Magnesium in PDB 1e79: Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide)
Enzymatic activity of Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide)
All present enzymatic activity of Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide):
3.6.1.34;
Protein crystallography data
The structure of Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide), PDB code: 1e79
was solved by
C.Gibbons,
M.G.Montgomery,
A.G.W.Leslie,
J.E.Walker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20 /
2.4
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
267.200,
107.200,
135.900,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.5 /
28.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide)
(pdb code 1e79). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide), PDB code: 1e79:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 1e79
Go back to
Magnesium Binding Sites List in 1e79
Magnesium binding site 1 out
of 5 in the Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:44.7
occ:1.00
|
O2G
|
A:ATP600
|
2.1
|
53.5
|
1.0
|
O2B
|
A:ATP600
|
2.1
|
45.2
|
1.0
|
OG1
|
A:THR176
|
2.1
|
40.4
|
1.0
|
O
|
A:HOH2075
|
2.2
|
38.7
|
1.0
|
O
|
A:HOH2163
|
2.2
|
35.1
|
1.0
|
CB
|
A:THR176
|
3.2
|
40.0
|
1.0
|
PG
|
A:ATP600
|
3.2
|
56.7
|
1.0
|
PB
|
A:ATP600
|
3.3
|
46.0
|
1.0
|
O3B
|
A:ATP600
|
3.6
|
50.0
|
1.0
|
O3G
|
A:ATP600
|
3.7
|
56.2
|
1.0
|
N
|
A:THR176
|
3.8
|
39.2
|
1.0
|
OD2
|
A:ASP269
|
4.0
|
33.5
|
1.0
|
CA
|
A:THR176
|
4.1
|
39.2
|
1.0
|
O2A
|
A:ATP600
|
4.1
|
42.6
|
1.0
|
OD1
|
A:ASP269
|
4.2
|
39.0
|
1.0
|
CG2
|
A:THR176
|
4.2
|
36.9
|
1.0
|
O3A
|
A:ATP600
|
4.3
|
45.5
|
1.0
|
O1B
|
A:ATP600
|
4.3
|
46.2
|
1.0
|
O1G
|
A:ATP600
|
4.4
|
56.6
|
1.0
|
O
|
A:HOH2076
|
4.5
|
46.3
|
1.0
|
CG
|
A:ASP269
|
4.5
|
41.2
|
1.0
|
O
|
A:HOH2022
|
4.5
|
42.5
|
1.0
|
PA
|
A:ATP600
|
4.6
|
42.5
|
1.0
|
O1A
|
A:ATP600
|
4.6
|
43.7
|
1.0
|
O
|
A:HOH2110
|
4.7
|
30.1
|
1.0
|
O
|
A:HOH2077
|
4.8
|
45.8
|
1.0
|
O
|
A:HOH2160
|
4.9
|
67.6
|
1.0
|
C
|
A:LYS175
|
5.0
|
40.3
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 1e79
Go back to
Magnesium Binding Sites List in 1e79
Magnesium binding site 2 out
of 5 in the Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:46.5
occ:1.00
|
O
|
B:HOH2049
|
2.1
|
53.9
|
1.0
|
O
|
B:HOH2048
|
2.1
|
38.8
|
1.0
|
O
|
B:HOH2134
|
2.1
|
39.5
|
1.0
|
O2B
|
B:ADP600
|
2.1
|
45.7
|
1.0
|
OG1
|
B:THR176
|
2.1
|
45.5
|
1.0
|
O
|
B:HOH2137
|
2.3
|
34.2
|
1.0
|
PB
|
B:ADP600
|
3.2
|
44.4
|
1.0
|
CB
|
B:THR176
|
3.3
|
46.7
|
1.0
|
O3B
|
B:ADP600
|
3.3
|
44.1
|
1.0
|
N
|
B:THR176
|
4.1
|
43.3
|
1.0
|
O2A
|
B:ADP600
|
4.1
|
46.0
|
1.0
|
O1B
|
B:ADP600
|
4.2
|
46.2
|
1.0
|
O3A
|
B:ADP600
|
4.2
|
46.5
|
1.0
|
CA
|
B:THR176
|
4.3
|
43.9
|
1.0
|
CG2
|
B:THR176
|
4.3
|
45.6
|
1.0
|
OD1
|
B:ASP269
|
4.3
|
44.6
|
1.0
|
OD2
|
B:ASP269
|
4.3
|
43.8
|
1.0
|
O
|
B:HOH2105
|
4.4
|
42.2
|
1.0
|
O
|
B:HOH2106
|
4.5
|
40.7
|
1.0
|
PA
|
B:ADP600
|
4.6
|
46.7
|
1.0
|
CG
|
B:ASP269
|
4.7
|
43.1
|
1.0
|
O
|
B:HOH2072
|
4.7
|
35.2
|
1.0
|
NZ
|
B:LYS175
|
4.7
|
39.4
|
1.0
|
O1A
|
B:ADP600
|
4.8
|
47.4
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 1e79
Go back to
Magnesium Binding Sites List in 1e79
Magnesium binding site 3 out
of 5 in the Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:43.2
occ:1.00
|
OG1
|
C:THR176
|
2.1
|
37.9
|
1.0
|
O2G
|
C:ATP600
|
2.1
|
48.4
|
1.0
|
O
|
C:HOH2162
|
2.1
|
42.0
|
1.0
|
O2B
|
C:ATP600
|
2.1
|
42.7
|
1.0
|
O
|
C:HOH2075
|
2.2
|
42.8
|
1.0
|
CB
|
C:THR176
|
3.3
|
42.0
|
1.0
|
PG
|
C:ATP600
|
3.3
|
52.2
|
1.0
|
PB
|
C:ATP600
|
3.4
|
42.3
|
1.0
|
O3B
|
C:ATP600
|
3.7
|
47.4
|
1.0
|
O3G
|
C:ATP600
|
4.0
|
51.4
|
1.0
|
N
|
C:THR176
|
4.0
|
40.7
|
1.0
|
OD2
|
C:ASP269
|
4.0
|
39.6
|
1.0
|
O
|
C:HOH2076
|
4.1
|
49.0
|
1.0
|
OD1
|
C:ASP269
|
4.1
|
42.1
|
1.0
|
CA
|
C:THR176
|
4.2
|
40.8
|
1.0
|
O
|
C:HOH2060
|
4.2
|
60.5
|
1.0
|
O2A
|
C:ATP600
|
4.2
|
36.5
|
1.0
|
CG2
|
C:THR176
|
4.3
|
41.8
|
1.0
|
O1B
|
C:ATP600
|
4.3
|
43.6
|
1.0
|
O3A
|
C:ATP600
|
4.5
|
41.7
|
1.0
|
O1G
|
C:ATP600
|
4.5
|
51.4
|
1.0
|
CG
|
C:ASP269
|
4.5
|
41.7
|
1.0
|
O
|
C:HOH2079
|
4.5
|
61.9
|
1.0
|
PA
|
C:ATP600
|
4.7
|
39.5
|
1.0
|
O1A
|
C:ATP600
|
4.8
|
40.0
|
1.0
|
O
|
C:HOH2103
|
5.0
|
29.4
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 1e79
Go back to
Magnesium Binding Sites List in 1e79
Magnesium binding site 4 out
of 5 in the Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:35.2
occ:1.00
|
O
|
D:HOH2148
|
2.1
|
31.4
|
1.0
|
O
|
D:HOH2073
|
2.1
|
45.2
|
1.0
|
O
|
D:HOH2147
|
2.1
|
34.1
|
1.0
|
OG1
|
D:THR163
|
2.2
|
37.6
|
1.0
|
O2B
|
D:ADP600
|
2.2
|
37.6
|
1.0
|
CB
|
D:THR163
|
3.2
|
37.5
|
1.0
|
NH1
|
D:ARG189
|
3.5
|
38.3
|
1.0
|
PB
|
D:ADP600
|
3.5
|
37.5
|
1.0
|
O3B
|
D:ADP600
|
3.9
|
37.4
|
1.0
|
OD2
|
D:ASP256
|
4.0
|
38.8
|
1.0
|
OE2
|
D:GLU192
|
4.0
|
36.4
|
1.0
|
OE1
|
D:GLU188
|
4.0
|
45.8
|
1.0
|
O
|
D:HOH2056
|
4.1
|
33.2
|
1.0
|
CG2
|
D:THR163
|
4.1
|
41.0
|
1.0
|
OE1
|
D:GLU192
|
4.2
|
45.3
|
1.0
|
OD1
|
D:ASP256
|
4.2
|
40.3
|
1.0
|
N
|
D:THR163
|
4.3
|
38.4
|
1.0
|
CA
|
D:THR163
|
4.3
|
39.5
|
1.0
|
O2A
|
D:ADP600
|
4.3
|
37.9
|
1.0
|
O
|
D:HOH2055
|
4.4
|
37.2
|
1.0
|
O3A
|
D:ADP600
|
4.4
|
39.0
|
1.0
|
NH1
|
C:ARG373
|
4.5
|
29.4
|
1.0
|
CD
|
D:GLU192
|
4.5
|
42.3
|
1.0
|
O1B
|
D:ADP600
|
4.5
|
37.5
|
1.0
|
CD
|
D:GLU188
|
4.5
|
44.6
|
1.0
|
CG
|
D:ASP256
|
4.5
|
42.4
|
1.0
|
PA
|
D:ADP600
|
4.8
|
38.8
|
1.0
|
CZ
|
D:ARG189
|
4.8
|
41.1
|
1.0
|
O1A
|
D:ADP600
|
4.9
|
39.4
|
1.0
|
CE
|
D:LYS162
|
4.9
|
30.6
|
1.0
|
O
|
D:HOH2072
|
4.9
|
33.1
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 1e79
Go back to
Magnesium Binding Sites List in 1e79
Magnesium binding site 5 out
of 5 in the Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg601
b:34.7
occ:1.00
|
OG1
|
F:THR163
|
2.1
|
32.5
|
1.0
|
O
|
F:HOH2059
|
2.1
|
28.4
|
1.0
|
O
|
F:HOH2162
|
2.1
|
33.1
|
1.0
|
O2B
|
F:ADP600
|
2.1
|
41.5
|
1.0
|
O
|
F:HOH2062
|
2.1
|
38.8
|
1.0
|
O
|
F:HOH2086
|
2.1
|
28.0
|
1.0
|
PB
|
F:ADP600
|
3.2
|
42.7
|
1.0
|
CB
|
F:THR163
|
3.3
|
36.9
|
1.0
|
O3B
|
F:ADP600
|
3.3
|
41.9
|
1.0
|
NH1
|
F:ARG189
|
3.8
|
28.9
|
1.0
|
N
|
F:THR163
|
4.0
|
36.0
|
1.0
|
O3A
|
F:ADP600
|
4.0
|
41.3
|
1.0
|
O2A
|
F:ADP600
|
4.1
|
41.4
|
1.0
|
OE2
|
F:GLU192
|
4.2
|
42.8
|
1.0
|
CA
|
F:THR163
|
4.2
|
35.6
|
1.0
|
CG2
|
F:THR163
|
4.3
|
28.7
|
1.0
|
O
|
F:HOH2063
|
4.3
|
31.8
|
1.0
|
OE1
|
F:GLU188
|
4.3
|
48.8
|
1.0
|
O1A
|
F:ADP600
|
4.3
|
41.0
|
1.0
|
PA
|
F:ADP600
|
4.4
|
41.2
|
1.0
|
O1B
|
F:ADP600
|
4.4
|
42.1
|
1.0
|
OE1
|
F:GLU192
|
4.4
|
43.9
|
1.0
|
OD2
|
F:ASP256
|
4.4
|
40.6
|
1.0
|
OD1
|
F:ASP256
|
4.5
|
38.6
|
1.0
|
O
|
F:HOH2161
|
4.7
|
41.4
|
1.0
|
O
|
F:HOH2163
|
4.7
|
33.9
|
1.0
|
CD
|
F:GLU192
|
4.8
|
43.3
|
1.0
|
CG
|
F:ASP256
|
4.9
|
40.7
|
1.0
|
|
Reference:
C.Gibbons,
M.G.Montgomery,
A.G.W.Leslie,
J.E.Walker.
The Structure of the Central Stalk in Bovine F(1)- Atpase at 2.4 A Resolution. Nat.Struct.Biol. V. 7 1055 2000.
ISSN: ISSN 1072-8368
PubMed: 11062563
DOI: 10.1038/80981
Page generated: Tue Aug 13 02:51:58 2024
|