Magnesium in PDB 4a01: Crystal Structure of the H-Translocating Pyrophosphatase
Enzymatic activity of Crystal Structure of the H-Translocating Pyrophosphatase
All present enzymatic activity of Crystal Structure of the H-Translocating Pyrophosphatase:
3.6.1.1;
Protein crystallography data
The structure of Crystal Structure of the H-Translocating Pyrophosphatase, PDB code: 4a01
was solved by
S.-M.Lin,
J.-Y.Tsai,
C.-D.Hsiao,
C.-L.Chiu,
R.-L.Pan,
Y.-J.Sun,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
30.00 /
2.35
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
218.619,
88.241,
159.105,
90.00,
125.53,
90.00
|
|
R / Rfree (%)
|
16.803 /
20.314
|
Other elements in 4a01:
The structure of Crystal Structure of the H-Translocating Pyrophosphatase also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the H-Translocating Pyrophosphatase
(pdb code 4a01). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the
Crystal Structure of the H-Translocating Pyrophosphatase, PDB code: 4a01:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 4a01
Go back to
Magnesium Binding Sites List in 4a01
Magnesium binding site 1 out
of 10 in the Crystal Structure of the H-Translocating Pyrophosphatase
 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 H-Translocating Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1767
b:36.9
occ:1.00
|
OD1
|
A:ASP253
|
1.9
|
37.4
|
1.0
|
|
OD2
|
A:ASP257
|
2.0
|
32.9
|
1.0
|
|
O5
|
A:2PN1773
|
2.1
|
32.3
|
1.0
|
|
O
|
A:HOH2112
|
2.1
|
31.0
|
1.0
|
|
O
|
A:HOH2109
|
2.2
|
30.8
|
1.0
|
|
O
|
A:HOH2108
|
2.2
|
30.0
|
1.0
|
|
CG
|
A:ASP253
|
3.0
|
34.6
|
1.0
|
|
CG
|
A:ASP257
|
3.0
|
31.1
|
1.0
|
|
MG
|
A:MG1769
|
3.3
|
34.0
|
1.0
|
|
OD2
|
A:ASP253
|
3.3
|
37.5
|
1.0
|
|
OD1
|
A:ASP257
|
3.4
|
30.1
|
1.0
|
|
P2
|
A:2PN1773
|
3.4
|
35.2
|
1.0
|
|
O4
|
A:2PN1773
|
3.7
|
31.9
|
1.0
|
|
O
|
A:HOH2113
|
3.9
|
29.6
|
1.0
|
|
OD2
|
A:ASP723
|
4.0
|
33.3
|
1.0
|
|
O
|
A:HOH2106
|
4.1
|
29.7
|
1.0
|
|
O6
|
A:2PN1773
|
4.2
|
31.9
|
1.0
|
|
CB
|
A:ASP257
|
4.2
|
33.0
|
1.0
|
|
OD2
|
A:ASP727
|
4.2
|
31.4
|
1.0
|
|
OD2
|
A:ASP279
|
4.3
|
37.5
|
1.0
|
|
O
|
A:HOH2299
|
4.3
|
27.7
|
1.0
|
|
OE1
|
A:GLU268
|
4.3
|
38.3
|
1.0
|
|
O
|
A:HOH2127
|
4.3
|
26.3
|
1.0
|
|
CB
|
A:ASP253
|
4.3
|
34.0
|
1.0
|
|
O
|
A:ASP253
|
4.4
|
31.9
|
1.0
|
|
N1
|
A:2PN1773
|
4.7
|
36.2
|
1.0
|
|
CA
|
A:ASP253
|
4.7
|
31.4
|
1.0
|
|
NZ
|
A:LYS694
|
4.7
|
29.0
|
1.0
|
|
CD
|
A:GLU268
|
4.7
|
38.6
|
1.0
|
|
C
|
A:ASP253
|
4.8
|
31.2
|
1.0
|
|
OD1
|
A:ASP727
|
4.8
|
31.7
|
1.0
|
|
CG
|
A:ASP727
|
4.9
|
29.9
|
1.0
|
|
O1
|
A:2PN1773
|
4.9
|
32.4
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 4a01
Go back to
Magnesium Binding Sites List in 4a01
Magnesium binding site 2 out
of 10 in the Crystal Structure of the H-Translocating Pyrophosphatase
 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 H-Translocating Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1768
b:44.7
occ:1.00
|
O
|
A:HOH2129
|
1.9
|
32.2
|
1.0
|
|
O
|
A:HOH2127
|
2.0
|
26.3
|
1.0
|
|
OD1
|
A:ASP507
|
2.1
|
33.2
|
1.0
|
|
O
|
A:HOH2134
|
2.1
|
35.9
|
1.0
|
|
O
|
A:HOH2128
|
2.1
|
31.3
|
1.0
|
|
O6
|
A:2PN1773
|
2.1
|
31.9
|
1.0
|
|
CG
|
A:ASP507
|
3.0
|
31.8
|
1.0
|
|
OD2
|
A:ASP507
|
3.2
|
34.3
|
1.0
|
|
MG
|
A:MG1770
|
3.4
|
35.8
|
1.0
|
|
P2
|
A:2PN1773
|
3.4
|
35.2
|
1.0
|
|
O4
|
A:2PN1773
|
3.6
|
31.9
|
1.0
|
|
O
|
A:HOH2215
|
3.9
|
35.8
|
1.0
|
|
OD2
|
A:ASP269
|
3.9
|
41.3
|
1.0
|
|
OD1
|
A:ASP279
|
4.1
|
38.5
|
1.0
|
|
O
|
A:HOH2106
|
4.1
|
29.7
|
1.0
|
|
OD2
|
A:ASP283
|
4.2
|
35.1
|
1.0
|
|
O
|
A:HOH2108
|
4.2
|
30.0
|
1.0
|
|
O
|
A:ASP507
|
4.2
|
35.2
|
1.0
|
|
OD1
|
A:ASP269
|
4.3
|
40.1
|
1.0
|
|
OE2
|
A:GLU268
|
4.4
|
34.8
|
1.0
|
|
CB
|
A:ASP507
|
4.4
|
34.8
|
1.0
|
|
O5
|
A:2PN1773
|
4.4
|
32.3
|
1.0
|
|
ND2
|
A:ASN280
|
4.5
|
34.5
|
1.0
|
|
CG
|
A:ASP269
|
4.6
|
40.3
|
1.0
|
|
C
|
A:ASP507
|
4.6
|
34.7
|
1.0
|
|
OD1
|
A:ASP283
|
4.6
|
34.3
|
1.0
|
|
N1
|
A:2PN1773
|
4.6
|
36.2
|
1.0
|
|
CA
|
A:ASP507
|
4.7
|
34.4
|
1.0
|
|
CG
|
A:ASP283
|
4.8
|
36.0
|
1.0
|
|
O
|
A:HOH2216
|
4.8
|
36.4
|
1.0
|
|
OD2
|
A:ASP279
|
4.9
|
37.5
|
1.0
|
|
CG
|
A:ASP279
|
4.9
|
37.5
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 4a01
Go back to
Magnesium Binding Sites List in 4a01
Magnesium binding site 3 out
of 10 in the Crystal Structure of the H-Translocating Pyrophosphatase
 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 H-Translocating Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1769
b:34.0
occ:1.00
|
O
|
A:HOH2299
|
2.0
|
27.7
|
1.0
|
|
O1
|
A:2PN1773
|
2.0
|
32.4
|
1.0
|
|
OD1
|
A:ASP727
|
2.1
|
31.7
|
1.0
|
|
O5
|
A:2PN1773
|
2.2
|
32.3
|
1.0
|
|
O
|
A:HOH2109
|
2.3
|
30.8
|
1.0
|
|
OD2
|
A:ASP253
|
2.3
|
37.5
|
1.0
|
|
CG
|
A:ASP727
|
3.0
|
29.9
|
1.0
|
|
P1
|
A:2PN1773
|
3.1
|
42.7
|
1.0
|
|
N1
|
A:2PN1773
|
3.2
|
36.2
|
1.0
|
|
CG
|
A:ASP253
|
3.2
|
34.6
|
1.0
|
|
OD2
|
A:ASP727
|
3.2
|
31.4
|
1.0
|
|
P2
|
A:2PN1773
|
3.2
|
35.2
|
1.0
|
|
MG
|
A:MG1767
|
3.3
|
36.9
|
1.0
|
|
OD1
|
A:ASP253
|
3.4
|
37.4
|
1.0
|
|
NZ
|
A:LYS730
|
3.5
|
26.7
|
1.0
|
|
O
|
A:HOH2106
|
4.0
|
29.7
|
1.0
|
|
CE
|
A:LYS250
|
4.0
|
23.7
|
1.0
|
|
OD1
|
A:ASP723
|
4.0
|
30.9
|
1.0
|
|
O2
|
A:2PN1773
|
4.1
|
30.4
|
1.0
|
|
NZ
|
A:LYS250
|
4.1
|
26.0
|
1.0
|
|
OD2
|
A:ASP723
|
4.1
|
33.3
|
1.0
|
|
O4
|
A:2PN1773
|
4.3
|
31.9
|
1.0
|
|
O3
|
A:2PN1773
|
4.3
|
37.6
|
1.0
|
|
O
|
A:HOH2112
|
4.3
|
31.0
|
1.0
|
|
CB
|
A:ASP727
|
4.4
|
28.0
|
1.0
|
|
O6
|
A:2PN1773
|
4.4
|
31.9
|
1.0
|
|
OD2
|
A:ASP691
|
4.4
|
31.3
|
1.0
|
|
CG
|
A:ASP723
|
4.4
|
32.3
|
1.0
|
|
CB
|
A:ASP253
|
4.6
|
34.0
|
1.0
|
|
OD2
|
A:ASP731
|
4.7
|
35.2
|
1.0
|
|
O
|
A:HOH2298
|
4.7
|
25.2
|
1.0
|
|
MG
|
A:MG1770
|
4.7
|
35.8
|
1.0
|
|
CE
|
A:LYS730
|
4.8
|
32.6
|
1.0
|
|
MG
|
A:MG1771
|
4.8
|
34.0
|
1.0
|
|
O
|
A:HOH2105
|
4.8
|
24.9
|
1.0
|
|
CA
|
A:ASP727
|
4.9
|
29.0
|
1.0
|
|
OD2
|
A:ASP257
|
4.9
|
32.9
|
1.0
|
|
O
|
A:ASP723
|
4.9
|
31.2
|
1.0
|
|
CG
|
A:ASP691
|
5.0
|
31.7
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 4a01
Go back to
Magnesium Binding Sites List in 4a01
Magnesium binding site 4 out
of 10 in the Crystal Structure of the H-Translocating Pyrophosphatase
 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 H-Translocating Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1770
b:35.8
occ:1.00
|
O2
|
A:2PN1773
|
2.1
|
30.4
|
1.0
|
|
O6
|
A:2PN1773
|
2.1
|
31.9
|
1.0
|
|
O
|
A:HOH2106
|
2.1
|
29.7
|
1.0
|
|
OD1
|
A:ASP283
|
2.1
|
34.3
|
1.0
|
|
OD2
|
A:ASP507
|
2.2
|
34.3
|
1.0
|
|
O
|
A:HOH2134
|
2.3
|
35.9
|
1.0
|
|
P2
|
A:2PN1773
|
3.1
|
35.2
|
1.0
|
|
CG
|
A:ASP283
|
3.1
|
36.0
|
1.0
|
|
P1
|
A:2PN1773
|
3.2
|
42.7
|
1.0
|
|
CG
|
A:ASP507
|
3.3
|
31.8
|
1.0
|
|
MG
|
A:MG1768
|
3.4
|
44.7
|
1.0
|
|
N1
|
A:2PN1773
|
3.4
|
36.2
|
1.0
|
|
OD2
|
A:ASP283
|
3.6
|
35.1
|
1.0
|
|
OD1
|
A:ASP507
|
3.6
|
33.2
|
1.0
|
|
O
|
A:HOH2103
|
3.6
|
28.1
|
1.0
|
|
O5
|
A:2PN1773
|
3.7
|
32.3
|
1.0
|
|
O
|
A:HOH2137
|
3.8
|
43.8
|
1.0
|
|
O1
|
A:2PN1773
|
4.0
|
32.4
|
1.0
|
|
O
|
A:HOH2102
|
4.2
|
32.1
|
1.0
|
|
O
|
A:HOH2216
|
4.3
|
36.4
|
1.0
|
|
NZ
|
A:LYS250
|
4.3
|
26.0
|
1.0
|
|
OD1
|
A:ASP279
|
4.4
|
38.5
|
1.0
|
|
O3
|
A:2PN1773
|
4.4
|
37.6
|
1.0
|
|
OD2
|
A:ASP253
|
4.4
|
37.5
|
1.0
|
|
CB
|
A:ASP283
|
4.4
|
33.1
|
1.0
|
|
O4
|
A:2PN1773
|
4.5
|
31.9
|
1.0
|
|
O
|
A:HOH2127
|
4.5
|
26.3
|
1.0
|
|
CB
|
A:ASP507
|
4.6
|
34.8
|
1.0
|
|
O
|
A:HOH2105
|
4.6
|
24.9
|
1.0
|
|
MG
|
A:MG1769
|
4.7
|
34.0
|
1.0
|
|
O
|
A:HOH2128
|
4.8
|
31.3
|
1.0
|
|
OD2
|
A:ASP287
|
4.9
|
34.6
|
1.0
|
|
MG
|
A:MG1771
|
4.9
|
34.0
|
1.0
|
|
CG
|
A:ASP253
|
5.0
|
34.6
|
1.0
|
|
O
|
A:HOH2129
|
5.0
|
32.2
|
1.0
|
|
CA
|
A:ASP283
|
5.0
|
33.6
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 4a01
Go back to
Magnesium Binding Sites List in 4a01
Magnesium binding site 5 out
of 10 in the Crystal Structure of the H-Translocating Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of the H-Translocating Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1771
b:34.0
occ:1.00
|
OD2
|
A:ASP691
|
2.0
|
31.3
|
1.0
|
|
N1
|
A:2PN1773
|
2.1
|
36.2
|
1.0
|
|
O
|
A:HOH2216
|
2.1
|
36.4
|
1.0
|
|
OD1
|
A:ASN534
|
2.1
|
40.4
|
1.0
|
|
O3
|
A:2PN1773
|
2.2
|
37.6
|
1.0
|
|
O
|
A:HOH2234
|
2.2
|
29.2
|
1.0
|
|
P1
|
A:2PN1773
|
2.8
|
42.7
|
1.0
|
|
CG
|
A:ASN534
|
3.0
|
32.0
|
1.0
|
|
CG
|
A:ASP691
|
3.2
|
31.7
|
1.0
|
|
ND2
|
A:ASN534
|
3.3
|
33.4
|
1.0
|
|
P2
|
A:2PN1773
|
3.4
|
35.2
|
1.0
|
|
OD1
|
A:ASP691
|
3.6
|
32.3
|
1.0
|
|
O4
|
A:2PN1773
|
3.7
|
31.9
|
1.0
|
|
O2
|
A:2PN1773
|
3.8
|
30.4
|
1.0
|
|
O
|
A:HOH2299
|
3.9
|
27.7
|
1.0
|
|
K
|
A:K1772
|
3.9
|
62.8
|
1.0
|
|
O
|
A:HOH2236
|
3.9
|
27.1
|
1.0
|
|
O1
|
A:2PN1773
|
4.0
|
32.4
|
1.0
|
|
OD2
|
A:ASP530
|
4.1
|
35.3
|
1.0
|
|
O6
|
A:2PN1773
|
4.2
|
31.9
|
1.0
|
|
CB
|
A:ASP691
|
4.4
|
29.6
|
1.0
|
|
CB
|
A:ASN534
|
4.4
|
30.6
|
1.0
|
|
OD1
|
A:ASP530
|
4.4
|
38.9
|
1.0
|
|
O5
|
A:2PN1773
|
4.5
|
32.3
|
1.0
|
|
CG
|
A:ASP530
|
4.7
|
36.3
|
1.0
|
|
O
|
A:HOH2105
|
4.7
|
24.9
|
1.0
|
|
O
|
A:HOH2214
|
4.8
|
34.5
|
1.0
|
|
O
|
A:HOH2137
|
4.8
|
43.8
|
1.0
|
|
MG
|
A:MG1769
|
4.8
|
34.0
|
1.0
|
|
CE
|
A:LYS730
|
4.8
|
32.6
|
1.0
|
|
OD2
|
A:ASP507
|
4.9
|
34.3
|
1.0
|
|
CA
|
A:ASN534
|
4.9
|
32.1
|
1.0
|
|
MG
|
A:MG1770
|
4.9
|
35.8
|
1.0
|
|
NZ
|
A:LYS730
|
4.9
|
26.7
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 4a01
Go back to
Magnesium Binding Sites List in 4a01
Magnesium binding site 6 out
of 10 in the Crystal Structure of the H-Translocating Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of the H-Translocating Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1767
b:41.7
occ:1.00
|
OD2
|
B:ASP257
|
2.0
|
40.9
|
1.0
|
|
OD1
|
B:ASP253
|
2.0
|
43.8
|
1.0
|
|
O5
|
B:2PN1773
|
2.1
|
33.6
|
1.0
|
|
O
|
B:HOH2072
|
2.2
|
39.8
|
1.0
|
|
O
|
B:HOH2075
|
2.3
|
35.4
|
1.0
|
|
O
|
B:HOH2073
|
2.4
|
33.5
|
1.0
|
|
CG
|
B:ASP253
|
3.0
|
40.3
|
1.0
|
|
CG
|
B:ASP257
|
3.1
|
38.2
|
1.0
|
|
MG
|
B:MG1769
|
3.2
|
36.9
|
1.0
|
|
OD2
|
B:ASP253
|
3.3
|
35.7
|
1.0
|
|
P2
|
B:2PN1773
|
3.3
|
34.1
|
1.0
|
|
OD1
|
B:ASP257
|
3.5
|
32.0
|
1.0
|
|
O4
|
B:2PN1773
|
3.6
|
36.2
|
1.0
|
|
O6
|
B:2PN1773
|
3.9
|
34.8
|
1.0
|
|
OD2
|
B:ASP723
|
3.9
|
40.2
|
1.0
|
|
O
|
B:HOH2076
|
4.0
|
39.2
|
1.0
|
|
OD2
|
B:ASP727
|
4.3
|
31.7
|
1.0
|
|
OE1
|
B:GLU268
|
4.3
|
41.9
|
1.0
|
|
O
|
B:HOH2070
|
4.3
|
39.5
|
1.0
|
|
O
|
B:HOH2087
|
4.3
|
30.9
|
1.0
|
|
OD2
|
B:ASP279
|
4.3
|
38.4
|
1.0
|
|
O
|
B:HOH2232
|
4.3
|
30.5
|
1.0
|
|
CB
|
B:ASP257
|
4.4
|
38.2
|
1.0
|
|
CB
|
B:ASP253
|
4.4
|
38.9
|
1.0
|
|
O
|
B:ASP253
|
4.4
|
39.4
|
1.0
|
|
OD1
|
B:ASP727
|
4.6
|
34.6
|
1.0
|
|
N1
|
B:2PN1773
|
4.7
|
37.6
|
1.0
|
|
NZ
|
B:LYS694
|
4.7
|
35.1
|
1.0
|
|
CD
|
B:GLU268
|
4.7
|
42.6
|
1.0
|
|
CA
|
B:ASP253
|
4.7
|
39.3
|
1.0
|
|
C
|
B:ASP253
|
4.8
|
39.2
|
1.0
|
|
O1
|
B:2PN1773
|
4.9
|
34.6
|
1.0
|
|
CG
|
B:ASP727
|
4.9
|
32.7
|
1.0
|
|
OE2
|
B:GLU268
|
5.0
|
39.8
|
1.0
|
|
CG
|
B:ASP723
|
5.0
|
36.3
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 4a01
Go back to
Magnesium Binding Sites List in 4a01
Magnesium binding site 7 out
of 10 in the Crystal Structure of the H-Translocating Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of the H-Translocating Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1768
b:40.2
occ:1.00
|
OD1
|
B:ASP507
|
1.7
|
35.0
|
1.0
|
|
O
|
B:HOH2089
|
2.0
|
37.3
|
1.0
|
|
O
|
B:HOH2087
|
2.0
|
30.9
|
1.0
|
|
O
|
B:HOH2094
|
2.0
|
36.5
|
1.0
|
|
O
|
B:HOH2088
|
2.1
|
40.5
|
1.0
|
|
O6
|
B:2PN1773
|
2.2
|
34.8
|
1.0
|
|
CG
|
B:ASP507
|
2.8
|
38.5
|
1.0
|
|
OD2
|
B:ASP507
|
3.1
|
39.9
|
1.0
|
|
MG
|
B:MG1770
|
3.4
|
41.3
|
1.0
|
|
P2
|
B:2PN1773
|
3.6
|
34.1
|
1.0
|
|
O4
|
B:2PN1773
|
3.8
|
36.2
|
1.0
|
|
O
|
B:ASP507
|
3.9
|
40.2
|
1.0
|
|
OD2
|
B:ASP269
|
4.0
|
45.9
|
1.0
|
|
OD1
|
B:ASP279
|
4.0
|
36.6
|
1.0
|
|
O
|
B:HOH2168
|
4.0
|
46.1
|
1.0
|
|
CB
|
B:ASP507
|
4.1
|
39.1
|
1.0
|
|
OD2
|
B:ASP283
|
4.1
|
38.1
|
1.0
|
|
OE2
|
B:GLU268
|
4.2
|
39.8
|
1.0
|
|
O
|
B:HOH2070
|
4.2
|
39.5
|
1.0
|
|
OD1
|
B:ASP269
|
4.3
|
44.6
|
1.0
|
|
O
|
B:HOH2073
|
4.4
|
33.5
|
1.0
|
|
C
|
B:ASP507
|
4.4
|
40.5
|
1.0
|
|
CA
|
B:ASP507
|
4.5
|
40.4
|
1.0
|
|
ND2
|
B:ASN280
|
4.5
|
42.2
|
1.0
|
|
O5
|
B:2PN1773
|
4.5
|
33.6
|
1.0
|
|
N1
|
B:2PN1773
|
4.5
|
37.6
|
1.0
|
|
CG
|
B:ASP269
|
4.6
|
45.5
|
1.0
|
|
OD1
|
B:ASP283
|
4.7
|
40.3
|
1.0
|
|
O
|
B:HOH2169
|
4.8
|
41.7
|
1.0
|
|
CG
|
B:ASP283
|
4.9
|
40.2
|
1.0
|
|
OD2
|
B:ASP530
|
4.9
|
41.7
|
1.0
|
|
CG
|
B:ASP279
|
4.9
|
38.2
|
1.0
|
|
CD
|
B:GLU268
|
5.0
|
42.6
|
1.0
|
|
OD2
|
B:ASP279
|
5.0
|
38.4
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 4a01
Go back to
Magnesium Binding Sites List in 4a01
Magnesium binding site 8 out
of 10 in the Crystal Structure of the H-Translocating Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of the H-Translocating Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1769
b:36.9
occ:1.00
|
O5
|
B:2PN1773
|
2.0
|
33.6
|
1.0
|
|
O
|
B:HOH2232
|
2.1
|
30.5
|
1.0
|
|
O1
|
B:2PN1773
|
2.1
|
34.6
|
1.0
|
|
OD1
|
B:ASP727
|
2.1
|
34.6
|
1.0
|
|
O
|
B:HOH2072
|
2.2
|
39.8
|
1.0
|
|
OD2
|
B:ASP253
|
2.2
|
35.7
|
1.0
|
|
P2
|
B:2PN1773
|
3.1
|
34.1
|
1.0
|
|
CG
|
B:ASP727
|
3.1
|
32.7
|
1.0
|
|
MG
|
B:MG1767
|
3.2
|
41.7
|
1.0
|
|
CG
|
B:ASP253
|
3.2
|
40.3
|
1.0
|
|
P1
|
B:2PN1773
|
3.3
|
47.6
|
1.0
|
|
N1
|
B:2PN1773
|
3.3
|
37.6
|
1.0
|
|
OD2
|
B:ASP727
|
3.4
|
31.7
|
1.0
|
|
NZ
|
B:LYS730
|
3.4
|
31.4
|
1.0
|
|
OD1
|
B:ASP253
|
3.6
|
43.8
|
1.0
|
|
NZ
|
B:LYS250
|
3.8
|
24.5
|
1.0
|
|
O4
|
B:2PN1773
|
4.0
|
36.2
|
1.0
|
|
OD2
|
B:ASP723
|
4.1
|
40.2
|
1.0
|
|
OD1
|
B:ASP723
|
4.1
|
39.8
|
1.0
|
|
O6
|
B:2PN1773
|
4.2
|
34.8
|
1.0
|
|
O
|
B:HOH2070
|
4.2
|
39.5
|
1.0
|
|
O2
|
B:2PN1773
|
4.2
|
40.5
|
1.0
|
|
O
|
B:HOH2075
|
4.4
|
35.4
|
1.0
|
|
OD2
|
B:ASP691
|
4.4
|
39.5
|
1.0
|
|
O3
|
B:2PN1773
|
4.4
|
38.5
|
1.0
|
|
CB
|
B:ASP727
|
4.5
|
34.3
|
1.0
|
|
CG
|
B:ASP723
|
4.5
|
36.3
|
1.0
|
|
CB
|
B:ASP253
|
4.6
|
38.9
|
1.0
|
|
OD2
|
B:ASP731
|
4.6
|
34.3
|
1.0
|
|
CE
|
B:LYS730
|
4.7
|
31.4
|
1.0
|
|
O
|
B:HOH2231
|
4.7
|
33.9
|
1.0
|
|
MG
|
B:MG1771
|
4.8
|
38.8
|
1.0
|
|
O
|
B:HOH2069
|
4.8
|
30.9
|
1.0
|
|
CE
|
B:LYS250
|
4.8
|
28.0
|
1.0
|
|
OD2
|
B:ASP257
|
4.8
|
40.9
|
1.0
|
|
CD
|
B:LYS250
|
4.9
|
26.9
|
1.0
|
|
CG
|
B:ASP691
|
4.9
|
39.1
|
1.0
|
|
MG
|
B:MG1770
|
5.0
|
41.3
|
1.0
|
|
CA
|
B:ASP727
|
5.0
|
33.6
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 4a01
Go back to
Magnesium Binding Sites List in 4a01
Magnesium binding site 9 out
of 10 in the Crystal Structure of the H-Translocating Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of the H-Translocating Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1770
b:41.3
occ:1.00
|
OD2
|
B:ASP507
|
1.9
|
39.9
|
1.0
|
|
OD1
|
B:ASP283
|
2.0
|
40.3
|
1.0
|
|
O2
|
B:2PN1773
|
2.0
|
40.5
|
1.0
|
|
O
|
B:HOH2070
|
2.1
|
39.5
|
1.0
|
|
O
|
B:HOH2094
|
2.3
|
36.5
|
1.0
|
|
O6
|
B:2PN1773
|
2.4
|
34.8
|
1.0
|
|
CG
|
B:ASP283
|
2.9
|
40.2
|
1.0
|
|
CG
|
B:ASP507
|
3.1
|
38.5
|
1.0
|
|
OD2
|
B:ASP283
|
3.2
|
38.1
|
1.0
|
|
P1
|
B:2PN1773
|
3.3
|
47.6
|
1.0
|
|
P2
|
B:2PN1773
|
3.4
|
34.1
|
1.0
|
|
MG
|
B:MG1768
|
3.4
|
40.2
|
1.0
|
|
O
|
B:HOH2068
|
3.4
|
28.6
|
1.0
|
|
OD1
|
B:ASP507
|
3.5
|
35.0
|
1.0
|
|
N1
|
B:2PN1773
|
3.5
|
37.6
|
1.0
|
|
O
|
B:HOH2098
|
3.6
|
46.7
|
1.0
|
|
O5
|
B:2PN1773
|
3.9
|
33.6
|
1.0
|
|
O1
|
B:2PN1773
|
4.0
|
34.6
|
1.0
|
|
O
|
B:HOH2067
|
4.1
|
35.9
|
1.0
|
|
OD1
|
B:ASP279
|
4.1
|
36.6
|
1.0
|
|
CB
|
B:ASP283
|
4.3
|
39.8
|
1.0
|
|
O
|
B:HOH2169
|
4.3
|
41.7
|
1.0
|
|
CB
|
B:ASP507
|
4.3
|
39.1
|
1.0
|
|
NZ
|
B:LYS250
|
4.4
|
24.5
|
1.0
|
|
O3
|
B:2PN1773
|
4.5
|
38.5
|
1.0
|
|
O
|
B:HOH2087
|
4.5
|
30.9
|
1.0
|
|
O
|
B:HOH2069
|
4.7
|
30.9
|
1.0
|
|
O4
|
B:2PN1773
|
4.7
|
36.2
|
1.0
|
|
OD2
|
B:ASP253
|
4.8
|
35.7
|
1.0
|
|
CA
|
B:ASP283
|
4.8
|
39.7
|
1.0
|
|
O
|
B:ASP279
|
4.9
|
40.6
|
1.0
|
|
O
|
B:HOH2088
|
4.9
|
40.5
|
1.0
|
|
MG
|
B:MG1769
|
5.0
|
36.9
|
1.0
|
|
O
|
B:HOH2089
|
5.0
|
37.3
|
1.0
|
|
OD2
|
B:ASP287
|
5.0
|
45.4
|
1.0
|
|
CG
|
B:ASP279
|
5.0
|
38.2
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 4a01
Go back to
Magnesium Binding Sites List in 4a01
Magnesium binding site 10 out
of 10 in the Crystal Structure of the H-Translocating Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of the H-Translocating Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1771
b:38.8
occ:1.00
|
N1
|
B:2PN1773
|
2.0
|
37.6
|
1.0
|
|
OD1
|
B:ASN534
|
2.1
|
40.9
|
1.0
|
|
O
|
B:HOH2169
|
2.1
|
41.7
|
1.0
|
|
O3
|
B:2PN1773
|
2.2
|
38.5
|
1.0
|
|
OD2
|
B:ASP691
|
2.3
|
39.5
|
1.0
|
|
O
|
B:HOH2179
|
2.4
|
38.9
|
1.0
|
|
P1
|
B:2PN1773
|
2.8
|
47.6
|
1.0
|
|
CG
|
B:ASN534
|
3.0
|
38.4
|
1.0
|
|
CG
|
B:ASP691
|
3.3
|
39.1
|
1.0
|
|
ND2
|
B:ASN534
|
3.3
|
37.7
|
1.0
|
|
P2
|
B:2PN1773
|
3.5
|
34.1
|
1.0
|
|
K
|
B:K1772
|
3.6
|
60.1
|
1.0
|
|
O4
|
B:2PN1773
|
3.7
|
36.2
|
1.0
|
|
O
|
B:HOH2181
|
3.7
|
28.3
|
1.0
|
|
OD1
|
B:ASP691
|
3.7
|
36.4
|
1.0
|
|
O1
|
B:2PN1773
|
4.0
|
34.6
|
1.0
|
|
O2
|
B:2PN1773
|
4.0
|
40.5
|
1.0
|
|
O
|
B:HOH2232
|
4.0
|
30.5
|
1.0
|
|
OD1
|
B:ASP530
|
4.2
|
43.4
|
1.0
|
|
O6
|
B:2PN1773
|
4.3
|
34.8
|
1.0
|
|
CB
|
B:ASN534
|
4.3
|
39.4
|
1.0
|
|
OD2
|
B:ASP530
|
4.3
|
41.7
|
1.0
|
|
O5
|
B:2PN1773
|
4.5
|
33.6
|
1.0
|
|
CB
|
B:ASP691
|
4.6
|
36.2
|
1.0
|
|
O
|
B:HOH2167
|
4.6
|
34.5
|
1.0
|
|
CG
|
B:ASP530
|
4.6
|
42.5
|
1.0
|
|
O
|
B:HOH2069
|
4.7
|
30.9
|
1.0
|
|
CA
|
B:ASN534
|
4.7
|
39.2
|
1.0
|
|
O
|
B:HOH2098
|
4.8
|
46.7
|
1.0
|
|
MG
|
B:MG1769
|
4.8
|
36.9
|
1.0
|
|
OD2
|
B:ASP507
|
4.8
|
39.9
|
1.0
|
|
CE
|
B:LYS730
|
4.8
|
31.4
|
1.0
|
|
O
|
B:ASP530
|
5.0
|
40.3
|
1.0
|
|
Reference:
S.-M.Lin,
J.-Y.Tsai,
C.-D.Hsiao,
C.-L.Chiu,
R.-L.Pan,
Y.-J.Sun.
Crystal Structure of A Membrane Embedded H1-Translocating Pyrophosphatase Nature V. 484 399 2012.
ISSN: ISSN 0028-0836
PubMed: 22456709
DOI: 10.1038/NATURE10963
Page generated: Mon Dec 14 09:05:30 2020
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