Magnesium in PDB 6afw: Proton Pyrophosphatase-T228D Mutant
Enzymatic activity of Proton Pyrophosphatase-T228D Mutant
All present enzymatic activity of Proton Pyrophosphatase-T228D Mutant:
3.6.1.1;
Protein crystallography data
The structure of Proton Pyrophosphatase-T228D Mutant, PDB code: 6afw
was solved by
J.-Y.Tsai,
K.-M.Li,
Y.-J.Sun,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
26.62 /
2.19
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
212.672,
88.101,
156.686,
90.00,
124.54,
90.00
|
|
R / Rfree (%)
|
19.9 /
23.5
|
Other elements in 6afw:
The structure of Proton Pyrophosphatase-T228D Mutant also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Proton Pyrophosphatase-T228D Mutant
(pdb code 6afw). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the
Proton Pyrophosphatase-T228D Mutant, PDB code: 6afw:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 6afw
Go back to
Magnesium Binding Sites List in 6afw
Magnesium binding site 1 out
of 10 in the Proton Pyrophosphatase-T228D Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1003
b:32.9
occ:1.00
|
O
|
A:HOH1114
|
2.1
|
27.8
|
1.0
|
|
OD2
|
A:ASP257
|
2.1
|
31.4
|
1.0
|
|
OD1
|
A:ASP253
|
2.1
|
30.5
|
1.0
|
|
O
|
A:HOH1196
|
2.1
|
28.7
|
1.0
|
|
O2
|
A:PO41002
|
2.2
|
31.5
|
1.0
|
|
O
|
A:HOH1142
|
2.3
|
27.2
|
1.0
|
|
CG
|
A:ASP257
|
3.0
|
31.9
|
1.0
|
|
CG
|
A:ASP253
|
3.1
|
31.8
|
1.0
|
|
MG
|
A:MG1005
|
3.3
|
28.9
|
1.0
|
|
OD1
|
A:ASP257
|
3.3
|
30.6
|
1.0
|
|
P
|
A:PO41002
|
3.3
|
34.7
|
1.0
|
|
O3
|
A:PO41002
|
3.4
|
31.5
|
1.0
|
|
OD2
|
A:ASP253
|
3.4
|
33.7
|
1.0
|
|
O
|
A:HOH1130
|
3.8
|
28.7
|
1.0
|
|
O
|
A:HOH1232
|
4.1
|
31.0
|
1.0
|
|
O4
|
A:PO41002
|
4.1
|
29.6
|
1.0
|
|
OD2
|
A:ASP723
|
4.1
|
31.9
|
1.0
|
|
O
|
A:HOH1167
|
4.1
|
27.1
|
1.0
|
|
OE1
|
A:GLU268
|
4.1
|
30.0
|
1.0
|
|
OD2
|
A:ASP279
|
4.2
|
31.6
|
1.0
|
|
O
|
A:ASP253
|
4.3
|
29.9
|
1.0
|
|
CB
|
A:ASP257
|
4.3
|
32.3
|
1.0
|
|
O1
|
A:PO41002
|
4.4
|
36.5
|
1.0
|
|
OD2
|
A:ASP727
|
4.5
|
29.0
|
1.0
|
|
O
|
A:HOH1115
|
4.5
|
26.8
|
1.0
|
|
CB
|
A:ASP253
|
4.5
|
32.2
|
1.0
|
|
CD
|
A:GLU268
|
4.5
|
35.0
|
1.0
|
|
NZ
|
A:LYS694
|
4.7
|
31.2
|
1.0
|
|
C
|
A:ASP253
|
4.8
|
28.9
|
1.0
|
|
CA
|
A:ASP253
|
4.8
|
31.3
|
1.0
|
|
OD1
|
A:ASP727
|
4.9
|
28.1
|
1.0
|
|
O4
|
A:PO41001
|
5.0
|
27.8
|
1.0
|
|
OE2
|
A:GLU268
|
5.0
|
36.0
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 6afw
Go back to
Magnesium Binding Sites List in 6afw
Magnesium binding site 2 out
of 10 in the Proton Pyrophosphatase-T228D Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1004
b:35.4
occ:1.00
|
OD1
|
A:ASP507
|
2.0
|
34.7
|
1.0
|
|
O
|
A:HOH1133
|
2.0
|
34.5
|
1.0
|
|
O
|
A:HOH1232
|
2.1
|
31.0
|
1.0
|
|
O
|
A:HOH1107
|
2.2
|
31.2
|
1.0
|
|
O
|
A:HOH1162
|
2.2
|
33.8
|
1.0
|
|
O4
|
A:PO41002
|
2.3
|
29.6
|
1.0
|
|
CG
|
A:ASP507
|
2.9
|
33.3
|
1.0
|
|
OD2
|
A:ASP507
|
3.2
|
32.6
|
1.0
|
|
MG
|
A:MG1006
|
3.4
|
34.1
|
1.0
|
|
P
|
A:PO41002
|
3.5
|
34.7
|
1.0
|
|
O3
|
A:PO41002
|
3.6
|
31.5
|
1.0
|
|
O
|
A:HOH1279
|
3.7
|
35.3
|
1.0
|
|
OD2
|
A:ASP269
|
4.0
|
31.6
|
1.0
|
|
OD1
|
A:ASP279
|
4.0
|
32.0
|
1.0
|
|
OD2
|
A:ASP283
|
4.1
|
32.2
|
1.0
|
|
O
|
A:ASP507
|
4.1
|
35.2
|
1.0
|
|
O
|
A:HOH1196
|
4.2
|
28.7
|
1.0
|
|
O
|
A:HOH1167
|
4.3
|
27.1
|
1.0
|
|
CB
|
A:ASP507
|
4.3
|
32.9
|
1.0
|
|
OD1
|
A:ASP269
|
4.4
|
33.9
|
1.0
|
|
O2
|
A:PO41002
|
4.4
|
31.5
|
1.0
|
|
OE2
|
A:GLU268
|
4.4
|
36.0
|
1.0
|
|
C
|
A:ASP507
|
4.5
|
33.7
|
1.0
|
|
ND2
|
A:ASN280
|
4.6
|
34.9
|
1.0
|
|
O1
|
A:PO41002
|
4.6
|
36.5
|
1.0
|
|
CG
|
A:ASP269
|
4.6
|
36.5
|
1.0
|
|
CA
|
A:ASP507
|
4.6
|
36.3
|
1.0
|
|
O2
|
A:PO41001
|
4.7
|
30.0
|
1.0
|
|
O
|
A:HOH1146
|
4.8
|
30.9
|
1.0
|
|
CG
|
A:ASP283
|
4.9
|
35.5
|
1.0
|
|
OD2
|
A:ASP530
|
4.9
|
35.2
|
1.0
|
|
OD1
|
A:ASP283
|
4.9
|
37.1
|
1.0
|
|
CG
|
A:ASP279
|
4.9
|
32.7
|
1.0
|
|
OD2
|
A:ASP279
|
5.0
|
31.6
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 6afw
Go back to
Magnesium Binding Sites List in 6afw
Magnesium binding site 3 out
of 10 in the Proton Pyrophosphatase-T228D Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1005
b:28.9
occ:1.00
|
O2
|
A:PO41002
|
2.1
|
31.5
|
1.0
|
|
OD1
|
A:ASP727
|
2.1
|
28.1
|
1.0
|
|
O
|
A:HOH1142
|
2.2
|
27.2
|
1.0
|
|
O
|
A:HOH1115
|
2.2
|
26.8
|
1.0
|
|
O4
|
A:PO41001
|
2.2
|
27.8
|
1.0
|
|
OD2
|
A:ASP253
|
2.3
|
33.7
|
1.0
|
|
CG
|
A:ASP727
|
3.0
|
30.1
|
1.0
|
|
CG
|
A:ASP253
|
3.2
|
31.8
|
1.0
|
|
O1
|
A:PO41002
|
3.2
|
36.5
|
1.0
|
|
P
|
A:PO41002
|
3.2
|
34.7
|
1.0
|
|
MG
|
A:MG1003
|
3.3
|
32.9
|
1.0
|
|
OD2
|
A:ASP727
|
3.3
|
29.0
|
1.0
|
|
OD1
|
A:ASP253
|
3.4
|
30.5
|
1.0
|
|
NZ
|
A:LYS730
|
3.7
|
26.6
|
1.0
|
|
P
|
A:PO41001
|
3.7
|
48.8
|
1.0
|
|
OD2
|
A:ASP723
|
4.0
|
31.9
|
1.0
|
|
O
|
A:HOH1167
|
4.0
|
27.1
|
1.0
|
|
OD1
|
A:ASP723
|
4.1
|
28.1
|
1.0
|
|
O3
|
A:PO41002
|
4.1
|
31.5
|
1.0
|
|
O
|
A:HOH1114
|
4.2
|
27.8
|
1.0
|
|
O2
|
A:PO41001
|
4.3
|
30.0
|
1.0
|
|
NZ
|
A:LYS250
|
4.3
|
28.7
|
1.0
|
|
CE
|
A:LYS250
|
4.3
|
25.4
|
1.0
|
|
O4
|
A:PO41002
|
4.3
|
29.6
|
1.0
|
|
O3
|
A:PO41001
|
4.4
|
35.0
|
1.0
|
|
CB
|
A:ASP727
|
4.4
|
27.4
|
1.0
|
|
CG
|
A:ASP723
|
4.4
|
28.2
|
1.0
|
|
OD2
|
A:ASP691
|
4.5
|
30.9
|
1.0
|
|
CB
|
A:ASP253
|
4.5
|
32.2
|
1.0
|
|
O1
|
A:PO41001
|
4.7
|
34.0
|
1.0
|
|
CE
|
A:LYS730
|
4.8
|
30.2
|
1.0
|
|
OD2
|
A:ASP257
|
4.8
|
31.4
|
1.0
|
|
O
|
A:HOH1137
|
4.8
|
29.9
|
1.0
|
|
O
|
A:ASP723
|
4.9
|
24.9
|
1.0
|
|
OD2
|
A:ASP731
|
4.9
|
28.5
|
1.0
|
|
CA
|
A:ASP727
|
5.0
|
29.2
|
1.0
|
|
MG
|
A:MG1006
|
5.0
|
34.1
|
1.0
|
|
CG
|
A:ASP691
|
5.0
|
31.1
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 6afw
Go back to
Magnesium Binding Sites List in 6afw
Magnesium binding site 4 out
of 10 in the Proton Pyrophosphatase-T228D Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1006
b:34.1
occ:1.00
|
O
|
A:HOH1167
|
2.1
|
27.1
|
1.0
|
|
OD1
|
A:ASP283
|
2.1
|
37.1
|
1.0
|
|
O2
|
A:PO41001
|
2.2
|
30.0
|
1.0
|
|
O
|
A:HOH1107
|
2.2
|
31.2
|
1.0
|
|
OD2
|
A:ASP507
|
2.2
|
32.6
|
1.0
|
|
O4
|
A:PO41002
|
2.3
|
29.6
|
1.0
|
|
CG
|
A:ASP283
|
2.8
|
35.5
|
1.0
|
|
OD2
|
A:ASP283
|
2.9
|
32.2
|
1.0
|
|
CG
|
A:ASP507
|
3.3
|
33.3
|
1.0
|
|
MG
|
A:MG1004
|
3.4
|
35.4
|
1.0
|
|
P
|
A:PO41002
|
3.4
|
34.7
|
1.0
|
|
O
|
A:HOH1135
|
3.5
|
29.1
|
1.0
|
|
P
|
A:PO41001
|
3.6
|
48.8
|
1.0
|
|
OD1
|
A:ASP507
|
3.7
|
34.7
|
1.0
|
|
O2
|
A:PO41002
|
3.7
|
31.5
|
1.0
|
|
O1
|
A:PO41002
|
3.9
|
36.5
|
1.0
|
|
O
|
A:HOH1219
|
3.9
|
29.9
|
1.0
|
|
O4
|
A:PO41001
|
3.9
|
27.8
|
1.0
|
|
OD1
|
A:ASP279
|
4.0
|
32.0
|
1.0
|
|
O
|
A:HOH1247
|
4.1
|
35.9
|
1.0
|
|
CB
|
A:ASP283
|
4.3
|
29.3
|
1.0
|
|
O
|
A:HOH1146
|
4.3
|
30.9
|
1.0
|
|
OD2
|
A:ASP253
|
4.4
|
33.7
|
1.0
|
|
O
|
A:HOH1232
|
4.4
|
31.0
|
1.0
|
|
O1
|
A:PO41001
|
4.4
|
34.0
|
1.0
|
|
CB
|
A:ASP507
|
4.5
|
32.9
|
1.0
|
|
NZ
|
A:LYS250
|
4.6
|
28.7
|
1.0
|
|
O3
|
A:PO41001
|
4.6
|
35.0
|
1.0
|
|
O3
|
A:PO41002
|
4.7
|
31.5
|
1.0
|
|
CG
|
A:ASP279
|
4.8
|
32.7
|
1.0
|
|
O
|
A:ASP279
|
4.8
|
32.4
|
1.0
|
|
OD2
|
A:ASP279
|
4.9
|
31.6
|
1.0
|
|
CA
|
A:ASP283
|
4.9
|
32.9
|
1.0
|
|
CG
|
A:ASP253
|
4.9
|
31.8
|
1.0
|
|
MG
|
A:MG1005
|
5.0
|
28.9
|
1.0
|
|
O
|
A:HOH1133
|
5.0
|
34.5
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 6afw
Go back to
Magnesium Binding Sites List in 6afw
Magnesium binding site 5 out
of 10 in the Proton Pyrophosphatase-T228D Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1007
b:34.9
occ:1.00
|
O
|
A:HOH1146
|
2.0
|
30.9
|
1.0
|
|
O
|
A:HOH1152
|
2.1
|
29.5
|
1.0
|
|
OD1
|
A:ASN534
|
2.1
|
33.6
|
1.0
|
|
O3
|
A:PO41001
|
2.1
|
35.0
|
1.0
|
|
OD2
|
A:ASP691
|
2.2
|
30.9
|
1.0
|
|
O1
|
A:PO41002
|
2.2
|
36.5
|
1.0
|
|
CG
|
A:ASN534
|
3.0
|
32.6
|
1.0
|
|
CG
|
A:ASP691
|
3.2
|
31.1
|
1.0
|
|
ND2
|
A:ASN534
|
3.3
|
29.4
|
1.0
|
|
P
|
A:PO41001
|
3.4
|
48.8
|
1.0
|
|
P
|
A:PO41002
|
3.6
|
34.7
|
1.0
|
|
OD1
|
A:ASP691
|
3.6
|
30.6
|
1.0
|
|
O2
|
A:PO41001
|
3.8
|
30.0
|
1.0
|
|
K
|
A:K1008
|
3.8
|
45.5
|
1.0
|
|
O3
|
A:PO41002
|
3.9
|
31.5
|
1.0
|
|
OD1
|
A:ASP530
|
3.9
|
36.3
|
1.0
|
|
O
|
A:HOH1115
|
4.0
|
26.8
|
1.0
|
|
O4
|
A:PO41001
|
4.0
|
27.8
|
1.0
|
|
O
|
A:HOH1281
|
4.1
|
28.8
|
1.0
|
|
OD2
|
A:ASP530
|
4.1
|
35.2
|
1.0
|
|
O4
|
A:PO41002
|
4.2
|
29.6
|
1.0
|
|
CB
|
A:ASN534
|
4.4
|
31.8
|
1.0
|
|
CG
|
A:ASP530
|
4.4
|
36.6
|
1.0
|
|
CB
|
A:ASP691
|
4.5
|
27.0
|
1.0
|
|
O1
|
A:PO41001
|
4.6
|
34.0
|
1.0
|
|
O2
|
A:PO41002
|
4.7
|
31.5
|
1.0
|
|
OD2
|
A:ASP507
|
4.8
|
32.6
|
1.0
|
|
O
|
A:HOH1218
|
4.8
|
31.1
|
1.0
|
|
O
|
A:ASP530
|
4.8
|
35.9
|
1.0
|
|
CA
|
A:ASN534
|
4.8
|
32.6
|
1.0
|
|
O
|
A:HOH1247
|
4.9
|
35.9
|
1.0
|
|
CE
|
A:LYS730
|
4.9
|
30.2
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 6afw
Go back to
Magnesium Binding Sites List in 6afw
Magnesium binding site 6 out
of 10 in the Proton Pyrophosphatase-T228D Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1003
b:40.7
occ:1.00
|
OD2
|
B:ASP257
|
2.0
|
38.9
|
1.0
|
|
OD1
|
B:ASP253
|
2.0
|
38.1
|
1.0
|
|
O
|
B:HOH1110
|
2.1
|
38.7
|
1.0
|
|
O
|
B:HOH1141
|
2.3
|
38.1
|
1.0
|
|
O2
|
B:PO41002
|
2.3
|
34.8
|
1.0
|
|
O
|
B:HOH1131
|
2.4
|
36.8
|
1.0
|
|
CG
|
B:ASP253
|
3.0
|
39.0
|
1.0
|
|
CG
|
B:ASP257
|
3.0
|
38.9
|
1.0
|
|
OD2
|
B:ASP253
|
3.3
|
39.0
|
1.0
|
|
MG
|
B:MG1005
|
3.4
|
37.6
|
1.0
|
|
P
|
B:PO41002
|
3.4
|
39.8
|
1.0
|
|
OD1
|
B:ASP257
|
3.5
|
36.4
|
1.0
|
|
O4
|
B:PO41002
|
3.6
|
37.6
|
1.0
|
|
O
|
B:HOH1162
|
3.9
|
36.1
|
1.0
|
|
O3
|
B:PO41002
|
4.0
|
37.6
|
1.0
|
|
OD2
|
B:ASP723
|
4.0
|
36.6
|
1.0
|
|
O
|
B:HOH1220
|
4.1
|
37.7
|
1.0
|
|
OE1
|
B:GLU268
|
4.2
|
39.8
|
1.0
|
|
OD2
|
B:ASP279
|
4.2
|
38.4
|
1.0
|
|
O
|
B:HOH1234
|
4.2
|
32.1
|
1.0
|
|
CB
|
B:ASP257
|
4.3
|
39.1
|
1.0
|
|
CB
|
B:ASP253
|
4.4
|
34.5
|
1.0
|
|
OD2
|
B:ASP727
|
4.4
|
34.4
|
1.0
|
|
O
|
B:ASP253
|
4.4
|
38.2
|
1.0
|
|
O
|
B:HOH1128
|
4.5
|
28.8
|
1.0
|
|
O1
|
B:PO41002
|
4.7
|
41.0
|
1.0
|
|
CA
|
B:ASP253
|
4.7
|
39.4
|
1.0
|
|
CD
|
B:GLU268
|
4.7
|
40.0
|
1.0
|
|
C
|
B:ASP253
|
4.7
|
40.2
|
1.0
|
|
NZ
|
B:LYS694
|
4.8
|
36.9
|
1.0
|
|
OD1
|
B:ASP727
|
4.8
|
32.9
|
1.0
|
|
O2
|
B:PO41001
|
4.9
|
32.3
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 6afw
Go back to
Magnesium Binding Sites List in 6afw
Magnesium binding site 7 out
of 10 in the Proton Pyrophosphatase-T228D Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1004
b:43.7
occ:1.00
|
O
|
B:HOH1220
|
1.9
|
37.7
|
1.0
|
|
OD1
|
B:ASP507
|
2.0
|
40.6
|
1.0
|
|
O
|
B:HOH1163
|
2.1
|
40.0
|
1.0
|
|
O
|
B:HOH1119
|
2.1
|
34.5
|
1.0
|
|
O
|
B:HOH1112
|
2.2
|
42.2
|
1.0
|
|
O3
|
B:PO41002
|
2.2
|
37.6
|
1.0
|
|
CG
|
B:ASP507
|
3.0
|
43.4
|
1.0
|
|
OD2
|
B:ASP507
|
3.3
|
38.4
|
1.0
|
|
P
|
B:PO41002
|
3.4
|
39.8
|
1.0
|
|
MG
|
B:MG1006
|
3.4
|
37.3
|
1.0
|
|
O4
|
B:PO41002
|
3.4
|
37.6
|
1.0
|
|
O
|
B:HOH1235
|
3.9
|
42.0
|
1.0
|
|
OD2
|
B:ASP269
|
4.1
|
42.6
|
1.0
|
|
O
|
B:HOH1131
|
4.1
|
36.8
|
1.0
|
|
OD1
|
B:ASP279
|
4.1
|
38.9
|
1.0
|
|
OD1
|
B:ASP269
|
4.2
|
40.0
|
1.0
|
|
O
|
B:ASP507
|
4.2
|
44.9
|
1.0
|
|
OE2
|
B:GLU268
|
4.2
|
41.1
|
1.0
|
|
O1
|
B:PO41002
|
4.3
|
41.0
|
1.0
|
|
O2
|
B:PO41002
|
4.4
|
34.8
|
1.0
|
|
CB
|
B:ASP507
|
4.4
|
40.5
|
1.0
|
|
O
|
B:HOH1234
|
4.4
|
32.1
|
1.0
|
|
OD2
|
B:ASP283
|
4.4
|
43.3
|
1.0
|
|
ND2
|
B:ASN280
|
4.6
|
43.6
|
1.0
|
|
CG
|
B:ASP269
|
4.6
|
44.0
|
1.0
|
|
C
|
B:ASP507
|
4.6
|
43.8
|
1.0
|
|
CA
|
B:ASP507
|
4.7
|
41.1
|
1.0
|
|
CD
|
B:GLU268
|
4.8
|
40.0
|
1.0
|
|
O
|
B:HOH1152
|
4.8
|
43.2
|
1.0
|
|
O
|
B:HOH1110
|
4.9
|
38.7
|
1.0
|
|
O4
|
B:PO41001
|
4.9
|
36.6
|
1.0
|
|
OD1
|
B:ASP283
|
4.9
|
42.2
|
1.0
|
|
OD2
|
B:ASP530
|
4.9
|
46.7
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 6afw
Go back to
Magnesium Binding Sites List in 6afw
Magnesium binding site 8 out
of 10 in the Proton Pyrophosphatase-T228D Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1005
b:37.6
occ:1.00
|
O
|
B:HOH1128
|
2.0
|
28.8
|
1.0
|
|
O
|
B:HOH1141
|
2.1
|
38.1
|
1.0
|
|
OD1
|
B:ASP727
|
2.1
|
32.9
|
1.0
|
|
O2
|
B:PO41002
|
2.1
|
34.8
|
1.0
|
|
O2
|
B:PO41001
|
2.2
|
32.3
|
1.0
|
|
OD2
|
B:ASP253
|
2.3
|
39.0
|
1.0
|
|
CG
|
B:ASP727
|
3.0
|
34.5
|
1.0
|
|
CG
|
B:ASP253
|
3.3
|
39.0
|
1.0
|
|
OD2
|
B:ASP727
|
3.3
|
34.4
|
1.0
|
|
P
|
B:PO41002
|
3.4
|
39.8
|
1.0
|
|
MG
|
B:MG1003
|
3.4
|
40.7
|
1.0
|
|
NZ
|
B:LYS730
|
3.5
|
31.7
|
1.0
|
|
O1
|
B:PO41002
|
3.5
|
41.0
|
1.0
|
|
OD1
|
B:ASP253
|
3.6
|
38.1
|
1.0
|
|
P
|
B:PO41001
|
3.6
|
54.2
|
1.0
|
|
OD2
|
B:ASP723
|
4.0
|
36.6
|
1.0
|
|
OD1
|
B:ASP723
|
4.0
|
37.2
|
1.0
|
|
NZ
|
B:LYS250
|
4.1
|
35.9
|
1.0
|
|
O
|
B:HOH1234
|
4.2
|
32.1
|
1.0
|
|
CE
|
B:LYS250
|
4.2
|
33.5
|
1.0
|
|
O4
|
B:PO41001
|
4.3
|
36.6
|
1.0
|
|
O3
|
B:PO41001
|
4.3
|
40.1
|
1.0
|
|
O4
|
B:PO41002
|
4.3
|
37.6
|
1.0
|
|
O3
|
B:PO41002
|
4.3
|
37.6
|
1.0
|
|
OD2
|
B:ASP691
|
4.4
|
39.6
|
1.0
|
|
CB
|
B:ASP727
|
4.4
|
33.6
|
1.0
|
|
O
|
B:HOH1110
|
4.4
|
38.7
|
1.0
|
|
CG
|
B:ASP723
|
4.4
|
36.5
|
1.0
|
|
CB
|
B:ASP253
|
4.6
|
34.5
|
1.0
|
|
CE
|
B:LYS730
|
4.6
|
31.7
|
1.0
|
|
O1
|
B:PO41001
|
4.6
|
41.9
|
1.0
|
|
OD2
|
B:ASP731
|
4.7
|
34.5
|
1.0
|
|
O
|
B:HOH1199
|
4.8
|
30.6
|
1.0
|
|
O
|
B:ASP723
|
4.8
|
31.9
|
1.0
|
|
CA
|
B:ASP727
|
4.9
|
34.4
|
1.0
|
|
CG
|
B:ASP691
|
4.9
|
38.2
|
1.0
|
|
OD2
|
B:ASP257
|
4.9
|
38.9
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 6afw
Go back to
Magnesium Binding Sites List in 6afw
Magnesium binding site 9 out
of 10 in the Proton Pyrophosphatase-T228D Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1006
b:37.3
occ:1.00
|
O
|
B:HOH1234
|
2.1
|
32.1
|
1.0
|
|
OD1
|
B:ASP283
|
2.1
|
42.2
|
1.0
|
|
O3
|
B:PO41002
|
2.1
|
37.6
|
1.0
|
|
OD2
|
B:ASP507
|
2.1
|
38.4
|
1.0
|
|
O4
|
B:PO41001
|
2.3
|
36.6
|
1.0
|
|
O
|
B:HOH1112
|
2.3
|
42.2
|
1.0
|
|
CG
|
B:ASP283
|
3.0
|
43.3
|
1.0
|
|
CG
|
B:ASP507
|
3.2
|
43.4
|
1.0
|
|
OD2
|
B:ASP283
|
3.2
|
43.3
|
1.0
|
|
P
|
B:PO41002
|
3.3
|
39.8
|
1.0
|
|
MG
|
B:MG1004
|
3.4
|
43.7
|
1.0
|
|
OD1
|
B:ASP507
|
3.5
|
40.6
|
1.0
|
|
P
|
B:PO41001
|
3.7
|
54.2
|
1.0
|
|
O1
|
B:PO41002
|
3.7
|
41.0
|
1.0
|
|
O
|
B:HOH1142
|
3.7
|
34.4
|
1.0
|
|
O2
|
B:PO41002
|
3.8
|
34.8
|
1.0
|
|
OD1
|
B:ASP279
|
3.9
|
38.9
|
1.0
|
|
O
|
B:HOH1217
|
4.0
|
36.4
|
1.0
|
|
O2
|
B:PO41001
|
4.0
|
32.3
|
1.0
|
|
O
|
B:HOH1242
|
4.2
|
44.4
|
1.0
|
|
O
|
B:HOH1152
|
4.3
|
43.2
|
1.0
|
|
O
|
B:HOH1220
|
4.3
|
37.7
|
1.0
|
|
CB
|
B:ASP283
|
4.3
|
41.7
|
1.0
|
|
CB
|
B:ASP507
|
4.5
|
40.5
|
1.0
|
|
O1
|
B:PO41001
|
4.6
|
41.9
|
1.0
|
|
O4
|
B:PO41002
|
4.6
|
37.6
|
1.0
|
|
O3
|
B:PO41001
|
4.6
|
40.1
|
1.0
|
|
OD2
|
B:ASP253
|
4.6
|
39.0
|
1.0
|
|
NZ
|
B:LYS250
|
4.6
|
35.9
|
1.0
|
|
O
|
B:ASP279
|
4.8
|
41.6
|
1.0
|
|
CG
|
B:ASP279
|
4.8
|
40.5
|
1.0
|
|
O
|
B:HOH1119
|
4.9
|
34.5
|
1.0
|
|
CA
|
B:ASP283
|
5.0
|
41.8
|
1.0
|
|
O
|
B:HOH1163
|
5.0
|
40.0
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 6afw
Go back to
Magnesium Binding Sites List in 6afw
Magnesium binding site 10 out
of 10 in the Proton Pyrophosphatase-T228D Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1007
b:43.7
occ:1.00
|
OD1
|
B:ASN534
|
2.0
|
37.8
|
1.0
|
|
O
|
B:HOH1152
|
2.1
|
43.2
|
1.0
|
|
O1
|
B:PO41002
|
2.2
|
41.0
|
1.0
|
|
O
|
B:HOH1167
|
2.2
|
37.8
|
1.0
|
|
O3
|
B:PO41001
|
2.2
|
40.1
|
1.0
|
|
OD2
|
B:ASP691
|
2.4
|
39.6
|
1.0
|
|
CG
|
B:ASN534
|
2.9
|
42.3
|
1.0
|
|
ND2
|
B:ASN534
|
3.2
|
42.5
|
1.0
|
|
CG
|
B:ASP691
|
3.3
|
38.2
|
1.0
|
|
P
|
B:PO41001
|
3.5
|
54.2
|
1.0
|
|
P
|
B:PO41002
|
3.6
|
39.8
|
1.0
|
|
K
|
B:K1008
|
3.7
|
56.1
|
1.0
|
|
OD1
|
B:ASP691
|
3.7
|
39.9
|
1.0
|
|
O4
|
B:PO41001
|
3.9
|
36.6
|
1.0
|
|
O4
|
B:PO41002
|
3.9
|
37.6
|
1.0
|
|
O
|
B:HOH1231
|
3.9
|
40.1
|
1.0
|
|
OD2
|
B:ASP530
|
4.0
|
46.7
|
1.0
|
|
O2
|
B:PO41001
|
4.0
|
32.3
|
1.0
|
|
OD1
|
B:ASP530
|
4.1
|
47.4
|
1.0
|
|
O
|
B:HOH1128
|
4.1
|
28.8
|
1.0
|
|
CB
|
B:ASN534
|
4.2
|
40.0
|
1.0
|
|
CG
|
B:ASP530
|
4.4
|
46.7
|
1.0
|
|
O3
|
B:PO41002
|
4.4
|
37.6
|
1.0
|
|
O2
|
B:PO41002
|
4.6
|
34.8
|
1.0
|
|
O
|
B:HOH1219
|
4.6
|
38.2
|
1.0
|
|
CB
|
B:ASP691
|
4.6
|
34.6
|
1.0
|
|
O1
|
B:PO41001
|
4.7
|
41.9
|
1.0
|
|
CA
|
B:ASN534
|
4.8
|
41.3
|
1.0
|
|
OD2
|
B:ASP507
|
4.9
|
38.4
|
1.0
|
|
O
|
B:ASP530
|
4.9
|
45.0
|
1.0
|
|
CE
|
B:LYS730
|
4.9
|
31.7
|
1.0
|
|
Reference:
J.Y.Tsai,
K.Z.Tang,
K.M.Li,
B.L.Hsu,
Y.W.Chiang,
A.Goldman,
Y.J.Sun.
Roles of the Hydrophobic Gate and Exit Channel in Vigna Radiata Pyrophosphatase Ion Translocation. J. Mol. Biol. V. 431 1619 2019.
ISSN: ESSN 1089-8638
PubMed: 30878480
DOI: 10.1016/J.JMB.2019.03.009
Page generated: Wed Aug 13 02:11:27 2025
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