Calcium in PDB 5cvw: 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: 5cvw
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)
|
29.24 /
1.25
|
|
Space group
|
I 2 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.824,
62.983,
77.627,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
13.9 /
16.6
|
Other elements in 5cvw:
The structure of Crystal Structure of Rtx Domain Block V of Adenylate Cyclase Toxin From Bordetella Pertussis also contains other interesting chemical elements:
Calcium 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 5cvw). 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 Rtx Domain Block V of Adenylate Cyclase Toxin From Bordetella Pertussis, PDB code: 5cvw:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 5cvw
Go back to
Calcium Binding Sites List in 5cvw
Calcium binding site 1 out
of 8 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:11.8
occ:1.00
|
O
|
A:ALA1558
|
2.3
|
13.3
|
1.0
|
|
O
|
A:ASP1539
|
2.3
|
13.6
|
1.0
|
|
O
|
A:GLY1556
|
2.4
|
11.8
|
1.0
|
|
O
|
A:GLY1541
|
2.4
|
13.7
|
1.0
|
|
OD1
|
A:ASN1543
|
2.4
|
12.2
|
1.0
|
|
OD1
|
A:ASP1561
|
2.4
|
11.4
|
1.0
|
|
OD2
|
A:ASP1561
|
2.9
|
10.8
|
1.0
|
|
CG
|
A:ASP1561
|
3.0
|
9.9
|
1.0
|
|
CG
|
A:ASN1543
|
3.4
|
12.1
|
1.0
|
|
C
|
A:GLY1556
|
3.5
|
10.9
|
1.0
|
|
C
|
A:ALA1558
|
3.5
|
12.1
|
1.0
|
|
C
|
A:ASP1539
|
3.5
|
14.0
|
1.0
|
|
C
|
A:GLY1541
|
3.6
|
12.7
|
1.0
|
|
C
|
A:GLY1557
|
3.8
|
11.8
|
1.0
|
|
O
|
A:GLY1557
|
3.8
|
11.6
|
1.0
|
|
N
|
A:ASP1539
|
3.9
|
14.3
|
1.0
|
|
N
|
A:GLY1541
|
4.1
|
14.3
|
1.0
|
|
N
|
A:ALA1558
|
4.1
|
11.8
|
1.0
|
|
C
|
A:ALA1540
|
4.2
|
15.3
|
1.0
|
|
CA
|
A:GLY1557
|
4.2
|
12.1
|
1.0
|
|
CB
|
A:ASN1543
|
4.2
|
11.7
|
1.0
|
|
N
|
A:ASN1543
|
4.2
|
11.7
|
1.0
|
|
N
|
A:GLY1557
|
4.3
|
11.8
|
1.0
|
|
ND2
|
A:ASN1543
|
4.3
|
16.1
|
1.0
|
|
CA
|
A:GLY1559
|
4.3
|
12.9
|
1.0
|
|
O
|
A:GLY1559
|
4.4
|
10.8
|
1.0
|
|
CA
|
A:ASP1539
|
4.4
|
14.9
|
1.0
|
|
N
|
A:GLY1559
|
4.4
|
13.9
|
1.0
|
|
CA
|
A:GLY1556
|
4.4
|
11.6
|
1.0
|
|
N
|
A:ALA1540
|
4.4
|
15.2
|
1.0
|
|
CA
|
A:GLY1541
|
4.4
|
14.1
|
1.0
|
|
C
|
A:GLY1559
|
4.5
|
10.8
|
1.0
|
|
CA
|
A:ALA1558
|
4.5
|
12.9
|
1.0
|
|
OD1
|
A:ASP1539
|
4.5
|
14.5
|
1.0
|
|
CA
|
A:CA1702
|
4.5
|
10.7
|
1.0
|
|
CB
|
A:ASP1561
|
4.5
|
10.3
|
1.0
|
|
CA
|
A:ALA1540
|
4.5
|
14.8
|
1.0
|
|
N
|
A:ALA1542
|
4.5
|
13.8
|
1.0
|
|
C
|
A:GLY1538
|
4.6
|
14.8
|
1.0
|
|
O
|
A:ALA1540
|
4.6
|
16.7
|
1.0
|
|
CA
|
A:GLY1538
|
4.7
|
12.8
|
1.0
|
|
CA
|
A:ALA1542
|
4.7
|
13.6
|
1.0
|
|
C
|
A:ALA1542
|
4.8
|
13.6
|
1.0
|
|
CA
|
A:ASN1543
|
4.9
|
11.9
|
1.0
|
|
Calcium binding site 2 out
of 8 in 5cvw
Go back to
Calcium Binding Sites List in 5cvw
Calcium binding site 2 out
of 8 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:10.7
occ:1.00
|
O
|
A:ALA1576
|
2.3
|
11.6
|
1.0
|
|
OD2
|
A:ASP1561
|
2.3
|
10.8
|
1.0
|
|
O
|
A:GLY1559
|
2.4
|
10.8
|
1.0
|
|
O
|
A:GLY1574
|
2.4
|
10.8
|
1.0
|
|
O
|
A:GLY1557
|
2.4
|
11.6
|
1.0
|
|
OD1
|
A:ASP1579
|
2.4
|
11.2
|
1.0
|
|
OD2
|
A:ASP1579
|
3.0
|
11.0
|
1.0
|
|
CG
|
A:ASP1579
|
3.1
|
10.3
|
1.0
|
|
CG
|
A:ASP1561
|
3.4
|
9.9
|
1.0
|
|
C
|
A:ALA1576
|
3.5
|
11.9
|
1.0
|
|
C
|
A:GLY1574
|
3.5
|
10.0
|
1.0
|
|
C
|
A:GLY1557
|
3.6
|
11.8
|
1.0
|
|
C
|
A:GLY1559
|
3.6
|
10.8
|
1.0
|
|
O
|
A:ALA1558
|
3.7
|
13.3
|
1.0
|
|
C
|
A:ALA1558
|
3.7
|
12.1
|
1.0
|
|
CA
|
A:ALA1558
|
4.1
|
12.9
|
1.0
|
|
C
|
A:ASP1575
|
4.1
|
11.2
|
1.0
|
|
N
|
A:GLY1559
|
4.1
|
13.9
|
1.0
|
|
CB
|
A:ASP1561
|
4.1
|
10.3
|
1.0
|
|
N
|
A:ALA1576
|
4.2
|
11.9
|
1.0
|
|
O
|
A:ASP1575
|
4.2
|
11.0
|
1.0
|
|
N
|
A:ASP1561
|
4.3
|
10.1
|
1.0
|
|
N
|
A:ALA1558
|
4.3
|
11.8
|
1.0
|
|
OD1
|
A:ASP1561
|
4.3
|
11.4
|
1.0
|
|
CA
|
A:GLY1577
|
4.3
|
11.1
|
1.0
|
|
CA
|
A:GLY1574
|
4.3
|
11.1
|
1.0
|
|
C
|
A:GLY1556
|
4.4
|
10.9
|
1.0
|
|
N
|
A:GLY1577
|
4.4
|
11.5
|
1.0
|
|
CA
|
A:GLY1559
|
4.4
|
12.9
|
1.0
|
|
N
|
A:ASP1575
|
4.4
|
10.4
|
1.0
|
|
O
|
A:GLY1556
|
4.5
|
11.8
|
1.0
|
|
N
|
A:GLY1557
|
4.5
|
11.8
|
1.0
|
|
CA
|
A:CA1701
|
4.5
|
11.8
|
1.0
|
|
CA
|
A:ALA1576
|
4.5
|
12.2
|
1.0
|
|
CB
|
A:ASP1579
|
4.5
|
11.0
|
1.0
|
|
N
|
A:ASP1560
|
4.5
|
11.5
|
1.0
|
|
CA
|
A:ASP1575
|
4.6
|
11.0
|
1.0
|
|
C
|
A:GLY1577
|
4.6
|
10.7
|
1.0
|
|
CB
|
A:ASP1575
|
4.7
|
12.8
|
1.0
|
|
CA
|
A:CA1703
|
4.7
|
10.9
|
1.0
|
|
CA
|
A:GLY1557
|
4.7
|
12.1
|
1.0
|
|
CA
|
A:ASP1560
|
4.7
|
11.3
|
1.0
|
|
CA
|
A:GLY1556
|
4.7
|
11.6
|
1.0
|
|
O
|
A:GLY1577
|
4.7
|
12.1
|
1.0
|
|
CA
|
A:ASP1561
|
4.9
|
10.4
|
1.0
|
|
C
|
A:ASP1560
|
4.9
|
11.4
|
1.0
|
|
Calcium binding site 3 out
of 8 in 5cvw
Go back to
Calcium Binding Sites List in 5cvw
Calcium binding site 3 out
of 8 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:10.9
occ:1.00
|
O
|
A:TYR1596
|
2.3
|
11.4
|
1.0
|
|
O
|
A:GLY1577
|
2.3
|
12.1
|
1.0
|
|
O
|
A:ASP1575
|
2.3
|
11.0
|
1.0
|
|
OD2
|
A:ASP1579
|
2.3
|
11.0
|
1.0
|
|
OD1
|
A:ASP1599
|
2.3
|
10.5
|
1.0
|
|
OD2
|
A:ASP1599
|
2.5
|
10.9
|
1.0
|
|
CG
|
A:ASP1599
|
2.8
|
10.2
|
1.0
|
|
C
|
A:TYR1596
|
3.4
|
11.4
|
1.0
|
|
CG
|
A:ASP1579
|
3.4
|
10.3
|
1.0
|
|
C
|
A:GLY1577
|
3.4
|
10.7
|
1.0
|
|
C
|
A:ASP1575
|
3.5
|
11.2
|
1.0
|
|
C
|
A:ALA1576
|
3.8
|
11.9
|
1.0
|
|
O
|
A:ALA1576
|
3.9
|
11.6
|
1.0
|
|
CA
|
A:TYR1596
|
4.0
|
11.3
|
1.0
|
|
N
|
A:GLY1577
|
4.0
|
11.5
|
1.0
|
|
C
|
A:GLY1574
|
4.0
|
10.0
|
1.0
|
|
CB
|
A:ASP1579
|
4.1
|
11.0
|
1.0
|
|
N
|
A:ASP1575
|
4.1
|
10.4
|
1.0
|
|
N
|
A:ASP1579
|
4.1
|
9.7
|
1.0
|
|
CB
|
A:TYR1596
|
4.2
|
11.5
|
1.0
|
|
O
|
A:GLY1574
|
4.2
|
10.8
|
1.0
|
|
CA
|
A:ALA1576
|
4.3
|
12.2
|
1.0
|
|
CB
|
A:ASP1599
|
4.3
|
10.7
|
1.0
|
|
CA
|
A:GLY1577
|
4.3
|
11.1
|
1.0
|
|
N
|
A:ASN1578
|
4.3
|
11.3
|
1.0
|
|
N
|
A:ALA1576
|
4.3
|
11.9
|
1.0
|
|
OD1
|
A:ASP1579
|
4.4
|
11.2
|
1.0
|
|
CA
|
A:ASN1578
|
4.4
|
11.8
|
1.0
|
|
N
|
A:GLY1597
|
4.4
|
11.8
|
1.0
|
|
CA
|
A:ASP1575
|
4.4
|
11.0
|
1.0
|
|
CA
|
A:GLY1574
|
4.5
|
11.1
|
1.0
|
|
CD2
|
A:TYR1596
|
4.5
|
12.3
|
1.0
|
|
CA
|
A:GLY1597
|
4.6
|
12.5
|
1.0
|
|
CA
|
A:CA1702
|
4.7
|
10.7
|
1.0
|
|
O
|
A:HOH1849
|
4.7
|
11.6
|
1.0
|
|
C
|
A:ASN1578
|
4.7
|
10.7
|
1.0
|
|
CG
|
A:TYR1596
|
4.8
|
12.1
|
1.0
|
|
C
|
A:GLY1597
|
4.8
|
11.1
|
1.0
|
|
CA
|
A:ASP1579
|
4.8
|
10.0
|
1.0
|
|
N
|
A:HIS1598
|
4.9
|
12.0
|
1.0
|
|
CA
|
A:ASP1599
|
5.0
|
10.9
|
1.0
|
|
O
|
A:HOH1839
|
5.0
|
17.6
|
1.0
|
|
Calcium binding site 4 out
of 8 in 5cvw
Go back to
Calcium Binding Sites List in 5cvw
Calcium binding site 4 out
of 8 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:11.4
occ:1.00
|
O
|
A:ALA1549
|
2.3
|
12.6
|
1.0
|
|
O
|
A:SER1530
|
2.3
|
12.9
|
1.0
|
|
O
|
A:ARG1532
|
2.3
|
12.8
|
1.0
|
|
O
|
A:GLY1547
|
2.3
|
11.7
|
1.0
|
|
OD2
|
A:ASP1534
|
2.3
|
13.2
|
1.0
|
|
OD1
|
A:ASP1552
|
2.4
|
11.2
|
1.0
|
|
OD2
|
A:ASP1552
|
2.9
|
11.3
|
1.0
|
|
CG
|
A:ASP1552
|
3.0
|
11.1
|
1.0
|
|
CG
|
A:ASP1534
|
3.4
|
12.9
|
1.0
|
|
C
|
A:ALA1549
|
3.5
|
11.4
|
1.0
|
|
C
|
A:GLY1547
|
3.5
|
11.2
|
1.0
|
|
C
|
A:SER1530
|
3.5
|
13.7
|
1.0
|
|
C
|
A:ARG1532
|
3.5
|
14.3
|
1.0
|
|
O
|
A:LEU1548
|
3.9
|
10.7
|
0.7
|
|
C
|
A:LEU1548
|
3.9
|
11.0
|
0.7
|
|
C
|
A:LEU1548
|
4.0
|
10.8
|
0.3
|
|
N
|
A:SER1530
|
4.0
|
13.5
|
1.0
|
|
O
|
A:LEU1548
|
4.0
|
11.3
|
0.3
|
|
N
|
A:ARG1532
|
4.1
|
16.2
|
1.0
|
|
N
|
A:ASP1534
|
4.1
|
11.3
|
1.0
|
|
C
|
A:ALA1531
|
4.1
|
15.8
|
1.0
|
|
OD1
|
A:ASP1534
|
4.2
|
16.0
|
1.0
|
|
CB
|
A:ASP1534
|
4.2
|
13.3
|
1.0
|
|
CA
|
A:GLY1550
|
4.2
|
12.5
|
1.0
|
|
CA
|
A:GLY1547
|
4.3
|
11.6
|
1.0
|
|
N
|
A:ALA1549
|
4.3
|
10.4
|
1.0
|
|
CB
|
A:LEU1548
|
4.3
|
12.8
|
0.3
|
|
N
|
A:GLY1550
|
4.3
|
11.8
|
1.0
|
|
CA
|
A:SER1530
|
4.4
|
13.2
|
1.0
|
|
N
|
A:ASP1533
|
4.4
|
13.4
|
1.0
|
|
N
|
A:ALA1531
|
4.4
|
13.7
|
1.0
|
|
CA
|
A:ALA1531
|
4.4
|
16.1
|
1.0
|
|
CB
|
A:ASP1552
|
4.4
|
10.6
|
1.0
|
|
CA
|
A:ASP1533
|
4.4
|
12.5
|
1.0
|
|
N
|
A:LEU1548
|
4.4
|
11.4
|
0.3
|
|
CA
|
A:LEU1548
|
4.5
|
11.5
|
0.3
|
|
O
|
A:ALA1531
|
4.5
|
17.9
|
1.0
|
|
CA
|
A:LEU1548
|
4.5
|
11.1
|
0.7
|
|
N
|
A:LEU1548
|
4.5
|
10.9
|
0.7
|
|
C
|
A:GLY1550
|
4.5
|
10.9
|
1.0
|
|
OG
|
A:SER1530
|
4.5
|
15.0
|
1.0
|
|
CA
|
A:ARG1532
|
4.5
|
17.9
|
1.0
|
|
O
|
A:GLY1550
|
4.5
|
11.3
|
1.0
|
|
CA
|
A:ALA1549
|
4.5
|
11.4
|
1.0
|
|
CA
|
A:CA1705
|
4.5
|
9.9
|
1.0
|
|
CB
|
A:LEU1548
|
4.5
|
11.7
|
0.7
|
|
C
|
A:ASP1533
|
4.6
|
12.5
|
1.0
|
|
CA
|
A:ASP1534
|
4.8
|
11.7
|
1.0
|
|
Calcium binding site 5 out
of 8 in 5cvw
Go back to
Calcium Binding Sites List in 5cvw
Calcium binding site 5 out
of 8 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:9.9
occ:1.00
|
O
|
A:GLY1565
|
2.3
|
10.0
|
1.0
|
|
O
|
A:GLU1567
|
2.3
|
10.4
|
1.0
|
|
OD2
|
A:ASP1552
|
2.3
|
11.3
|
1.0
|
|
O
|
A:LEU1548
|
2.4
|
11.3
|
0.3
|
|
O
|
A:GLY1550
|
2.4
|
11.3
|
1.0
|
|
OD1
|
A:ASP1570
|
2.4
|
10.2
|
1.0
|
|
O
|
A:LEU1548
|
2.4
|
10.7
|
0.7
|
|
CG
|
A:ASP1570
|
3.1
|
9.8
|
1.0
|
|
OD2
|
A:ASP1570
|
3.1
|
10.1
|
1.0
|
|
CG
|
A:ASP1552
|
3.3
|
11.1
|
1.0
|
|
C
|
A:GLY1565
|
3.5
|
9.2
|
1.0
|
|
C
|
A:GLU1567
|
3.5
|
10.7
|
1.0
|
|
C
|
A:GLY1550
|
3.6
|
10.9
|
1.0
|
|
C
|
A:LEU1548
|
3.6
|
10.8
|
0.3
|
|
C
|
A:LEU1548
|
3.6
|
11.0
|
0.7
|
|
C
|
A:ALA1549
|
3.7
|
11.4
|
1.0
|
|
O
|
A:ALA1549
|
3.7
|
12.6
|
1.0
|
|
N
|
A:GLY1550
|
4.0
|
11.8
|
1.0
|
|
CA
|
A:ALA1549
|
4.0
|
11.4
|
1.0
|
|
C
|
A:ASP1566
|
4.1
|
9.3
|
1.0
|
|
CB
|
A:ASP1552
|
4.1
|
10.6
|
1.0
|
|
O
|
A:ASP1566
|
4.2
|
9.5
|
1.0
|
|
N
|
A:GLU1567
|
4.2
|
10.4
|
1.0
|
|
N
|
A:ASP1552
|
4.2
|
10.1
|
1.0
|
|
OD1
|
A:ASP1552
|
4.3
|
11.2
|
1.0
|
|
N
|
A:ALA1549
|
4.3
|
10.4
|
1.0
|
|
CA
|
A:GLY1568
|
4.3
|
11.4
|
1.0
|
|
CA
|
A:GLY1565
|
4.3
|
9.7
|
1.0
|
|
N
|
A:GLY1568
|
4.3
|
10.9
|
1.0
|
|
CA
|
A:GLY1550
|
4.3
|
12.5
|
1.0
|
|
C
|
A:GLY1547
|
4.3
|
11.2
|
1.0
|
|
O
|
A:GLY1547
|
4.4
|
11.7
|
1.0
|
|
N
|
A:ASP1566
|
4.4
|
9.4
|
1.0
|
|
CA
|
A:GLU1567
|
4.5
|
11.0
|
1.0
|
|
N
|
A:ASN1551
|
4.5
|
11.0
|
1.0
|
|
CB
|
A:ASP1570
|
4.5
|
10.1
|
1.0
|
|
CA
|
A:CA1704
|
4.5
|
11.4
|
1.0
|
|
N
|
A:LEU1548
|
4.6
|
11.4
|
0.3
|
|
N
|
A:LEU1548
|
4.6
|
10.9
|
0.7
|
|
CA
|
A:ASP1566
|
4.6
|
9.9
|
1.0
|
|
CA
|
A:GLY1547
|
4.7
|
11.6
|
1.0
|
|
CB
|
A:ASP1566
|
4.7
|
11.8
|
1.0
|
|
CA
|
A:LEU1548
|
4.7
|
11.5
|
0.3
|
|
C
|
A:GLY1568
|
4.7
|
10.3
|
1.0
|
|
CA
|
A:ASN1551
|
4.7
|
11.7
|
1.0
|
|
CA
|
A:LEU1548
|
4.7
|
11.1
|
0.7
|
|
CA
|
A:ASP1552
|
4.9
|
10.3
|
1.0
|
|
C
|
A:ASN1551
|
5.0
|
11.6
|
1.0
|
|
CA
|
A:CA1706
|
5.0
|
9.4
|
1.0
|
|
Calcium binding site 6 out
of 8 in 5cvw
Go back to
Calcium Binding Sites List in 5cvw
Calcium binding site 6 out
of 8 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:9.4
occ:1.00
|
OD2
|
A:ASP1570
|
2.3
|
10.1
|
1.0
|
|
O
|
A:GLN1585
|
2.3
|
10.7
|
1.0
|
|
O
|
A:GLY1583
|
2.3
|
10.1
|
1.0
|
|
O
|
A:GLY1568
|
2.4
|
11.3
|
1.0
|
|
O
|
A:ASP1566
|
2.4
|
9.5
|
1.0
|
|
OD1
|
A:ASP1588
|
2.4
|
10.0
|
1.0
|
|
OD2
|
A:ASP1588
|
3.0
|
9.6
|
1.0
|
|
CG
|
A:ASP1588
|
3.1
|
9.0
|
1.0
|
|
C
|
A:GLY1568
|
3.4
|
10.3
|
1.0
|
|
CG
|
A:ASP1570
|
3.5
|
9.8
|
1.0
|
|
C
|
A:GLY1583
|
3.5
|
9.2
|
1.0
|
|
C
|
A:GLN1585
|
3.5
|
9.8
|
1.0
|
|
C
|
A:ASP1566
|
3.6
|
9.3
|
1.0
|
|
N
|
A:GLY1568
|
3.9
|
10.9
|
1.0
|
|
C
|
A:GLY1584
|
3.9
|
9.6
|
1.0
|
|
C
|
A:GLU1567
|
4.0
|
10.7
|
1.0
|
|
CB
|
A:ASP1570
|
4.1
|
10.1
|
1.0
|
|
CA
|
A:GLY1584
|
4.1
|
9.5
|
1.0
|
|
O
|
A:GLY1584
|
4.1
|
9.2
|
1.0
|
|
C
|
A:GLY1565
|
4.2
|
9.2
|
1.0
|
|
N
|
A:GLN1585
|
4.2
|
9.6
|
1.0
|
|
N
|
A:ASP1570
|
4.2
|
9.8
|
1.0
|
|
N
|
A:GLY1584
|
4.2
|
9.1
|
1.0
|
|
CA
|
A:GLY1568
|
4.2
|
11.4
|
1.0
|
|
N
|
A:ASP1566
|
4.2
|
9.4
|
1.0
|
|
O
|
A:GLU1567
|
4.3
|
10.4
|
1.0
|
|
CA
|
A:GLY1586
|
4.3
|
10.1
|
1.0
|
|
O
|
A:GLY1565
|
4.4
|
10.0
|
1.0
|
|
N
|
A:GLY1586
|
4.4
|
10.4
|
1.0
|
|
N
|
A:SER1569
|
4.4
|
11.0
|
0.5
|
|
N
|
A:SER1569
|
4.4
|
11.1
|
0.5
|
|
CA
|
A:GLU1567
|
4.5
|
11.0
|
1.0
|
|
CB
|
A:ASP1588
|
4.5
|
9.4
|
1.0
|
|
OD1
|
A:ASP1570
|
4.5
|
10.2
|
1.0
|
|
CA
|
A:GLY1565
|
4.5
|
9.7
|
1.0
|
|
N
|
A:GLU1567
|
4.5
|
10.4
|
1.0
|
|
CA
|
A:GLY1583
|
4.5
|
9.7
|
1.0
|
|
CA
|
A:GLN1585
|
4.5
|
9.8
|
1.0
|
|
C
|
A:GLY1586
|
4.5
|
10.2
|
1.0
|
|
CA
|
A:ASP1566
|
4.5
|
9.9
|
1.0
|
|
O
|
A:GLY1586
|
4.6
|
10.9
|
1.0
|
|
CA
|
A:SER1569
|
4.6
|
11.9
|
0.5
|
|
CA
|
A:SER1569
|
4.7
|
12.1
|
0.5
|
|
CA
|
A:ASP1570
|
4.8
|
10.2
|
1.0
|
|
CA
|
A:CA1707
|
4.8
|
9.6
|
1.0
|
|
C
|
A:SER1569
|
4.8
|
11.3
|
0.5
|
|
C
|
A:SER1569
|
4.8
|
11.2
|
0.5
|
|
CA
|
A:CA1705
|
5.0
|
9.9
|
1.0
|
|
Calcium binding site 7 out
of 8 in 5cvw
Go back to
Calcium Binding Sites List in 5cvw
Calcium binding site 7 out
of 8 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:9.6
occ:1.00
|
O
|
A:GLY1605
|
2.3
|
10.8
|
1.0
|
|
OD2
|
A:ASP1588
|
2.3
|
9.6
|
1.0
|
|
O
|
A:GLY1584
|
2.4
|
9.2
|
1.0
|
|
OD1
|
A:ASP1609
|
2.4
|
10.6
|
1.0
|
|
O
|
A:GLY1586
|
2.4
|
10.9
|
1.0
|
|
OE2
|
A:GLU1603
|
2.5
|
10.3
|
1.0
|
|
OE1
|
A:GLU1603
|
2.6
|
10.0
|
1.0
|
|
CD
|
A:GLU1603
|
2.9
|
9.2
|
1.0
|
|
CG
|
A:ASP1609
|
3.3
|
10.5
|
1.0
|
|
OD2
|
A:ASP1609
|
3.3
|
11.5
|
1.0
|
|
CG
|
A:ASP1588
|
3.4
|
9.0
|
1.0
|
|
C
|
A:GLY1605
|
3.6
|
11.0
|
1.0
|
|
C
|
A:GLY1584
|
3.6
|
9.6
|
1.0
|
|
C
|
A:GLY1586
|
3.6
|
10.2
|
1.0
|
|
C
|
A:GLN1585
|
3.9
|
9.8
|
1.0
|
|
CB
|
A:ASP1588
|
4.0
|
9.4
|
1.0
|
|
O
|
A:GLN1585
|
4.0
|
10.7
|
1.0
|
|
N
|
A:GLY1586
|
4.1
|
10.4
|
1.0
|
|
N
|
A:ASP1588
|
4.1
|
9.7
|
1.0
|
|
N
|
A:GLY1605
|
4.2
|
11.6
|
1.0
|
|
CA
|
A:GLN1585
|
4.3
|
9.8
|
1.0
|
|
O
|
A:HOH1836
|
4.4
|
12.4
|
1.0
|
|
CG
|
A:GLU1603
|
4.4
|
10.0
|
1.0
|
|
OD1
|
A:ASP1588
|
4.4
|
10.0
|
1.0
|
|
N
|
A:GLN1585
|
4.4
|
9.6
|
1.0
|
|
N
|
A:GLY1584
|
4.4
|
9.1
|
1.0
|
|
N
|
A:GLY1606
|
4.4
|
13.0
|
1.0
|
|
CA
|
A:GLY1586
|
4.4
|
10.1
|
1.0
|
|
CA
|
A:GLY1606
|
4.4
|
12.9
|
1.0
|
|
C
|
A:GLY1583
|
4.5
|
9.2
|
1.0
|
|
N
|
A:ASP1587
|
4.5
|
10.6
|
1.0
|
|
CA
|
A:GLY1605
|
4.5
|
12.7
|
1.0
|
|
CB
|
A:ASP1609
|
4.6
|
11.1
|
1.0
|
|
CA
|
A:GLY1584
|
4.7
|
9.5
|
1.0
|
|
O
|
A:GLY1583
|
4.7
|
10.1
|
1.0
|
|
CA
|
A:ASP1588
|
4.7
|
9.4
|
1.0
|
|
CA
|
A:ASP1587
|
4.7
|
10.8
|
1.0
|
|
CA
|
A:CA1706
|
4.8
|
9.4
|
1.0
|
|
C
|
A:ASP1587
|
4.9
|
10.3
|
1.0
|
|
N
|
A:SER1604
|
4.9
|
11.3
|
1.0
|
|
OH
|
A:TYR1590
|
4.9
|
9.9
|
1.0
|
|
CA
|
A:GLY1583
|
5.0
|
9.7
|
1.0
|
|
Calcium binding site 8 out
of 8 in 5cvw
Go back to
Calcium Binding Sites List in 5cvw
Calcium binding site 8 out
of 8 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:11.8
occ:1.00
|
O
|
A:GLY1606
|
2.3
|
13.7
|
1.0
|
|
OD2
|
A:ASP1609
|
2.3
|
11.5
|
1.0
|
|
O
|
A:ARG1652
|
2.4
|
13.8
|
0.5
|
|
O
|
A:ARG1652
|
2.4
|
13.8
|
0.5
|
|
OE2
|
A:GLU1654
|
2.4
|
15.6
|
1.0
|
|
O
|
A:HOH1836
|
2.4
|
12.4
|
1.0
|
|
O
|
A:HOH1830
|
2.4
|
14.2
|
1.0
|
|
OE1
|
A:GLU1654
|
2.6
|
12.4
|
1.0
|
|
CD
|
A:GLU1654
|
2.9
|
13.7
|
1.0
|
|
CG
|
A:ASP1609
|
3.4
|
10.5
|
1.0
|
|
C
|
A:GLY1606
|
3.5
|
12.5
|
1.0
|
|
C
|
A:ARG1652
|
3.6
|
12.2
|
0.5
|
|
C
|
A:ARG1652
|
3.6
|
12.0
|
0.5
|
|
CB
|
A:ASP1609
|
4.1
|
11.1
|
1.0
|
|
N
|
A:GLY1606
|
4.2
|
13.0
|
1.0
|
|
CA
|
A:GLY1606
|
4.2
|
12.9
|
1.0
|
|
C
|
A:GLY1605
|
4.3
|
11.0
|
1.0
|
|
CA
|
A:VAL1653
|
4.4
|
13.9
|
1.0
|
|
CG
|
A:GLU1654
|
4.4
|
15.9
|
1.0
|
|
N
|
A:VAL1653
|
4.4
|
12.3
|
1.0
|
|
O
|
A:ALA1649
|
4.4
|
15.1
|
1.0
|
|
OD1
|
A:ASP1609
|
4.5
|
10.6
|
1.0
|
|
OE2
|
A:GLU1603
|
4.5
|
10.3
|
1.0
|
|
N
|
A:GLY1607
|
4.5
|
12.5
|
1.0
|
|
O
|
A:HOH1812
|
4.5
|
26.9
|
1.0
|
|
N
|
A:ASP1609
|
4.5
|
11.5
|
1.0
|
|
O
|
A:GLY1605
|
4.5
|
10.8
|
1.0
|
|
N
|
A:ARG1652
|
4.5
|
12.5
|
0.5
|
|
CA
|
A:ARG1652
|
4.6
|
12.6
|
0.5
|
|
N
|
A:ARG1652
|
4.6
|
12.2
|
0.5
|
|
CA
|
A:ARG1652
|
4.6
|
12.3
|
0.5
|
|
CA
|
A:GLY1607
|
4.6
|
13.7
|
1.0
|
|
O
|
A:ASP1650
|
4.6
|
12.4
|
1.0
|
|
CD
|
A:GLU1603
|
4.8
|
9.2
|
1.0
|
|
CG
|
A:GLU1603
|
4.9
|
10.0
|
1.0
|
|
C
|
A:GLY1607
|
4.9
|
13.6
|
1.0
|
|
N
|
A:GLU1654
|
4.9
|
12.7
|
1.0
|
|
CA
|
A:ASP1609
|
4.9
|
10.6
|
1.0
|
|
C
|
A:VAL1653
|
4.9
|
14.4
|
1.0
|
|
N
|
A:HIS1608
|
5.0
|
13.0
|
1.0
|
|
CA
|
A:GLY1605
|
5.0
|
12.7
|
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: Wed Jul 9 04:46:18 2025
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