Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Amp-Pnp, PDB code: 1ii9:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1ii9
Go back to
Magnesium Binding Sites List in 1ii9
Magnesium binding site 1 out
of 4 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 Magnesium with other atoms in the Mg 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:Mg592
b:17.3
occ:1.00
|
O3B
|
A:ADP590
|
2.0
|
45.7
|
1.0
|
OD1
|
A:ASP45
|
2.1
|
35.7
|
1.0
|
O
|
A:HOH3001
|
2.1
|
35.7
|
1.0
|
OG1
|
A:THR22
|
2.2
|
26.8
|
1.0
|
O
|
A:HOH3000
|
2.3
|
21.7
|
1.0
|
O
|
A:HOH2063
|
2.8
|
45.6
|
1.0
|
PB
|
A:ADP590
|
2.9
|
39.4
|
1.0
|
CG
|
A:ASP45
|
3.0
|
43.5
|
1.0
|
O1B
|
A:ADP590
|
3.1
|
42.9
|
1.0
|
OD2
|
A:ASP45
|
3.2
|
42.1
|
1.0
|
CB
|
A:THR22
|
3.5
|
33.2
|
1.0
|
O3A
|
A:ADP590
|
3.6
|
44.7
|
1.0
|
N
|
A:THR22
|
4.1
|
29.1
|
1.0
|
O
|
A:HOH3015
|
4.1
|
34.8
|
1.0
|
OD2
|
A:ASP142
|
4.2
|
33.2
|
1.0
|
O1A
|
A:ADP590
|
4.3
|
43.8
|
1.0
|
O2B
|
A:ADP590
|
4.3
|
37.0
|
1.0
|
CB
|
A:ASP45
|
4.3
|
44.5
|
1.0
|
CA
|
A:THR22
|
4.4
|
32.0
|
1.0
|
CG2
|
A:THR22
|
4.5
|
27.6
|
1.0
|
PA
|
A:ADP590
|
4.7
|
37.7
|
1.0
|
O
|
A:HOH2052
|
4.7
|
35.4
|
1.0
|
CE
|
A:LYS21
|
4.8
|
19.5
|
1.0
|
OG1
|
A:THR502
|
4.8
|
48.1
|
1.0
|
NZ
|
A:LYS21
|
4.9
|
22.4
|
1.0
|
CB
|
A:LYS21
|
5.0
|
23.5
|
1.0
|
CG
|
A:ASP142
|
5.0
|
35.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1ii9
Go back to
Magnesium Binding Sites List in 1ii9
Magnesium binding site 2 out
of 4 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 Magnesium with other atoms in the Mg 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:Mg593
b:21.9
occ:1.00
|
O
|
A:HOH2011
|
2.0
|
33.5
|
1.0
|
O
|
A:HOH2030
|
2.0
|
26.6
|
1.0
|
O2G
|
A:ANP591
|
2.0
|
29.8
|
1.0
|
O1B
|
A:ANP591
|
2.0
|
32.0
|
1.0
|
O
|
A:HOH3002
|
2.1
|
27.4
|
1.0
|
OG1
|
A:THR341
|
2.3
|
25.1
|
1.0
|
N3B
|
A:ANP591
|
3.0
|
38.4
|
1.0
|
PG
|
A:ANP591
|
3.1
|
36.9
|
1.0
|
PB
|
A:ANP591
|
3.2
|
36.2
|
1.0
|
CB
|
A:THR341
|
3.3
|
27.5
|
1.0
|
N
|
A:THR341
|
3.9
|
24.3
|
1.0
|
O3G
|
A:ANP591
|
3.9
|
34.5
|
1.0
|
O
|
A:HOH2304
|
4.1
|
31.3
|
1.0
|
OD2
|
A:ASP447
|
4.1
|
37.2
|
1.0
|
CA
|
A:THR341
|
4.2
|
29.0
|
1.0
|
O3A
|
A:ANP591
|
4.2
|
35.6
|
1.0
|
O1G
|
A:ANP591
|
4.3
|
27.6
|
1.0
|
O2B
|
A:ANP591
|
4.3
|
34.0
|
1.0
|
CG2
|
A:THR341
|
4.4
|
22.1
|
1.0
|
CG
|
A:ASP447
|
4.4
|
30.7
|
1.0
|
O2A
|
A:ANP591
|
4.4
|
41.5
|
1.0
|
CB
|
A:ASP364
|
4.7
|
57.3
|
1.0
|
OD2
|
A:ASP364
|
4.7
|
64.0
|
1.0
|
OG
|
A:SER363
|
4.7
|
40.4
|
1.0
|
NZ
|
A:LYS340
|
4.8
|
31.8
|
1.0
|
O
|
A:ASP447
|
4.8
|
30.7
|
1.0
|
CB
|
A:LYS340
|
4.8
|
28.3
|
1.0
|
OD1
|
A:ASP447
|
4.8
|
33.4
|
1.0
|
CB
|
A:ASP447
|
4.9
|
30.1
|
1.0
|
PA
|
A:ANP591
|
4.9
|
37.2
|
1.0
|
CE
|
A:LYS340
|
4.9
|
28.1
|
1.0
|
C
|
A:LYS340
|
5.0
|
24.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1ii9
Go back to
Magnesium Binding Sites List in 1ii9
Magnesium binding site 3 out
of 4 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 Magnesium with other atoms in the Mg 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
|
B:Mg1592
b:25.0
occ:1.00
|
OD1
|
B:ASP1045
|
1.7
|
53.5
|
1.0
|
O3B
|
B:ADP1590
|
2.0
|
35.8
|
1.0
|
O
|
B:HOH3003
|
2.1
|
23.8
|
1.0
|
OG1
|
B:THR1022
|
2.2
|
28.4
|
1.0
|
O
|
B:HOH2006
|
2.2
|
25.4
|
1.0
|
O
|
B:HOH2186
|
2.4
|
35.0
|
1.0
|
CG
|
B:ASP1045
|
2.8
|
57.9
|
1.0
|
PB
|
B:ADP1590
|
3.1
|
42.3
|
1.0
|
CB
|
B:THR1022
|
3.2
|
24.0
|
1.0
|
O1B
|
B:ADP1590
|
3.2
|
35.9
|
1.0
|
OD2
|
B:ASP1045
|
3.3
|
54.6
|
1.0
|
O1A
|
B:ADP1590
|
3.7
|
47.7
|
1.0
|
N
|
B:THR1022
|
4.0
|
28.7
|
1.0
|
O3A
|
B:ADP1590
|
4.1
|
42.6
|
1.0
|
CB
|
B:ASP1045
|
4.1
|
57.3
|
1.0
|
CA
|
B:THR1022
|
4.2
|
27.9
|
1.0
|
CG2
|
B:THR1022
|
4.2
|
22.6
|
1.0
|
OD2
|
B:ASP1142
|
4.3
|
37.4
|
1.0
|
O2B
|
B:ADP1590
|
4.3
|
37.0
|
1.0
|
PA
|
B:ADP1590
|
4.5
|
40.6
|
1.0
|
OG1
|
B:THR1502
|
4.7
|
37.8
|
1.0
|
O
|
B:HOH2022
|
4.9
|
35.0
|
1.0
|
CG
|
B:ASP1142
|
4.9
|
39.2
|
1.0
|
O
|
B:ASP1142
|
4.9
|
37.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1ii9
Go back to
Magnesium Binding Sites List in 1ii9
Magnesium binding site 4 out
of 4 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 Magnesium with other atoms in the Mg 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
|
B:Mg1593
b:14.2
occ:1.00
|
O
|
B:HOH3010
|
1.8
|
35.2
|
1.0
|
O
|
B:HOH3009
|
1.9
|
36.1
|
1.0
|
O1B
|
B:ANP1591
|
2.2
|
23.2
|
1.0
|
O2G
|
B:ANP1591
|
2.2
|
23.3
|
1.0
|
OG1
|
B:THR1341
|
2.3
|
30.2
|
1.0
|
O
|
B:HOH2018
|
2.3
|
37.6
|
1.0
|
N3B
|
B:ANP1591
|
2.9
|
35.4
|
1.0
|
PG
|
B:ANP1591
|
3.1
|
29.3
|
1.0
|
PB
|
B:ANP1591
|
3.2
|
30.1
|
1.0
|
CB
|
B:THR1341
|
3.4
|
34.1
|
1.0
|
O3G
|
B:ANP1591
|
3.7
|
39.2
|
1.0
|
O2A
|
B:ANP1591
|
4.1
|
32.2
|
1.0
|
OD2
|
B:ASP1447
|
4.2
|
23.7
|
1.0
|
O3A
|
B:ANP1591
|
4.2
|
25.1
|
1.0
|
N
|
B:THR1341
|
4.3
|
30.3
|
1.0
|
O1G
|
B:ANP1591
|
4.3
|
27.2
|
1.0
|
O
|
B:HOH3011
|
4.3
|
41.1
|
1.0
|
CG2
|
B:THR1341
|
4.4
|
25.1
|
1.0
|
OD2
|
B:ASP1364
|
4.4
|
66.7
|
1.0
|
CA
|
B:THR1341
|
4.5
|
29.5
|
1.0
|
O2B
|
B:ANP1591
|
4.6
|
34.2
|
1.0
|
CB
|
B:ASP1364
|
4.6
|
62.3
|
1.0
|
PA
|
B:ANP1591
|
4.7
|
32.7
|
1.0
|
NZ
|
B:LYS1340
|
4.8
|
34.8
|
1.0
|
O
|
B:ASP1447
|
4.8
|
32.2
|
1.0
|
CG
|
B:ASP1447
|
4.8
|
29.2
|
1.0
|
O1A
|
B:ANP1591
|
4.9
|
34.1
|
1.0
|
CE
|
B:LYS1340
|
4.9
|
38.4
|
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: Tue Aug 13 05:00:02 2024
|