Cadmium in PDB 1ii9: Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Enzymatic activity of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
All present enzymatic activity of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp:
3.6.3.16;
Protein crystallography data
The structure of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp, PDB code: 1ii9
was solved by
T.Zhou,
S.Radaev,
D.L.Gatti,
B.P.Rosen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.52 /
2.60
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.623,
222.527,
74.047,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
26.5
|
Other elements in 1ii9:
The structure of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp also contains other interesting chemical elements:
Cadmium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Cadmium atom in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
(pdb code 1ii9). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 18 binding sites of Cadmium where determined in the
Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp, PDB code: 1ii9:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 18 in 1ii9
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Cadmium Binding Sites List in 1ii9
Cadmium binding site 1 out
of 18 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd594
b:40.5
occ:1.00
|
SG
|
A:CYS172
|
2.4
|
33.9
|
1.0
|
CL
|
A:CL597
|
2.5
|
28.6
|
1.0
|
SG
|
A:CYS113
|
2.5
|
43.4
|
1.0
|
O
|
A:HOH2119
|
2.6
|
25.1
|
1.0
|
SG
|
A:CYS422
|
2.7
|
40.8
|
1.0
|
CB
|
A:CYS172
|
3.6
|
41.2
|
1.0
|
CB
|
A:CYS113
|
3.7
|
29.9
|
1.0
|
CD
|
A:CD595
|
3.7
|
34.0
|
1.0
|
CB
|
A:CYS422
|
3.8
|
43.9
|
1.0
|
OG
|
A:SER420
|
3.8
|
30.5
|
1.0
|
CB
|
A:SER420
|
4.1
|
33.2
|
1.0
|
CD
|
A:CD596
|
4.3
|
34.5
|
1.0
|
N
|
A:CYS113
|
4.5
|
26.9
|
1.0
|
N
|
A:CYS422
|
4.6
|
41.5
|
1.0
|
CA
|
A:CYS113
|
4.7
|
31.7
|
1.0
|
CA
|
A:CYS422
|
4.8
|
41.7
|
1.0
|
CL
|
A:CL598
|
4.9
|
35.7
|
1.0
|
CD
|
A:PRO421
|
5.0
|
39.4
|
1.0
|
CA
|
A:CYS172
|
5.0
|
43.0
|
1.0
|
|
Cadmium binding site 2 out
of 18 in 1ii9
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Cadmium Binding Sites List in 1ii9
Cadmium binding site 2 out
of 18 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd595
b:34.0
occ:1.00
|
O
|
A:HOH3024
|
2.3
|
34.6
|
1.0
|
NE2
|
A:HIS453
|
2.4
|
28.6
|
1.0
|
CL
|
A:CL598
|
2.4
|
35.7
|
1.0
|
CL
|
A:CL597
|
2.7
|
28.6
|
1.0
|
SG
|
A:CYS172
|
2.8
|
33.9
|
1.0
|
CE1
|
A:HIS453
|
3.3
|
26.9
|
1.0
|
CD2
|
A:HIS453
|
3.3
|
32.0
|
1.0
|
CB
|
A:CYS172
|
3.6
|
41.2
|
1.0
|
CD
|
A:CD594
|
3.7
|
40.5
|
1.0
|
CD2
|
A:LEU457
|
4.0
|
39.0
|
1.0
|
CA
|
A:GLY111
|
4.2
|
20.8
|
1.0
|
CA
|
A:CYS172
|
4.2
|
43.0
|
1.0
|
O
|
A:SER171
|
4.4
|
57.7
|
1.0
|
ND1
|
A:HIS453
|
4.4
|
34.3
|
1.0
|
CG
|
A:HIS453
|
4.4
|
33.7
|
1.0
|
O
|
A:GLN108
|
4.6
|
36.9
|
1.0
|
N
|
A:GLY111
|
4.6
|
29.0
|
1.0
|
CB
|
A:CYS113
|
4.7
|
29.9
|
1.0
|
N
|
A:CYS172
|
4.9
|
47.3
|
1.0
|
C
|
A:GLY111
|
4.9
|
22.6
|
1.0
|
C
|
A:SER171
|
4.9
|
53.3
|
1.0
|
|
Cadmium binding site 3 out
of 18 in 1ii9
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Cadmium Binding Sites List in 1ii9
Cadmium binding site 3 out
of 18 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd596
b:34.5
occ:1.00
|
O
|
A:HOH3023
|
2.1
|
23.9
|
1.0
|
OG
|
A:SER420
|
2.2
|
30.5
|
1.0
|
NE2
|
A:HIS148
|
2.3
|
26.8
|
1.0
|
CL
|
A:CL599
|
2.3
|
69.0
|
1.0
|
SG
|
A:CYS113
|
2.5
|
43.4
|
1.0
|
CD2
|
A:HIS148
|
3.2
|
30.1
|
1.0
|
CE1
|
A:HIS148
|
3.3
|
27.9
|
1.0
|
CB
|
A:CYS113
|
3.5
|
29.9
|
1.0
|
CB
|
A:SER420
|
3.6
|
33.2
|
1.0
|
O
|
A:HOH3005
|
3.9
|
41.3
|
1.0
|
CD1
|
A:LEU152
|
4.1
|
36.2
|
1.0
|
CB
|
A:CYS172
|
4.2
|
41.2
|
1.0
|
CD
|
A:CD594
|
4.3
|
40.5
|
1.0
|
OD1
|
A:ASP417
|
4.3
|
40.0
|
1.0
|
CG
|
A:HIS148
|
4.3
|
28.8
|
1.0
|
ND1
|
A:HIS148
|
4.4
|
27.0
|
1.0
|
CA
|
A:SER420
|
4.4
|
35.8
|
1.0
|
CA
|
A:CYS113
|
4.5
|
31.7
|
1.0
|
O
|
A:ASP417
|
4.8
|
29.4
|
1.0
|
CD
|
A:PRO421
|
4.8
|
39.4
|
1.0
|
SG
|
A:CYS172
|
4.9
|
33.9
|
1.0
|
O
|
A:CYS172
|
4.9
|
43.5
|
1.0
|
O
|
A:HOH2119
|
5.0
|
25.1
|
1.0
|
|
Cadmium binding site 4 out
of 18 in 1ii9
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Cadmium Binding Sites List in 1ii9
Cadmium binding site 4 out
of 18 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd600
b:29.9
occ:1.00
|
NE2
|
B:HIS1585
|
2.1
|
36.1
|
1.0
|
ND1
|
B:HIS1587
|
2.3
|
25.3
|
1.0
|
O
|
A:HOH2060
|
2.3
|
18.7
|
1.0
|
OD1
|
A:ASP320
|
2.4
|
26.2
|
1.0
|
OD2
|
A:ASP320
|
2.5
|
38.3
|
1.0
|
CL
|
A:CL2000
|
2.6
|
27.4
|
1.0
|
CG
|
A:ASP320
|
2.7
|
32.1
|
1.0
|
CE1
|
B:HIS1585
|
2.9
|
37.1
|
1.0
|
CE1
|
B:HIS1587
|
3.1
|
20.5
|
1.0
|
CD2
|
B:HIS1585
|
3.2
|
32.4
|
1.0
|
CG
|
B:HIS1587
|
3.3
|
24.1
|
1.0
|
CB
|
B:HIS1587
|
3.7
|
28.6
|
1.0
|
O
|
B:HOH2013
|
3.9
|
22.8
|
1.0
|
ND1
|
B:HIS1585
|
4.0
|
35.5
|
1.0
|
O
|
A:ASP320
|
4.1
|
23.1
|
1.0
|
CB
|
A:ASP320
|
4.2
|
28.6
|
1.0
|
CA
|
B:HIS1587
|
4.2
|
30.8
|
1.0
|
CG
|
B:HIS1585
|
4.2
|
36.1
|
1.0
|
NE2
|
B:HIS1587
|
4.3
|
24.7
|
1.0
|
CD2
|
B:HIS1587
|
4.4
|
27.0
|
1.0
|
O
|
A:HOH2058
|
4.6
|
24.0
|
1.0
|
CE1
|
A:HIS585
|
4.6
|
24.8
|
1.0
|
C
|
A:ASP320
|
4.6
|
27.4
|
1.0
|
CA
|
A:ASP320
|
4.7
|
29.3
|
1.0
|
O
|
B:HOH2216
|
4.7
|
31.9
|
1.0
|
N
|
B:HIS1587
|
4.9
|
25.9
|
1.0
|
O
|
A:HOH3030
|
4.9
|
22.1
|
1.0
|
|
Cadmium binding site 5 out
of 18 in 1ii9
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Cadmium Binding Sites List in 1ii9
Cadmium binding site 5 out
of 18 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd601
b:31.0
occ:1.00
|
O
|
A:HOH3030
|
2.0
|
22.1
|
1.0
|
NE2
|
A:HIS585
|
2.3
|
27.2
|
1.0
|
NE2
|
A:HIS588
|
2.4
|
31.8
|
1.0
|
O
|
A:HOH2098
|
2.4
|
21.5
|
1.0
|
O
|
A:HOH2117
|
2.5
|
21.1
|
1.0
|
O
|
A:HOH2042
|
2.8
|
26.5
|
1.0
|
CD2
|
A:HIS585
|
3.3
|
25.0
|
1.0
|
CE1
|
A:HIS588
|
3.3
|
33.8
|
1.0
|
CE1
|
A:HIS585
|
3.3
|
24.8
|
1.0
|
CD2
|
A:HIS588
|
3.4
|
27.0
|
1.0
|
OD1
|
A:ASP320
|
4.3
|
26.2
|
1.0
|
OD1
|
A:ASP321
|
4.3
|
29.4
|
1.0
|
OD2
|
A:ASP321
|
4.4
|
28.7
|
1.0
|
ND1
|
A:HIS585
|
4.4
|
26.4
|
1.0
|
ND1
|
A:HIS588
|
4.4
|
26.9
|
1.0
|
CG
|
A:HIS585
|
4.4
|
27.6
|
1.0
|
CG
|
A:HIS588
|
4.5
|
29.9
|
1.0
|
NH2
|
A:ARG324
|
4.6
|
26.3
|
1.0
|
CG
|
A:ASP321
|
4.7
|
29.6
|
1.0
|
O
|
A:HOH3052
|
4.8
|
38.3
|
1.0
|
CG
|
A:ASP320
|
4.9
|
32.1
|
1.0
|
O
|
A:HOH2055
|
4.9
|
36.2
|
1.0
|
|
Cadmium binding site 6 out
of 18 in 1ii9
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Cadmium Binding Sites List in 1ii9
Cadmium binding site 6 out
of 18 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd602
b:39.4
occ:1.00
|
OE1
|
B:GLU1326
|
1.8
|
53.2
|
1.0
|
NE2
|
A:HIS584
|
2.2
|
32.1
|
1.0
|
NE2
|
A:HIS586
|
2.3
|
32.5
|
1.0
|
O
|
B:HOH2015
|
2.3
|
28.6
|
1.0
|
O
|
B:HOH2003
|
2.3
|
39.5
|
1.0
|
CD
|
B:GLU1326
|
2.6
|
51.6
|
1.0
|
OE2
|
B:GLU1326
|
2.7
|
52.5
|
1.0
|
CD2
|
A:HIS586
|
3.1
|
29.0
|
1.0
|
CD2
|
A:HIS584
|
3.2
|
33.0
|
1.0
|
CE1
|
A:HIS584
|
3.2
|
37.4
|
1.0
|
CE1
|
A:HIS586
|
3.3
|
30.1
|
1.0
|
CG
|
B:GLU1326
|
4.0
|
47.5
|
1.0
|
ND1
|
A:HIS584
|
4.3
|
30.8
|
1.0
|
CG
|
A:HIS586
|
4.3
|
30.5
|
1.0
|
CG
|
A:HIS584
|
4.3
|
29.2
|
1.0
|
ND1
|
A:HIS586
|
4.4
|
23.9
|
1.0
|
O
|
A:HOH2153
|
4.6
|
40.9
|
1.0
|
|
Cadmium binding site 7 out
of 18 in 1ii9
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Cadmium Binding Sites List in 1ii9
Cadmium binding site 7 out
of 18 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd603
b:98.6
occ:1.00
|
O
|
A:HOH2053
|
2.5
|
51.7
|
1.0
|
NE2
|
A:HIS397
|
2.5
|
53.5
|
1.0
|
O
|
A:HOH2112
|
2.9
|
55.0
|
1.0
|
O
|
A:HOH2062
|
3.1
|
32.6
|
1.0
|
CE1
|
A:HIS397
|
3.3
|
51.5
|
1.0
|
CD2
|
A:HIS397
|
3.5
|
49.2
|
1.0
|
ND1
|
A:HIS397
|
4.5
|
50.7
|
1.0
|
CG
|
A:HIS397
|
4.6
|
50.6
|
1.0
|
|
Cadmium binding site 8 out
of 18 in 1ii9
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Cadmium Binding Sites List in 1ii9
Cadmium binding site 8 out
of 18 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd604
b:46.7
occ:1.00
|
OD1
|
A:ASP386
|
2.2
|
52.9
|
1.0
|
ND1
|
A:HIS388
|
2.3
|
45.9
|
1.0
|
OD2
|
A:ASP386
|
2.8
|
52.9
|
1.0
|
CG
|
A:ASP386
|
2.8
|
47.6
|
1.0
|
CG
|
A:HIS388
|
3.2
|
48.2
|
1.0
|
CB
|
A:HIS388
|
3.3
|
42.3
|
1.0
|
CE1
|
A:HIS388
|
3.3
|
56.0
|
1.0
|
CB
|
A:ASP386
|
4.3
|
42.8
|
1.0
|
CD2
|
A:HIS388
|
4.3
|
49.6
|
1.0
|
NE2
|
A:HIS388
|
4.4
|
57.6
|
1.0
|
CA
|
A:HIS388
|
4.6
|
37.1
|
1.0
|
N
|
A:HIS388
|
4.6
|
40.1
|
1.0
|
|
Cadmium binding site 9 out
of 18 in 1ii9
Go back to
Cadmium Binding Sites List in 1ii9
Cadmium binding site 9 out
of 18 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd605
b:60.6
occ:0.50
|
CE1
|
A:HIS520
|
2.5
|
53.7
|
1.0
|
NE2
|
A:HIS520
|
2.7
|
47.1
|
1.0
|
O
|
A:HOH3017
|
2.9
|
48.1
|
1.0
|
OE1
|
A:GLU515
|
3.7
|
45.2
|
1.0
|
ND1
|
A:HIS520
|
3.8
|
54.0
|
1.0
|
CD2
|
A:HIS520
|
4.1
|
51.5
|
1.0
|
CG
|
A:HIS520
|
4.6
|
53.4
|
1.0
|
CD
|
A:GLU515
|
4.8
|
40.9
|
1.0
|
|
Cadmium binding site 10 out
of 18 in 1ii9
Go back to
Cadmium Binding Sites List in 1ii9
Cadmium binding site 10 out
of 18 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 10 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd1594
b:35.7
occ:1.00
|
SG
|
B:CYS1113
|
2.4
|
30.9
|
1.0
|
SG
|
B:CYS1422
|
2.5
|
34.3
|
1.0
|
SG
|
B:CYS1172
|
2.5
|
41.6
|
1.0
|
CL
|
B:CL1597
|
2.5
|
28.7
|
1.0
|
O
|
B:HOH2145
|
2.8
|
29.6
|
1.0
|
OG
|
B:SER1420
|
3.2
|
35.9
|
1.0
|
CB
|
B:CYS1172
|
3.6
|
46.1
|
1.0
|
CB
|
B:CYS1422
|
3.6
|
37.1
|
1.0
|
CB
|
B:CYS1113
|
3.6
|
23.1
|
1.0
|
CD
|
B:CD1595
|
3.6
|
30.4
|
1.0
|
CB
|
B:SER1420
|
4.2
|
44.1
|
1.0
|
CD
|
B:CD1596
|
4.2
|
36.2
|
1.0
|
N
|
B:CYS1422
|
4.4
|
41.6
|
1.0
|
N
|
B:CYS1113
|
4.6
|
24.0
|
1.0
|
CA
|
B:CYS1422
|
4.6
|
40.8
|
1.0
|
CA
|
B:CYS1113
|
4.7
|
26.5
|
1.0
|
O
|
B:HOH3025
|
4.9
|
16.8
|
1.0
|
CD
|
B:PRO1421
|
4.9
|
39.5
|
1.0
|
CA
|
B:CYS1172
|
5.0
|
47.1
|
1.0
|
|
Reference:
T.Zhou,
S.Radaev,
B.P.Rosen,
D.L.Gatti.
Conformational Changes in Four Regions of the Escherichia Coli Arsa Atpase Link Atp Hydrolysis to Ion Translocation. J.Biol.Chem. V. 276 30414 2001.
ISSN: ISSN 0021-9258
PubMed: 11395509
DOI: 10.1074/JBC.M103671200
Page generated: Fri Jul 19 13:32:51 2024
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