Calcium in PDB 5cxl: Crystal Structure of Rtx Domain Block V of Adenylate Cyclase Toxin From Bordetella Pertussis
Enzymatic activity of Crystal Structure of Rtx Domain Block V of Adenylate Cyclase Toxin From Bordetella Pertussis
All present enzymatic activity of Crystal Structure of Rtx Domain Block V of Adenylate Cyclase Toxin From Bordetella Pertussis:
4.6.1.1;
Protein crystallography data
The structure of Crystal Structure of Rtx Domain Block V of Adenylate Cyclase Toxin From Bordetella Pertussis, PDB code: 5cxl
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)
|
32.15 /
1.45
|
|
Space group
|
P 41 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.225,
52.225,
195.952,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
14.8 /
20.7
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Rtx Domain Block V of Adenylate Cyclase Toxin From Bordetella Pertussis
(pdb code 5cxl). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the
Crystal Structure of Rtx Domain Block V of Adenylate Cyclase Toxin From Bordetella Pertussis, PDB code: 5cxl:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 16 in 5cxl
Go back to
Calcium Binding Sites List in 5cxl
Calcium binding site 1 out
of 16 in the Crystal Structure of Rtx Domain Block 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 Block V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1701
b:17.9
occ:1.00
|
O
|
A:ALA1558
|
2.3
|
20.0
|
1.0
|
|
OD1
|
A:ASN1543
|
2.3
|
19.6
|
1.0
|
|
O
|
A:GLY1541
|
2.3
|
20.8
|
1.0
|
|
O
|
A:GLY1556
|
2.4
|
17.9
|
1.0
|
|
OD1
|
A:ASP1561
|
2.4
|
15.8
|
1.0
|
|
O
|
A:ASP1539
|
2.4
|
21.5
|
1.0
|
|
OD2
|
A:ASP1561
|
3.0
|
16.9
|
1.0
|
|
CG
|
A:ASP1561
|
3.0
|
16.7
|
1.0
|
|
CG
|
A:ASN1543
|
3.4
|
18.4
|
1.0
|
|
C
|
A:GLY1556
|
3.5
|
16.7
|
1.0
|
|
C
|
A:ALA1558
|
3.5
|
20.0
|
1.0
|
|
C
|
A:GLY1541
|
3.6
|
19.9
|
1.0
|
|
C
|
A:ASP1539
|
3.6
|
23.5
|
1.0
|
|
C
|
A:GLY1557
|
3.8
|
16.4
|
1.0
|
|
O
|
A:GLY1557
|
3.9
|
16.6
|
1.0
|
|
N
|
A:ASP1539
|
4.0
|
23.9
|
1.0
|
|
N
|
A:ALA1558
|
4.0
|
18.5
|
1.0
|
|
N
|
A:GLY1541
|
4.1
|
23.4
|
1.0
|
|
C
|
A:ALA1540
|
4.1
|
21.8
|
1.0
|
|
N
|
A:ASN1543
|
4.2
|
18.9
|
1.0
|
|
CB
|
A:ASN1543
|
4.2
|
18.1
|
1.0
|
|
ND2
|
A:ASN1543
|
4.3
|
21.7
|
1.0
|
|
CA
|
A:GLY1557
|
4.3
|
16.4
|
1.0
|
|
N
|
A:GLY1557
|
4.3
|
15.3
|
1.0
|
|
CA
|
A:GLY1556
|
4.4
|
15.0
|
1.0
|
|
CA
|
A:ALA1558
|
4.4
|
18.5
|
1.0
|
|
N
|
A:GLY1559
|
4.4
|
20.6
|
1.0
|
|
O
|
A:GLY1559
|
4.4
|
17.1
|
1.0
|
|
CA
|
A:ALA1540
|
4.5
|
23.6
|
1.0
|
|
CA
|
A:GLY1541
|
4.5
|
24.6
|
1.0
|
|
CA
|
A:ASP1539
|
4.5
|
25.1
|
1.0
|
|
CB
|
A:ASP1561
|
4.5
|
14.3
|
1.0
|
|
N
|
A:ALA1540
|
4.5
|
25.1
|
1.0
|
|
CA
|
A:GLY1559
|
4.5
|
21.2
|
1.0
|
|
O
|
A:ALA1540
|
4.5
|
24.9
|
1.0
|
|
N
|
A:ALA1542
|
4.5
|
21.8
|
1.0
|
|
OD1
|
A:ASP1539
|
4.5
|
22.2
|
1.0
|
|
CA
|
A:CA1702
|
4.6
|
15.7
|
1.0
|
|
C
|
A:GLY1538
|
4.6
|
22.6
|
1.0
|
|
C
|
A:GLY1559
|
4.6
|
18.3
|
1.0
|
|
CA
|
A:ALA1542
|
4.7
|
19.7
|
1.0
|
|
CA
|
A:GLY1538
|
4.7
|
20.2
|
1.0
|
|
C
|
A:ALA1542
|
4.7
|
18.4
|
1.0
|
|
CA
|
A:ASN1543
|
4.9
|
17.0
|
1.0
|
|
Calcium binding site 2 out
of 16 in 5cxl
Go back to
Calcium Binding Sites List in 5cxl
Calcium binding site 2 out
of 16 in the Crystal Structure of Rtx Domain Block 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 Block V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1702
b:15.7
occ:1.00
|
OD2
|
A:ASP1561
|
2.3
|
16.9
|
1.0
|
|
O
|
A:ALA1576
|
2.3
|
16.6
|
1.0
|
|
O
|
A:GLY1557
|
2.3
|
16.6
|
1.0
|
|
O
|
A:GLY1574
|
2.4
|
14.4
|
1.0
|
|
O
|
A:GLY1559
|
2.4
|
17.1
|
1.0
|
|
OD1
|
A:ASP1579
|
2.4
|
15.0
|
1.0
|
|
OD2
|
A:ASP1579
|
3.1
|
14.8
|
1.0
|
|
CG
|
A:ASP1579
|
3.1
|
14.4
|
1.0
|
|
CG
|
A:ASP1561
|
3.4
|
16.7
|
1.0
|
|
C
|
A:GLY1574
|
3.5
|
11.9
|
1.0
|
|
C
|
A:ALA1576
|
3.6
|
17.1
|
1.0
|
|
C
|
A:GLY1557
|
3.6
|
16.4
|
1.0
|
|
C
|
A:GLY1559
|
3.6
|
18.3
|
1.0
|
|
C
|
A:ALA1558
|
3.8
|
20.0
|
1.0
|
|
O
|
A:ALA1558
|
3.8
|
20.0
|
1.0
|
|
C
|
A:ASP1575
|
4.1
|
15.3
|
1.0
|
|
CB
|
A:ASP1561
|
4.1
|
14.3
|
1.0
|
|
N
|
A:GLY1559
|
4.1
|
20.6
|
1.0
|
|
N
|
A:ALA1576
|
4.2
|
17.8
|
1.0
|
|
CA
|
A:ALA1558
|
4.2
|
18.5
|
1.0
|
|
O
|
A:ASP1575
|
4.2
|
15.6
|
1.0
|
|
N
|
A:ASP1561
|
4.2
|
14.7
|
1.0
|
|
C
|
A:GLY1556
|
4.3
|
16.7
|
1.0
|
|
OD1
|
A:ASP1561
|
4.3
|
15.8
|
1.0
|
|
CA
|
A:GLY1574
|
4.4
|
12.8
|
1.0
|
|
CA
|
A:GLY1577
|
4.4
|
17.6
|
1.0
|
|
N
|
A:GLY1557
|
4.4
|
15.3
|
1.0
|
|
N
|
A:ALA1558
|
4.4
|
18.5
|
1.0
|
|
N
|
A:GLY1577
|
4.4
|
17.0
|
1.0
|
|
CA
|
A:GLY1559
|
4.5
|
21.2
|
1.0
|
|
N
|
A:ASP1575
|
4.5
|
14.4
|
1.0
|
|
O
|
A:GLY1556
|
4.5
|
17.9
|
1.0
|
|
C
|
A:GLY1577
|
4.5
|
16.7
|
1.0
|
|
CA
|
A:ALA1576
|
4.5
|
17.1
|
1.0
|
|
CB
|
A:ASP1579
|
4.5
|
13.5
|
1.0
|
|
CA
|
A:ASP1575
|
4.6
|
14.2
|
1.0
|
|
CA
|
A:GLY1556
|
4.6
|
15.0
|
1.0
|
|
CA
|
A:CA1701
|
4.6
|
17.9
|
1.0
|
|
N
|
A:ASP1560
|
4.6
|
17.0
|
1.0
|
|
CA
|
A:GLY1557
|
4.6
|
16.4
|
1.0
|
|
CB
|
A:ASP1575
|
4.6
|
15.8
|
1.0
|
|
CA
|
A:CA1703
|
4.6
|
13.8
|
1.0
|
|
O
|
A:GLY1577
|
4.7
|
16.5
|
1.0
|
|
CA
|
A:ASP1560
|
4.7
|
17.4
|
1.0
|
|
CA
|
A:ASP1561
|
4.8
|
12.6
|
1.0
|
|
C
|
A:ASP1560
|
4.9
|
15.7
|
1.0
|
|
Calcium binding site 3 out
of 16 in 5cxl
Go back to
Calcium Binding Sites List in 5cxl
Calcium binding site 3 out
of 16 in the Crystal Structure of Rtx Domain Block 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 Block V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1703
b:13.8
occ:1.00
|
O
|
A:ASP1575
|
2.2
|
15.6
|
1.0
|
|
O
|
A:TYR1596
|
2.2
|
15.5
|
1.0
|
|
OD2
|
A:ASP1579
|
2.3
|
14.8
|
1.0
|
|
O
|
A:GLY1577
|
2.3
|
16.5
|
1.0
|
|
OD1
|
A:ASP1599
|
2.4
|
14.3
|
1.0
|
|
OD2
|
A:ASP1599
|
2.5
|
13.1
|
1.0
|
|
CG
|
A:ASP1599
|
2.8
|
12.9
|
1.0
|
|
C
|
A:TYR1596
|
3.4
|
15.1
|
1.0
|
|
C
|
A:GLY1577
|
3.4
|
16.7
|
1.0
|
|
CG
|
A:ASP1579
|
3.4
|
14.4
|
1.0
|
|
C
|
A:ASP1575
|
3.5
|
15.3
|
1.0
|
|
O
|
A:ALA1576
|
3.7
|
16.6
|
1.0
|
|
C
|
A:ALA1576
|
3.8
|
17.1
|
1.0
|
|
CA
|
A:TYR1596
|
4.0
|
15.5
|
1.0
|
|
N
|
A:GLY1577
|
4.0
|
17.0
|
1.0
|
|
C
|
A:GLY1574
|
4.1
|
11.9
|
1.0
|
|
CB
|
A:ASP1579
|
4.1
|
13.5
|
1.0
|
|
N
|
A:ASP1579
|
4.1
|
14.0
|
1.0
|
|
N
|
A:ASP1575
|
4.1
|
14.4
|
1.0
|
|
CB
|
A:TYR1596
|
4.1
|
15.2
|
1.0
|
|
CA
|
A:ALA1576
|
4.2
|
17.1
|
1.0
|
|
O
|
A:GLY1574
|
4.2
|
14.4
|
1.0
|
|
N
|
A:ALA1576
|
4.3
|
17.8
|
1.0
|
|
N
|
A:ASN1578
|
4.3
|
15.3
|
1.0
|
|
CB
|
A:ASP1599
|
4.3
|
12.3
|
1.0
|
|
CA
|
A:GLY1577
|
4.3
|
17.6
|
1.0
|
|
CD1
|
A:TYR1596
|
4.4
|
14.3
|
1.0
|
|
OD1
|
A:ASP1579
|
4.4
|
15.0
|
1.0
|
|
CA
|
A:ASP1575
|
4.4
|
14.2
|
1.0
|
|
CA
|
A:GLY1574
|
4.4
|
12.8
|
1.0
|
|
CA
|
A:ASN1578
|
4.4
|
16.4
|
1.0
|
|
N
|
A:GLY1597
|
4.4
|
14.9
|
1.0
|
|
CA
|
A:CA1702
|
4.6
|
15.7
|
1.0
|
|
CG
|
A:TYR1596
|
4.7
|
16.2
|
1.0
|
|
CA
|
A:GLY1597
|
4.7
|
15.9
|
1.0
|
|
C
|
A:ASN1578
|
4.7
|
14.8
|
1.0
|
|
O
|
A:HOH1862
|
4.8
|
13.4
|
1.0
|
|
C
|
A:GLY1597
|
4.8
|
14.4
|
1.0
|
|
CA
|
A:ASP1579
|
4.8
|
13.5
|
1.0
|
|
N
|
A:HIS1598
|
4.9
|
14.1
|
1.0
|
|
CA
|
A:ASP1599
|
5.0
|
11.8
|
1.0
|
|
Calcium binding site 4 out
of 16 in 5cxl
Go back to
Calcium Binding Sites List in 5cxl
Calcium binding site 4 out
of 16 in the Crystal Structure of Rtx Domain Block 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 Block V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1704
b:16.9
occ:1.00
|
O
|
A:GLY1547
|
2.3
|
16.4
|
1.0
|
|
O
|
A:ALA1549
|
2.3
|
18.1
|
1.0
|
|
O
|
A:SER1530
|
2.3
|
19.3
|
1.0
|
|
OD2
|
A:ASP1534
|
2.4
|
19.8
|
1.0
|
|
OD1
|
A:ASP1552
|
2.4
|
16.1
|
1.0
|
|
O
|
A:ARG1532
|
2.4
|
18.6
|
1.0
|
|
OD2
|
A:ASP1552
|
2.9
|
16.2
|
1.0
|
|
CG
|
A:ASP1552
|
3.0
|
14.4
|
1.0
|
|
CG
|
A:ASP1534
|
3.4
|
19.2
|
1.0
|
|
C
|
A:GLY1547
|
3.5
|
15.9
|
1.0
|
|
C
|
A:SER1530
|
3.5
|
18.5
|
1.0
|
|
C
|
A:ALA1549
|
3.5
|
17.9
|
1.0
|
|
C
|
A:ARG1532
|
3.6
|
18.9
|
1.0
|
|
O
|
A:LEU1548
|
3.9
|
14.9
|
1.0
|
|
N
|
A:SER1530
|
3.9
|
20.1
|
1.0
|
|
C
|
A:LEU1548
|
3.9
|
16.2
|
1.0
|
|
N
|
A:ARG1532
|
4.1
|
20.6
|
1.0
|
|
C
|
A:ALA1531
|
4.1
|
21.2
|
1.0
|
|
N
|
A:ASP1534
|
4.1
|
18.7
|
1.0
|
|
CB
|
A:ASP1534
|
4.2
|
19.7
|
1.0
|
|
OD1
|
A:ASP1534
|
4.2
|
23.1
|
1.0
|
|
CA
|
A:GLY1550
|
4.2
|
19.8
|
1.0
|
|
N
|
A:ALA1549
|
4.3
|
16.1
|
1.0
|
|
CA
|
A:GLY1547
|
4.3
|
13.7
|
1.0
|
|
N
|
A:GLY1550
|
4.3
|
18.5
|
1.0
|
|
CA
|
A:SER1530
|
4.4
|
20.0
|
1.0
|
|
N
|
A:LEU1548
|
4.4
|
16.2
|
1.0
|
|
CA
|
A:ALA1531
|
4.4
|
20.9
|
1.0
|
|
CB
|
A:ASP1552
|
4.4
|
14.2
|
1.0
|
|
N
|
A:ALA1531
|
4.4
|
20.7
|
1.0
|
|
CB
|
A:LEU1548
|
4.4
|
15.8
|
1.0
|
|
CA
|
A:LEU1548
|
4.4
|
17.1
|
1.0
|
|
O
|
A:ALA1531
|
4.4
|
25.9
|
1.0
|
|
C
|
A:GLY1550
|
4.4
|
18.8
|
1.0
|
|
O
|
A:GLY1550
|
4.5
|
18.0
|
1.0
|
|
CA
|
A:ARG1532
|
4.5
|
21.9
|
1.0
|
|
N
|
A:ASP1533
|
4.5
|
20.5
|
1.0
|
|
OG
|
A:SER1530
|
4.5
|
21.2
|
1.0
|
|
CA
|
A:ASP1533
|
4.5
|
18.2
|
1.0
|
|
CA
|
A:ALA1549
|
4.5
|
17.4
|
1.0
|
|
CA
|
A:CA1705
|
4.6
|
14.0
|
1.0
|
|
C
|
A:ASP1533
|
4.7
|
21.3
|
1.0
|
|
CA
|
A:ASP1534
|
4.8
|
18.4
|
1.0
|
|
C
|
A:GLY1529
|
5.0
|
16.5
|
1.0
|
|
Calcium binding site 5 out
of 16 in 5cxl
Go back to
Calcium Binding Sites List in 5cxl
Calcium binding site 5 out
of 16 in the Crystal Structure of Rtx Domain Block 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 Block V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1705
b:14.0
occ:1.00
|
OD2
|
A:ASP1552
|
2.3
|
16.2
|
1.0
|
|
O
|
A:GLU1567
|
2.3
|
14.4
|
1.0
|
|
O
|
A:GLY1565
|
2.3
|
13.2
|
1.0
|
|
O
|
A:GLY1550
|
2.4
|
18.0
|
1.0
|
|
O
|
A:LEU1548
|
2.4
|
14.9
|
1.0
|
|
OD1
|
A:ASP1570
|
2.4
|
14.7
|
1.0
|
|
OD2
|
A:ASP1570
|
3.1
|
13.2
|
1.0
|
|
CG
|
A:ASP1570
|
3.1
|
12.0
|
1.0
|
|
CG
|
A:ASP1552
|
3.4
|
14.4
|
1.0
|
|
C
|
A:GLU1567
|
3.5
|
14.1
|
1.0
|
|
C
|
A:GLY1565
|
3.5
|
13.5
|
1.0
|
|
C
|
A:GLY1550
|
3.5
|
18.8
|
1.0
|
|
C
|
A:LEU1548
|
3.6
|
16.2
|
1.0
|
|
C
|
A:ALA1549
|
3.7
|
17.9
|
1.0
|
|
O
|
A:ALA1549
|
3.9
|
18.1
|
1.0
|
|
N
|
A:GLY1550
|
4.0
|
18.5
|
1.0
|
|
C
|
A:ASP1566
|
4.0
|
12.9
|
1.0
|
|
CA
|
A:ALA1549
|
4.1
|
17.4
|
1.0
|
|
O
|
A:ASP1566
|
4.1
|
12.8
|
1.0
|
|
CB
|
A:ASP1552
|
4.2
|
14.2
|
1.0
|
|
N
|
A:GLU1567
|
4.2
|
15.4
|
1.0
|
|
N
|
A:ASP1552
|
4.3
|
14.1
|
1.0
|
|
OD1
|
A:ASP1552
|
4.3
|
16.1
|
1.0
|
|
C
|
A:GLY1547
|
4.3
|
15.9
|
1.0
|
|
O
|
A:GLY1547
|
4.3
|
16.4
|
1.0
|
|
N
|
A:ALA1549
|
4.3
|
16.1
|
1.0
|
|
CA
|
A:GLY1568
|
4.3
|
16.9
|
1.0
|
|
N
|
A:GLY1568
|
4.4
|
15.1
|
1.0
|
|
CA
|
A:GLY1565
|
4.4
|
12.6
|
1.0
|
|
CA
|
A:GLY1550
|
4.4
|
19.8
|
1.0
|
|
CA
|
A:GLU1567
|
4.5
|
13.9
|
1.0
|
|
N
|
A:LEU1548
|
4.5
|
16.2
|
1.0
|
|
N
|
A:ASP1566
|
4.5
|
12.8
|
1.0
|
|
N
|
A:ASN1551
|
4.5
|
16.6
|
1.0
|
|
CB
|
A:ASP1570
|
4.5
|
11.7
|
1.0
|
|
CA
|
A:CA1704
|
4.6
|
16.9
|
1.0
|
|
CA
|
A:GLY1547
|
4.6
|
13.7
|
1.0
|
|
CA
|
A:ASP1566
|
4.6
|
12.4
|
1.0
|
|
CB
|
A:ASP1566
|
4.7
|
13.7
|
1.0
|
|
C
|
A:GLY1568
|
4.7
|
15.5
|
1.0
|
|
CA
|
A:ASN1551
|
4.7
|
14.7
|
1.0
|
|
CA
|
A:LEU1548
|
4.7
|
17.1
|
1.0
|
|
CA
|
A:ASP1552
|
4.9
|
13.8
|
1.0
|
|
CA
|
A:CA1706
|
4.9
|
12.6
|
1.0
|
|
O
|
A:GLY1568
|
4.9
|
15.2
|
1.0
|
|
C
|
A:ASN1551
|
4.9
|
14.2
|
1.0
|
|
Calcium binding site 6 out
of 16 in 5cxl
Go back to
Calcium Binding Sites List in 5cxl
Calcium binding site 6 out
of 16 in the Crystal Structure of Rtx Domain Block 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 Block V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1706
b:12.6
occ:1.00
|
OD2
|
A:ASP1570
|
2.3
|
13.2
|
1.0
|
|
O
|
A:GLN1585
|
2.3
|
13.8
|
1.0
|
|
O
|
A:ASP1566
|
2.4
|
12.8
|
1.0
|
|
O
|
A:GLY1583
|
2.4
|
12.6
|
1.0
|
|
O
|
A:GLY1568
|
2.4
|
15.2
|
1.0
|
|
OD1
|
A:ASP1588
|
2.4
|
12.6
|
1.0
|
|
OD2
|
A:ASP1588
|
3.0
|
12.1
|
1.0
|
|
CG
|
A:ASP1588
|
3.0
|
13.6
|
1.0
|
|
CG
|
A:ASP1570
|
3.5
|
12.0
|
1.0
|
|
C
|
A:GLY1583
|
3.5
|
12.1
|
1.0
|
|
C
|
A:GLY1568
|
3.5
|
15.5
|
1.0
|
|
C
|
A:GLN1585
|
3.6
|
13.3
|
1.0
|
|
C
|
A:ASP1566
|
3.6
|
12.9
|
1.0
|
|
C
|
A:GLY1584
|
3.9
|
11.4
|
1.0
|
|
N
|
A:GLY1568
|
3.9
|
15.1
|
1.0
|
|
C
|
A:GLU1567
|
4.0
|
14.1
|
1.0
|
|
N
|
A:GLN1585
|
4.1
|
12.8
|
1.0
|
|
CA
|
A:GLY1584
|
4.1
|
12.8
|
1.0
|
|
O
|
A:GLY1584
|
4.1
|
12.6
|
1.0
|
|
C
|
A:GLY1565
|
4.1
|
13.5
|
1.0
|
|
CB
|
A:ASP1570
|
4.1
|
11.7
|
1.0
|
|
N
|
A:ASP1570
|
4.2
|
13.7
|
1.0
|
|
N
|
A:GLY1584
|
4.2
|
12.2
|
1.0
|
|
N
|
A:ASP1566
|
4.2
|
12.8
|
1.0
|
|
O
|
A:GLU1567
|
4.3
|
14.4
|
1.0
|
|
CA
|
A:GLY1568
|
4.3
|
16.9
|
1.0
|
|
O
|
A:GLY1565
|
4.3
|
13.2
|
1.0
|
|
CA
|
A:GLY1586
|
4.4
|
14.1
|
1.0
|
|
N
|
A:GLY1586
|
4.5
|
13.4
|
1.0
|
|
CB
|
A:ASP1588
|
4.5
|
11.8
|
1.0
|
|
OD1
|
A:ASP1570
|
4.5
|
14.7
|
1.0
|
|
CA
|
A:GLN1585
|
4.5
|
13.1
|
1.0
|
|
N
|
A:SER1569
|
4.5
|
14.8
|
1.0
|
|
CA
|
A:GLY1565
|
4.5
|
12.6
|
1.0
|
|
CA
|
A:GLU1567
|
4.5
|
13.9
|
1.0
|
|
N
|
A:GLU1567
|
4.5
|
15.4
|
1.0
|
|
C
|
A:GLY1586
|
4.5
|
14.4
|
1.0
|
|
O
|
A:GLY1586
|
4.5
|
14.9
|
1.0
|
|
CA
|
A:ASP1566
|
4.6
|
12.4
|
1.0
|
|
CA
|
A:GLY1583
|
4.6
|
11.8
|
1.0
|
|
CA
|
A:SER1569
|
4.7
|
16.2
|
0.5
|
|
CA
|
A:SER1569
|
4.7
|
16.4
|
0.5
|
|
CA
|
A:CA1707
|
4.8
|
12.2
|
1.0
|
|
C
|
A:SER1569
|
4.9
|
15.2
|
1.0
|
|
CA
|
A:ASP1570
|
4.9
|
12.1
|
1.0
|
|
CA
|
A:CA1705
|
4.9
|
14.0
|
1.0
|
|
Calcium binding site 7 out
of 16 in 5cxl
Go back to
Calcium Binding Sites List in 5cxl
Calcium binding site 7 out
of 16 in the Crystal Structure of Rtx Domain Block 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 Block V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1707
b:12.2
occ:1.00
|
O
|
A:GLY1605
|
2.3
|
15.9
|
1.0
|
|
OD2
|
A:ASP1588
|
2.3
|
12.1
|
1.0
|
|
O
|
A:GLY1586
|
2.4
|
14.9
|
1.0
|
|
OD1
|
A:ASP1609
|
2.4
|
13.2
|
1.0
|
|
OE2
|
A:GLU1603
|
2.4
|
12.1
|
1.0
|
|
O
|
A:GLY1584
|
2.4
|
12.6
|
1.0
|
|
OE1
|
A:GLU1603
|
2.6
|
13.2
|
1.0
|
|
CD
|
A:GLU1603
|
2.9
|
11.6
|
1.0
|
|
CG
|
A:ASP1609
|
3.3
|
12.7
|
1.0
|
|
CG
|
A:ASP1588
|
3.4
|
13.6
|
1.0
|
|
OD2
|
A:ASP1609
|
3.5
|
14.5
|
1.0
|
|
C
|
A:GLY1605
|
3.5
|
13.2
|
1.0
|
|
C
|
A:GLY1586
|
3.6
|
14.4
|
1.0
|
|
C
|
A:GLY1584
|
3.6
|
11.4
|
1.0
|
|
C
|
A:GLN1585
|
3.8
|
13.3
|
1.0
|
|
O
|
A:GLN1585
|
3.9
|
13.8
|
1.0
|
|
CB
|
A:ASP1588
|
4.0
|
11.8
|
1.0
|
|
N
|
A:GLY1586
|
4.0
|
13.4
|
1.0
|
|
N
|
A:ASP1588
|
4.1
|
11.8
|
1.0
|
|
N
|
A:GLY1605
|
4.2
|
14.3
|
1.0
|
|
CA
|
A:GLN1585
|
4.2
|
13.1
|
1.0
|
|
CA
|
A:GLY1606
|
4.3
|
17.0
|
1.0
|
|
N
|
A:GLY1606
|
4.4
|
16.3
|
1.0
|
|
CG
|
A:GLU1603
|
4.4
|
12.2
|
1.0
|
|
N
|
A:GLN1585
|
4.4
|
12.8
|
1.0
|
|
CA
|
A:GLY1586
|
4.4
|
14.1
|
1.0
|
|
O
|
A:HOH1829
|
4.4
|
15.7
|
1.0
|
|
OD1
|
A:ASP1588
|
4.4
|
12.6
|
1.0
|
|
CA
|
A:GLY1605
|
4.5
|
14.7
|
1.0
|
|
N
|
A:GLY1584
|
4.5
|
12.2
|
1.0
|
|
C
|
A:GLY1583
|
4.5
|
12.1
|
1.0
|
|
N
|
A:ASP1587
|
4.6
|
14.1
|
1.0
|
|
CB
|
A:ASP1609
|
4.6
|
13.3
|
1.0
|
|
CA
|
A:GLY1584
|
4.7
|
12.8
|
1.0
|
|
CA
|
A:ASP1588
|
4.7
|
11.8
|
1.0
|
|
CA
|
A:ASP1587
|
4.7
|
12.9
|
1.0
|
|
O
|
A:GLY1583
|
4.7
|
12.6
|
1.0
|
|
C
|
A:ASP1587
|
4.8
|
13.9
|
1.0
|
|
CA
|
A:CA1706
|
4.8
|
12.6
|
1.0
|
|
OH
|
A:TYR1590
|
4.9
|
11.2
|
1.0
|
|
N
|
A:SER1604
|
4.9
|
14.5
|
1.0
|
|
Calcium binding site 8 out
of 16 in 5cxl
Go back to
Calcium Binding Sites List in 5cxl
Calcium binding site 8 out
of 16 in the Crystal Structure of Rtx Domain Block 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 Block V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1708
b:15.4
occ:1.00
|
O
|
A:GLY1606
|
2.3
|
17.9
|
1.0
|
|
OD2
|
A:ASP1609
|
2.3
|
14.5
|
1.0
|
|
O
|
A:ARG1652
|
2.4
|
15.6
|
0.7
|
|
O
|
A:ARG1652
|
2.4
|
15.9
|
0.3
|
|
O
|
A:HOH1829
|
2.4
|
15.7
|
1.0
|
|
OE2
|
A:GLU1654
|
2.4
|
21.6
|
1.0
|
|
O
|
A:HOH1824
|
2.4
|
18.6
|
1.0
|
|
OE1
|
A:GLU1654
|
2.5
|
16.5
|
1.0
|
|
CD
|
A:GLU1654
|
2.9
|
16.4
|
1.0
|
|
CG
|
A:ASP1609
|
3.5
|
12.7
|
1.0
|
|
C
|
A:GLY1606
|
3.5
|
16.5
|
1.0
|
|
C
|
A:ARG1652
|
3.6
|
15.6
|
0.7
|
|
C
|
A:ARG1652
|
3.6
|
15.8
|
0.3
|
|
CB
|
A:ASP1609
|
4.1
|
13.3
|
1.0
|
|
N
|
A:GLY1606
|
4.1
|
16.3
|
1.0
|
|
CA
|
A:GLY1606
|
4.2
|
17.0
|
1.0
|
|
O
|
A:ALA1649
|
4.3
|
21.0
|
1.0
|
|
C
|
A:GLY1605
|
4.4
|
13.2
|
1.0
|
|
CG
|
A:GLU1654
|
4.4
|
19.1
|
1.0
|
|
CA
|
A:VAL1653
|
4.4
|
17.2
|
1.0
|
|
N
|
A:VAL1653
|
4.4
|
15.3
|
1.0
|
|
O
|
A:HOH1805
|
4.4
|
39.9
|
1.0
|
|
N
|
A:ASP1609
|
4.5
|
15.0
|
1.0
|
|
OD1
|
A:ASP1609
|
4.5
|
13.2
|
1.0
|
|
OE2
|
A:GLU1603
|
4.5
|
12.1
|
1.0
|
|
CA
|
A:ARG1652
|
4.5
|
16.6
|
0.7
|
|
O
|
A:HOH1848
|
4.6
|
33.6
|
1.0
|
|
CA
|
A:ARG1652
|
4.6
|
16.6
|
0.3
|
|
N
|
A:GLY1607
|
4.6
|
17.7
|
1.0
|
|
O
|
A:ASP1650
|
4.6
|
15.4
|
1.0
|
|
N
|
A:ARG1652
|
4.6
|
16.6
|
0.3
|
|
N
|
A:ARG1652
|
4.6
|
16.6
|
0.7
|
|
O
|
A:GLY1605
|
4.7
|
15.9
|
1.0
|
|
CA
|
A:GLY1607
|
4.8
|
17.3
|
1.0
|
|
N
|
A:GLU1654
|
4.8
|
18.5
|
1.0
|
|
C
|
A:GLY1607
|
4.9
|
20.5
|
1.0
|
|
CD
|
A:GLU1603
|
4.9
|
11.6
|
1.0
|
|
CA
|
A:ASP1609
|
4.9
|
13.6
|
1.0
|
|
CA
|
A:GLY1605
|
5.0
|
14.7
|
1.0
|
|
C
|
A:VAL1653
|
5.0
|
18.7
|
1.0
|
|
Calcium binding site 9 out
of 16 in 5cxl
Go back to
Calcium Binding Sites List in 5cxl
Calcium binding site 9 out
of 16 in the Crystal Structure of Rtx Domain Block 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 Block V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1702
b:15.4
occ:1.00
|
O
|
B:ALA1558
|
2.3
|
15.7
|
1.0
|
|
O
|
B:GLY1541
|
2.3
|
17.7
|
1.0
|
|
O
|
B:ASP1539
|
2.3
|
17.1
|
1.0
|
|
O
|
B:GLY1556
|
2.3
|
13.9
|
1.0
|
|
OD1
|
B:ASN1543
|
2.4
|
14.2
|
1.0
|
|
OD1
|
B:ASP1561
|
2.4
|
14.7
|
1.0
|
|
OD2
|
B:ASP1561
|
2.9
|
15.8
|
1.0
|
|
CG
|
B:ASP1561
|
3.0
|
14.7
|
1.0
|
|
CG
|
B:ASN1543
|
3.4
|
15.4
|
1.0
|
|
C
|
B:GLY1556
|
3.5
|
14.3
|
1.0
|
|
C
|
B:ASP1539
|
3.5
|
17.8
|
1.0
|
|
C
|
B:GLY1541
|
3.6
|
17.9
|
1.0
|
|
C
|
B:ALA1558
|
3.6
|
14.5
|
1.0
|
|
C
|
B:GLY1557
|
3.8
|
14.3
|
1.0
|
|
O
|
B:GLY1557
|
3.9
|
14.7
|
1.0
|
|
N
|
B:ASP1539
|
4.0
|
18.2
|
1.0
|
|
N
|
B:GLY1541
|
4.0
|
16.7
|
1.0
|
|
N
|
B:ALA1558
|
4.0
|
15.7
|
1.0
|
|
C
|
B:ALA1540
|
4.1
|
19.2
|
1.0
|
|
N
|
B:ASN1543
|
4.2
|
15.9
|
1.0
|
|
CA
|
B:GLY1557
|
4.2
|
13.4
|
1.0
|
|
CB
|
B:ASN1543
|
4.3
|
15.6
|
1.0
|
|
N
|
B:GLY1557
|
4.3
|
13.0
|
1.0
|
|
ND2
|
B:ASN1543
|
4.3
|
17.6
|
1.0
|
|
CA
|
B:GLY1556
|
4.4
|
14.8
|
1.0
|
|
N
|
B:ALA1540
|
4.4
|
18.0
|
1.0
|
|
CB
|
B:ASP1561
|
4.4
|
13.3
|
1.0
|
|
CA
|
B:ALA1540
|
4.4
|
18.8
|
1.0
|
|
CA
|
B:ASP1539
|
4.4
|
16.5
|
1.0
|
|
CA
|
B:GLY1541
|
4.4
|
19.7
|
1.0
|
|
CA
|
B:ALA1558
|
4.4
|
16.1
|
1.0
|
|
O
|
B:GLY1559
|
4.5
|
16.4
|
1.0
|
|
N
|
B:GLY1559
|
4.5
|
16.6
|
1.0
|
|
OD1
|
B:ASP1539
|
4.5
|
19.9
|
1.0
|
|
O
|
B:ALA1540
|
4.5
|
21.4
|
1.0
|
|
CA
|
B:CA1703
|
4.5
|
14.3
|
1.0
|
|
C
|
B:GLY1538
|
4.5
|
17.1
|
1.0
|
|
N
|
B:ALA1542
|
4.5
|
16.8
|
1.0
|
|
CA
|
B:GLY1559
|
4.5
|
17.1
|
1.0
|
|
C
|
B:GLY1559
|
4.6
|
14.5
|
1.0
|
|
CA
|
B:ALA1542
|
4.6
|
16.6
|
1.0
|
|
CA
|
B:GLY1538
|
4.6
|
16.4
|
1.0
|
|
C
|
B:ALA1542
|
4.8
|
18.5
|
1.0
|
|
CA
|
B:ASN1543
|
4.9
|
13.0
|
1.0
|
|
Calcium binding site 10 out
of 16 in 5cxl
Go back to
Calcium Binding Sites List in 5cxl
Calcium binding site 10 out
of 16 in the Crystal Structure of Rtx Domain Block 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 Block V of Adenylate Cyclase Toxin From Bordetella Pertussis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1703
b:14.3
occ:1.00
|
O
|
B:ALA1576
|
2.3
|
15.4
|
1.0
|
|
O
|
B:GLY1559
|
2.3
|
16.4
|
1.0
|
|
OD2
|
B:ASP1561
|
2.3
|
15.8
|
1.0
|
|
O
|
B:GLY1557
|
2.4
|
14.7
|
1.0
|
|
O
|
B:GLY1574
|
2.4
|
15.5
|
1.0
|
|
OD1
|
B:ASP1579
|
2.4
|
13.2
|
1.0
|
|
OD2
|
B:ASP1579
|
3.1
|
13.3
|
1.0
|
|
CG
|
B:ASP1579
|
3.1
|
13.4
|
1.0
|
|
CG
|
B:ASP1561
|
3.4
|
14.7
|
1.0
|
|
C
|
B:GLY1574
|
3.5
|
13.2
|
1.0
|
|
C
|
B:GLY1559
|
3.6
|
14.5
|
1.0
|
|
C
|
B:ALA1576
|
3.6
|
15.4
|
1.0
|
|
C
|
B:GLY1557
|
3.6
|
14.3
|
1.0
|
|
C
|
B:ALA1558
|
3.7
|
14.5
|
1.0
|
|
O
|
B:ALA1558
|
3.7
|
15.7
|
1.0
|
|
N
|
B:GLY1559
|
4.1
|
16.6
|
1.0
|
|
C
|
B:ASP1575
|
4.1
|
12.6
|
1.0
|
|
CB
|
B:ASP1561
|
4.1
|
13.3
|
1.0
|
|
CA
|
B:ALA1558
|
4.1
|
16.1
|
1.0
|
|
N
|
B:ALA1576
|
4.2
|
14.4
|
1.0
|
|
N
|
B:ASP1561
|
4.2
|
15.2
|
1.0
|
|
O
|
B:ASP1575
|
4.2
|
14.7
|
1.0
|
|
CA
|
B:GLY1574
|
4.3
|
14.3
|
1.0
|
|
N
|
B:ALA1558
|
4.3
|
15.7
|
1.0
|
|
OD1
|
B:ASP1561
|
4.3
|
14.7
|
1.0
|
|
C
|
B:GLY1556
|
4.4
|
14.3
|
1.0
|
|
CA
|
B:GLY1577
|
4.4
|
19.3
|
1.0
|
|
CA
|
B:GLY1559
|
4.4
|
17.1
|
1.0
|
|
N
|
B:GLY1577
|
4.4
|
16.4
|
1.0
|
|
N
|
B:ASP1575
|
4.5
|
14.1
|
1.0
|
|
O
|
B:GLY1556
|
4.5
|
13.9
|
1.0
|
|
N
|
B:GLY1557
|
4.5
|
13.0
|
1.0
|
|
CA
|
B:CA1702
|
4.5
|
15.4
|
1.0
|
|
N
|
B:ASP1560
|
4.5
|
15.7
|
1.0
|
|
CA
|
B:ALA1576
|
4.5
|
16.0
|
1.0
|
|
CB
|
B:ASP1579
|
4.5
|
14.8
|
1.0
|
|
C
|
B:GLY1577
|
4.5
|
16.5
|
1.0
|
|
CB
|
B:ASP1575
|
4.6
|
15.6
|
1.0
|
|
CA
|
B:ASP1575
|
4.6
|
14.7
|
1.0
|
|
CA
|
B:GLY1556
|
4.6
|
14.8
|
1.0
|
|
CA
|
B:CA1704
|
4.7
|
14.7
|
1.0
|
|
CA
|
B:ASP1560
|
4.7
|
16.1
|
1.0
|
|
O
|
B:GLY1577
|
4.7
|
16.7
|
1.0
|
|
CA
|
B:GLY1557
|
4.7
|
13.4
|
1.0
|
|
CA
|
B:ASP1561
|
4.8
|
12.9
|
1.0
|
|
C
|
B:ASP1560
|
4.8
|
15.7
|
1.0
|
|
Reference:
L.Bumba,
J.Masin,
P.Macek,
T.Wald,
L.Motlova,
I.Bibova,
N.Klimova,
L.Bednarova,
V.Veverka,
M.Kachala,
D.I.Svergun,
C.Barinka,
P.Sebo.
Calcium-Driven Folding of Rtx Domain Beta-Rolls Ratchets Translocation of Rtx Proteins Through Type I Secretion Ducts. Mol.Cell V. 62 47 2016.
ISSN: ISSN 1097-2765
PubMed: 27058787
DOI: 10.1016/J.MOLCEL.2016.03.018
Page generated: Sat Dec 12 05:20:37 2020
|
