
 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 Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1704
b:26.8
occ:1.00
|
O
|
A:ALA1549
|
2.3
|
29.7
|
1.0
|
|
OD1
|
A:ASP1552
|
2.3
|
25.3
|
1.0
|
|
O
|
A:GLY1547
|
2.3
|
26.0
|
1.0
|
|
OD2
|
A:ASP1534
|
2.3
|
27.2
|
1.0
|
|
O
|
A:ARG1532
|
2.3
|
30.2
|
1.0
|
|
O
|
A:SER1530
|
2.4
|
28.1
|
1.0
|
|
OD2
|
A:ASP1552
|
3.0
|
26.0
|
1.0
|
|
CG
|
A:ASP1552
|
3.0
|
24.6
|
1.0
|
|
CG
|
A:ASP1534
|
3.3
|
25.7
|
1.0
|
|
C
|
A:GLY1547
|
3.5
|
26.2
|
1.0
|
|
C
|
A:ALA1549
|
3.5
|
30.5
|
1.0
|
|
C
|
A:SER1530
|
3.5
|
32.1
|
1.0
|
|
C
|
A:ARG1532
|
3.6
|
31.1
|
1.0
|
|
O
|
A:LEU1548
|
3.9
|
28.1
|
1.0
|
|
C
|
A:LEU1548
|
4.0
|
29.1
|
1.0
|
|
N
|
A:ARG1532
|
4.0
|
30.4
|
1.0
|
|
N
|
A:ASP1534
|
4.0
|
27.2
|
1.0
|
|
N
|
A:SER1530
|
4.0
|
28.7
|
1.0
|
|
OD1
|
A:ASP1534
|
4.1
|
29.1
|
1.0
|
|
CB
|
A:ASP1534
|
4.1
|
25.7
|
1.0
|
|
C
|
A:ALA1531
|
4.2
|
30.9
|
1.0
|
|
N
|
A:ALA1549
|
4.2
|
29.0
|
1.0
|
|
CA
|
A:GLY1547
|
4.3
|
25.2
|
1.0
|
|
CA
|
A:GLY1550
|
4.3
|
29.1
|
1.0
|
|
N
|
A:GLY1550
|
4.4
|
28.5
|
1.0
|
|
CA
|
A:SER1530
|
4.4
|
30.1
|
1.0
|
|
OG
|
A:SER1530
|
4.4
|
27.6
|
1.0
|
|
CA
|
A:ARG1532
|
4.4
|
31.4
|
1.0
|
|
N
|
A:ALA1531
|
4.4
|
30.3
|
1.0
|
|
N
|
A:LEU1548
|
4.4
|
26.6
|
1.0
|
|
CB
|
A:ASP1552
|
4.4
|
24.6
|
1.0
|
|
N
|
A:ASP1533
|
4.5
|
30.4
|
1.0
|
|
CA
|
A:ALA1549
|
4.5
|
29.1
|
1.0
|
|
CA
|
A:ALA1531
|
4.5
|
30.8
|
1.0
|
|
C
|
A:GLY1550
|
4.5
|
28.3
|
1.0
|
|
O
|
A:ALA1531
|
4.6
|
31.4
|
1.0
|
|
CA
|
A:ASP1533
|
4.6
|
31.6
|
1.0
|
|
CA
|
A:LEU1548
|
4.6
|
27.4
|
1.0
|
|
CB
|
A:LEU1548
|
4.6
|
27.6
|
1.0
|
|
C
|
A:ASP1533
|
4.6
|
33.1
|
1.0
|
|
O
|
A:GLY1550
|
4.6
|
28.7
|
1.0
|
|
CA
|
A:CA1705
|
4.7
|
27.9
|
1.0
|
|
CA
|
A:ASP1534
|
4.7
|
26.1
|
1.0
|
|
Calcium binding site 5 out
of 15 in 6sus
Go back to
Calcium Binding Sites List in 6sus
Calcium binding site 5 out
of 15 in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
 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 Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1705
b:27.9
occ:1.00
|
O
|
A:GLY1565
|
2.3
|
27.2
|
1.0
|
|
O
|
A:GLU1567
|
2.3
|
25.8
|
0.7
|
|
OD2
|
A:ASP1552
|
2.4
|
26.0
|
1.0
|
|
O
|
A:LEU1548
|
2.4
|
28.1
|
1.0
|
|
O
|
A:GLU1567
|
2.4
|
27.5
|
0.3
|
|
O
|
A:GLY1550
|
2.4
|
28.7
|
1.0
|
|
OD1
|
A:ASP1570
|
2.4
|
25.5
|
1.0
|
|
OD2
|
A:ASP1570
|
3.0
|
25.6
|
1.0
|
|
CG
|
A:ASP1570
|
3.1
|
25.3
|
1.0
|
|
CG
|
A:ASP1552
|
3.4
|
24.6
|
1.0
|
|
C
|
A:GLY1565
|
3.5
|
25.2
|
1.0
|
|
C
|
A:GLU1567
|
3.5
|
31.2
|
0.7
|
|
C
|
A:GLY1550
|
3.5
|
28.3
|
1.0
|
|
C
|
A:GLU1567
|
3.5
|
29.7
|
0.3
|
|
C
|
A:LEU1548
|
3.6
|
29.1
|
1.0
|
|
C
|
A:ALA1549
|
3.7
|
30.5
|
1.0
|
|
O
|
A:ALA1549
|
3.9
|
29.7
|
1.0
|
|
N
|
A:GLY1550
|
4.0
|
28.5
|
1.0
|
|
CA
|
A:ALA1549
|
4.1
|
29.1
|
1.0
|
|
C
|
A:ASP1566
|
4.1
|
29.1
|
1.0
|
|
O
|
A:ASP1566
|
4.1
|
27.2
|
1.0
|
|
CB
|
A:ASP1552
|
4.1
|
24.6
|
1.0
|
|
N
|
A:ASP1552
|
4.3
|
25.9
|
1.0
|
|
N
|
A:GLU1567
|
4.3
|
29.2
|
0.3
|
|
N
|
A:GLU1567
|
4.3
|
29.9
|
0.7
|
|
N
|
A:ALA1549
|
4.3
|
29.0
|
1.0
|
|
OD1
|
A:ASP1552
|
4.3
|
25.3
|
1.0
|
|
CA
|
A:GLY1568
|
4.3
|
28.0
|
1.0
|
|
CA
|
A:GLY1565
|
4.3
|
26.1
|
1.0
|
|
CA
|
A:GLY1550
|
4.3
|
29.1
|
1.0
|
|
N
|
A:GLY1568
|
4.3
|
27.6
|
1.0
|
|
C
|
A:GLY1547
|
4.4
|
26.2
|
1.0
|
|
O
|
A:GLY1547
|
4.4
|
26.0
|
1.0
|
|
CB
|
A:ASP1566
|
4.5
|
27.5
|
1.0
|
|
N
|
A:ASP1566
|
4.5
|
27.0
|
1.0
|
|
N
|
A:ASN1551
|
4.5
|
27.6
|
1.0
|
|
CB
|
A:ASP1570
|
4.5
|
25.5
|
1.0
|
|
CA
|
A:GLU1567
|
4.6
|
31.0
|
0.7
|
|
N
|
A:LEU1548
|
4.6
|
26.6
|
1.0
|
|
CA
|
A:GLU1567
|
4.6
|
29.7
|
0.3
|
|
CA
|
A:ASP1566
|
4.6
|
28.5
|
1.0
|
|
CA
|
A:CA1704
|
4.7
|
26.8
|
1.0
|
|
CA
|
A:LEU1548
|
4.7
|
27.4
|
1.0
|
|
C
|
A:GLY1568
|
4.7
|
27.3
|
1.0
|
|
CA
|
A:ASN1551
|
4.7
|
29.9
|
1.0
|
|
CA
|
A:GLY1547
|
4.8
|
25.2
|
1.0
|
|
CA
|
A:CA1706
|
4.9
|
27.8
|
1.0
|
|
CA
|
A:ASP1552
|
4.9
|
25.0
|
1.0
|
|
O
|
A:GLY1568
|
4.9
|
28.7
|
1.0
|
|
C
|
A:ASN1551
|
4.9
|
28.2
|
1.0
|
|
Calcium binding site 6 out
of 15 in 6sus
Go back to
Calcium Binding Sites List in 6sus
Calcium binding site 6 out
of 15 in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
 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 Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1706
b:27.8
occ:1.00
|
O
|
A:GLY1583
|
2.3
|
25.6
|
1.0
|
|
OD2
|
A:ASP1570
|
2.3
|
25.6
|
1.0
|
|
O
|
A:GLN1585
|
2.4
|
28.6
|
1.0
|
|
O
|
A:ASP1566
|
2.4
|
27.2
|
1.0
|
|
OD1
|
A:ASP1588
|
2.4
|
26.2
|
1.0
|
|
O
|
A:GLY1568
|
2.4
|
28.7
|
1.0
|
|
OD2
|
A:ASP1588
|
2.9
|
27.6
|
1.0
|
|
CG
|
A:ASP1588
|
3.0
|
28.2
|
1.0
|
|
C
|
A:GLY1583
|
3.4
|
25.2
|
1.0
|
|
CG
|
A:ASP1570
|
3.5
|
25.3
|
1.0
|
|
C
|
A:GLY1568
|
3.5
|
27.3
|
1.0
|
|
C
|
A:GLN1585
|
3.6
|
33.0
|
1.0
|
|
C
|
A:ASP1566
|
3.6
|
29.1
|
1.0
|
|
C
|
A:GLY1584
|
3.8
|
29.9
|
1.0
|
|
N
|
A:GLY1568
|
3.9
|
27.6
|
1.0
|
|
C
|
A:GLU1567
|
3.9
|
31.2
|
0.7
|
|
C
|
A:GLU1567
|
4.0
|
29.7
|
0.3
|
|
CB
|
A:ASP1570
|
4.0
|
25.5
|
1.0
|
|
CA
|
A:GLY1584
|
4.0
|
27.7
|
1.0
|
|
O
|
A:GLY1584
|
4.1
|
28.7
|
1.0
|
|
N
|
A:GLN1585
|
4.1
|
30.5
|
1.0
|
|
C
|
A:GLY1565
|
4.1
|
25.2
|
1.0
|
|
N
|
A:GLY1584
|
4.1
|
27.5
|
1.0
|
|
N
|
A:ASP1570
|
4.2
|
27.4
|
1.0
|
|
O
|
A:GLU1567
|
4.2
|
25.8
|
0.7
|
|
CA
|
A:GLY1568
|
4.3
|
28.0
|
1.0
|
|
N
|
A:ASP1566
|
4.3
|
27.0
|
1.0
|
|
O
|
A:GLY1565
|
4.3
|
27.2
|
1.0
|
|
O
|
A:GLU1567
|
4.3
|
27.5
|
0.3
|
|
CA
|
A:GLU1567
|
4.4
|
29.7
|
0.3
|
|
CA
|
A:GLY1586
|
4.4
|
30.4
|
1.0
|
|
CA
|
A:GLU1567
|
4.4
|
31.0
|
0.7
|
|
N
|
A:GLY1586
|
4.4
|
30.4
|
1.0
|
|
CB
|
A:ASP1588
|
4.5
|
27.4
|
1.0
|
|
N
|
A:GLU1567
|
4.5
|
29.2
|
0.3
|
|
N
|
A:GLU1567
|
4.5
|
29.9
|
0.7
|
|
OD1
|
A:ASP1570
|
4.5
|
25.5
|
1.0
|
|
CA
|
A:GLY1583
|
4.5
|
25.2
|
1.0
|
|
CA
|
A:GLN1585
|
4.5
|
34.2
|
1.0
|
|
CA
|
A:GLY1565
|
4.5
|
26.1
|
1.0
|
|
O
|
A:GLY1586
|
4.5
|
30.2
|
1.0
|
|
C
|
A:GLY1586
|
4.5
|
29.4
|
1.0
|
|
N
|
A:SER1569
|
4.5
|
29.2
|
0.5
|
|
N
|
A:SER1569
|
4.5
|
28.8
|
0.5
|
|
CA
|
A:ASP1566
|
4.6
|
28.5
|
1.0
|
|
CA
|
A:CA1707
|
4.7
|
29.6
|
1.0
|
|
CA
|
A:SER1569
|
4.8
|
29.3
|
0.5
|
|
CA
|
A:SER1569
|
4.8
|
28.6
|
0.5
|
|
CA
|
A:ASP1570
|
4.8
|
26.7
|
1.0
|
|
CA
|
A:CA1705
|
4.9
|
27.9
|
1.0
|
|
C
|
A:SER1569
|
4.9
|
28.4
|
0.5
|
|
C
|
A:SER1569
|
4.9
|
28.0
|
0.5
|
|
Calcium binding site 7 out
of 15 in 6sus
Go back to
Calcium Binding Sites List in 6sus
Calcium binding site 7 out
of 15 in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
 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 Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1707
b:29.6
occ:1.00
|
O
|
A:GLY1586
|
2.3
|
30.2
|
1.0
|
|
OD2
|
A:ASP1588
|
2.3
|
27.6
|
1.0
|
|
O
|
A:GLY1605
|
2.3
|
30.6
|
1.0
|
|
O
|
A:GLY1584
|
2.4
|
28.7
|
1.0
|
|
OD1
|
A:ASP1609
|
2.4
|
29.9
|
1.0
|
|
OE2
|
A:GLU1603
|
2.5
|
32.3
|
1.0
|
|
OE1
|
A:GLU1603
|
2.6
|
30.1
|
1.0
|
|
CD
|
A:GLU1603
|
2.9
|
33.1
|
1.0
|
|
CG
|
A:ASP1609
|
3.3
|
31.6
|
1.0
|
|
CG
|
A:ASP1588
|
3.4
|
28.2
|
1.0
|
|
OD2
|
A:ASP1609
|
3.5
|
31.7
|
1.0
|
|
C
|
A:GLY1586
|
3.5
|
29.4
|
1.0
|
|
C
|
A:GLY1605
|
3.5
|
39.1
|
1.0
|
|
C
|
A:GLY1584
|
3.6
|
29.9
|
1.0
|
|
C
|
A:GLN1585
|
3.8
|
33.0
|
1.0
|
|
CB
|
A:ASP1588
|
3.9
|
27.4
|
1.0
|
|
N
|
A:GLY1586
|
4.0
|
30.4
|
1.0
|
|
O
|
A:GLN1585
|
4.0
|
28.6
|
1.0
|
|
N
|
A:ASP1588
|
4.1
|
29.2
|
1.0
|
|
CA
|
A:GLN1585
|
4.3
|
34.2
|
1.0
|
|
CA
|
A:GLY1606
|
4.3
|
37.8
|
1.0
|
|
N
|
A:GLY1605
|
4.3
|
37.6
|
1.0
|
|
CG
|
A:GLU1603
|
4.4
|
31.6
|
1.0
|
|
N
|
A:GLY1606
|
4.4
|
36.8
|
1.0
|
|
CA
|
A:GLY1586
|
4.4
|
30.4
|
1.0
|
|
N
|
A:GLN1585
|
4.4
|
30.5
|
1.0
|
|
O
|
A:HOH1849
|
4.4
|
31.1
|
1.0
|
|
OD1
|
A:ASP1588
|
4.5
|
26.2
|
1.0
|
|
N
|
A:GLY1584
|
4.5
|
27.5
|
1.0
|
|
N
|
A:ASP1587
|
4.5
|
32.8
|
1.0
|
|
C
|
A:GLY1583
|
4.5
|
25.2
|
1.0
|
|
CA
|
A:GLY1605
|
4.5
|
38.0
|
1.0
|
|
CA
|
A:GLY1584
|
4.7
|
27.7
|
1.0
|
|
CB
|
A:ASP1609
|
4.7
|
32.3
|
1.0
|
|
CA
|
A:ASP1587
|
4.7
|
31.7
|
1.0
|
|
CA
|
A:ASP1588
|
4.7
|
28.6
|
1.0
|
|
O
|
A:GLY1583
|
4.7
|
25.6
|
1.0
|
|
CA
|
A:CA1706
|
4.7
|
27.8
|
1.0
|
|
C
|
A:ASP1587
|
4.8
|
29.1
|
1.0
|
|
OH
|
A:TYR1590
|
4.9
|
27.0
|
1.0
|
|
CA
|
A:GLY1583
|
5.0
|
25.2
|
1.0
|
|
Calcium binding site 8 out
of 15 in 6sus
Go back to
Calcium Binding Sites List in 6sus
Calcium binding site 8 out
of 15 in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
 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 Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1708
b:37.0
occ:1.00
|
O
|
A:GLY1606
|
2.2
|
40.0
|
1.0
|
|
O
|
A:HOH1864
|
2.4
|
37.5
|
1.0
|
|
OD2
|
A:ASP1609
|
2.4
|
31.7
|
1.0
|
|
O
|
A:HOH1849
|
2.4
|
31.1
|
1.0
|
|
OE2
|
A:GLU1654
|
2.4
|
34.9
|
1.0
|
|
O
|
A:ARG1652
|
2.5
|
36.5
|
1.0
|
|
OE1
|
A:GLU1654
|
2.5
|
36.4
|
1.0
|
|
CD
|
A:GLU1654
|
2.8
|
41.7
|
1.0
|
|
C
|
A:GLY1606
|
3.3
|
39.3
|
1.0
|
|
CG
|
A:ASP1609
|
3.5
|
31.6
|
1.0
|
|
C
|
A:ARG1652
|
3.7
|
34.1
|
1.0
|
|
CA
|
A:GLY1606
|
4.0
|
37.8
|
1.0
|
|
N
|
A:GLY1606
|
4.0
|
36.8
|
1.0
|
|
CB
|
A:ASP1609
|
4.1
|
32.3
|
1.0
|
|
CG
|
A:GLU1654
|
4.4
|
38.6
|
1.0
|
|
N
|
A:ASP1609
|
4.4
|
32.3
|
1.0
|
|
C
|
A:GLY1605
|
4.4
|
39.1
|
1.0
|
|
N
|
A:GLY1607
|
4.4
|
43.2
|
1.0
|
|
OD1
|
A:ASP1609
|
4.5
|
29.9
|
1.0
|
|
CA
|
A:VAL1653
|
4.5
|
34.6
|
1.0
|
|
OE2
|
A:GLU1603
|
4.5
|
32.3
|
1.0
|
|
N
|
A:VAL1653
|
4.6
|
34.4
|
1.0
|
|
O
|
A:ALA1649
|
4.6
|
43.8
|
1.0
|
|
O
|
A:ASP1650
|
4.6
|
38.0
|
1.0
|
|
N
|
A:ARG1652
|
4.7
|
36.6
|
1.0
|
|
O
|
A:HOH1866
|
4.7
|
59.5
|
1.0
|
|
O
|
A:GLY1605
|
4.7
|
30.6
|
1.0
|
|
CA
|
A:ARG1652
|
4.8
|
37.1
|
1.0
|
|
CA
|
A:GLY1607
|
4.8
|
43.5
|
1.0
|
|
C
|
A:GLY1607
|
4.9
|
45.5
|
1.0
|
|
CA
|
A:ASP1609
|
4.9
|
33.1
|
1.0
|
|
CD
|
A:GLU1603
|
4.9
|
33.1
|
1.0
|
|
N
|
A:GLU1654
|
4.9
|
37.9
|
1.0
|
|
N
|
A:HIS1608
|
5.0
|
42.4
|
1.0
|
|
CG
|
A:GLU1603
|
5.0
|
31.6
|
1.0
|
|
Calcium binding site 9 out
of 15 in 6sus
Go back to
Calcium Binding Sites List in 6sus
Calcium binding site 9 out
of 15 in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
 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 Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1709
b:26.1
occ:1.00
|
O
|
A:ASP1575
|
2.2
|
25.6
|
1.0
|
|
OD2
|
A:ASP1579
|
2.2
|
25.4
|
1.0
|
|
O
|
A:TYR1596
|
2.3
|
28.6
|
1.0
|
|
O
|
A:GLY1577
|
2.3
|
27.9
|
1.0
|
|
OD1
|
A:ASP1599
|
2.4
|
25.9
|
1.0
|
|
OD2
|
A:ASP1599
|
2.5
|
28.0
|
1.0
|
|
CG
|
A:ASP1599
|
2.8
|
26.0
|
1.0
|
|
C
|
A:GLY1577
|
3.4
|
26.2
|
1.0
|
|
C
|
A:TYR1596
|
3.4
|
30.2
|
1.0
|
|
CG
|
A:ASP1579
|
3.4
|
26.4
|
1.0
|
|
C
|
A:ASP1575
|
3.4
|
26.3
|
1.0
|
|
C
|
A:ALA1576
|
3.7
|
28.6
|
1.0
|
|
O
|
A:ALA1576
|
3.8
|
28.0
|
1.0
|
|
N
|
A:GLY1577
|
4.0
|
28.2
|
1.0
|
|
CA
|
A:TYR1596
|
4.0
|
29.0
|
1.0
|
|
C
|
A:GLY1574
|
4.1
|
23.1
|
1.0
|
|
CB
|
A:ASP1579
|
4.1
|
25.4
|
1.0
|
|
N
|
A:ASP1579
|
4.1
|
24.5
|
1.0
|
|
N
|
A:ASP1575
|
4.1
|
23.7
|
1.0
|
|
CB
|
A:TYR1596
|
4.2
|
27.4
|
1.0
|
|
CA
|
A:ALA1576
|
4.2
|
27.1
|
1.0
|
|
N
|
A:ALA1576
|
4.2
|
25.9
|
1.0
|
|
CB
|
A:ASP1599
|
4.3
|
26.8
|
1.0
|
|
CA
|
A:GLY1577
|
4.3
|
27.8
|
1.0
|
|
N
|
A:ASN1578
|
4.3
|
27.8
|
1.0
|
|
O
|
A:GLY1574
|
4.3
|
24.4
|
1.0
|
|
OD1
|
A:ASP1579
|
4.3
|
23.7
|
1.0
|
|
CA
|
A:ASP1575
|
4.4
|
25.3
|
1.0
|
|
CA
|
A:ASN1578
|
4.4
|
26.9
|
1.0
|
|
N
|
A:GLY1597
|
4.4
|
28.8
|
1.0
|
|
O
|
A:HOH1882
|
4.5
|
27.4
|
1.0
|
|
CA
|
A:GLY1574
|
4.5
|
24.3
|
1.0
|
|
CA
|
A:CA1710
|
4.6
|
24.8
|
1.0
|
|
CA
|
A:GLY1597
|
4.6
|
29.0
|
1.0
|
|
C
|
A:ASN1578
|
4.7
|
24.8
|
1.0
|
|
CA
|
A:ASP1579
|
4.8
|
25.5
|
1.0
|
|
C
|
A:GLY1597
|
4.8
|
29.4
|
1.0
|
|
N
|
A:HIS1598
|
4.9
|
30.3
|
0.5
|
|
CD2
|
A:TYR1596
|
4.9
|
29.3
|
1.0
|
|
CG
|
A:TYR1596
|
4.9
|
27.1
|
1.0
|
|
N
|
A:HIS1598
|
5.0
|
30.0
|
0.5
|
|
CA
|
A:ASP1599
|
5.0
|
28.2
|
1.0
|
|
Calcium binding site 10 out
of 15 in 6sus
Go back to
Calcium Binding Sites List in 6sus
Calcium binding site 10 out
of 15 in the Crystal Structure of Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis
 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 Rtx Domain Blocks IV and V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1710
b:24.8
occ:1.00
|
OD2
|
A:ASP1561
|
2.3
|
24.5
|
1.0
|
|
O
|
A:GLY1574
|
2.3
|
24.4
|
1.0
|
|
O
|
A:ALA1576
|
2.3
|
28.0
|
1.0
|
|
O
|
A:GLY1559
|
2.4
|
25.5
|
1.0
|
|
O
|
A:GLY1557
|
2.4
|
24.9
|
1.0
|
|
OD1
|
A:ASP1579
|
2.4
|
23.7
|
1.0
|
|
OD2
|
A:ASP1579
|
3.0
|
25.4
|
1.0
|
|
CG
|
A:ASP1579
|
3.1
|
26.4
|
1.0
|
|
CG
|
A:ASP1561
|
3.4
|
24.8
|
1.0
|
|
C
|
A:GLY1574
|
3.5
|
23.1
|
1.0
|
|
C
|
A:GLY1559
|
3.5
|
26.0
|
1.0
|
|
C
|
A:ALA1576
|
3.6
|
28.6
|
1.0
|
|
C
|
A:GLY1557
|
3.6
|
25.7
|
1.0
|
|
O
|
A:ALA1558
|
3.7
|
26.9
|
1.0
|
|
C
|
A:ALA1558
|
3.7
|
27.2
|
1.0
|
|
CB
|
A:ASP1561
|
4.1
|
22.8
|
1.0
|
|
N
|
A:GLY1559
|
4.1
|
25.5
|
1.0
|
|
C
|
A:ASP1575
|
4.1
|
26.3
|
1.0
|
|
CA
|
A:ALA1558
|
4.2
|
26.1
|
1.0
|
|
N
|
A:ASP1561
|
4.2
|
24.2
|
1.0
|
|
N
|
A:ALA1576
|
4.3
|
25.9
|
1.0
|
|
C
|
A:GLY1556
|
4.3
|
24.9
|
1.0
|
|
OD1
|
A:ASP1561
|
4.3
|
24.3
|
1.0
|
|
O
|
A:ASP1575
|
4.3
|
25.6
|
1.0
|
|
CA
|
A:GLY1574
|
4.3
|
24.3
|
1.0
|
|
CA
|
A:GLY1577
|
4.3
|
27.8
|
1.0
|
|
N
|
A:ALA1558
|
4.4
|
26.0
|
1.0
|
|
N
|
A:GLY1577
|
4.4
|
28.2
|
1.0
|
|
CA
|
A:GLY1559
|
4.4
|
26.9
|
1.0
|
|
N
|
A:ASP1575
|
4.4
|
23.7
|
1.0
|
|
N
|
A:GLY1557
|
4.4
|
24.0
|
1.0
|
|
O
|
A:GLY1556
|
4.4
|
24.0
|
1.0
|
|
CA
|
A:CA1711
|
4.5
|
25.2
|
1.0
|
|
CA
|
A:GLY1556
|
4.5
|
23.4
|
1.0
|
|
CB
|
A:ASP1579
|
4.5
|
25.4
|
1.0
|
|
N
|
A:ASP1560
|
4.5
|
26.1
|
1.0
|
|
C
|
A:GLY1577
|
4.6
|
26.2
|
1.0
|
|
CA
|
A:ALA1576
|
4.6
|
27.1
|
1.0
|
|
CA
|
A:ASP1575
|
4.6
|
25.3
|
1.0
|
|
CB
|
A:ASP1575
|
4.6
|
26.1
|
1.0
|
|
CA
|
A:CA1709
|
4.6
|
26.1
|
1.0
|
|
CA
|
A:ASP1560
|
4.6
|
25.1
|
1.0
|
|
CA
|
A:GLY1557
|
4.6
|
25.2
|
1.0
|
|
O
|
A:GLY1577
|
4.7
|
27.9
|
1.0
|
|
CA
|
A:ASP1561
|
4.8
|
24.1
|
1.0
|
|
C
|
A:ASP1560
|
4.8
|
25.7
|
1.0
|
|
Reference:
L.Motlova,
N.Klimova,
R.Fiser,
P.Sebo,
L.Bumba.
Continuous Assembly of Beta-Roll Structures Is Implicated in the Type I-Dependent Secretion of Large Repeat-in-Toxins (Rtx) Proteins. J.Mol.Biol. V. 432 5696 2020.
ISSN: ESSN 1089-8638
PubMed: 32860773
DOI: 10.1016/J.JMB.2020.08.020
Page generated: Tue Jul 16 14:53:40 2024
|
