Magnesium in PDB 6afx: Proton Pyrophosphatase - E225A
Enzymatic activity of Proton Pyrophosphatase - E225A
All present enzymatic activity of Proton Pyrophosphatase - E225A:
3.6.1.1;
Protein crystallography data
The structure of Proton Pyrophosphatase - E225A, PDB code: 6afx
was solved by
J.-Y.Tsai,
K.-Z.Tang,
Y.-J.Sun,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.80 /
2.30
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
217.197,
88.321,
158.843,
90.00,
125.14,
90.00
|
|
R / Rfree (%)
|
16.5 /
19.9
|
Other elements in 6afx:
The structure of Proton Pyrophosphatase - E225A also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Proton Pyrophosphatase - E225A
(pdb code 6afx). 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 - E225A, PDB code: 6afx:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 6afx
Go back to
Magnesium Binding Sites List in 6afx
Magnesium binding site 1 out
of 10 in the Proton Pyrophosphatase - E225A
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Proton Pyrophosphatase - E225A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1003
b:13.2
occ:1.00
|
OD2
|
A:ASP257
|
2.1
|
11.3
|
1.0
|
|
O
|
A:HOH1112
|
2.1
|
10.0
|
1.0
|
|
O2
|
A:PO41002
|
2.1
|
8.0
|
1.0
|
|
OD1
|
A:ASP253
|
2.1
|
11.2
|
1.0
|
|
O
|
A:HOH1130
|
2.2
|
11.2
|
1.0
|
|
O
|
A:HOH1127
|
2.2
|
8.4
|
1.0
|
|
CG
|
A:ASP257
|
3.0
|
10.3
|
1.0
|
|
CG
|
A:ASP253
|
3.1
|
11.5
|
1.0
|
|
P
|
A:PO41002
|
3.3
|
10.3
|
1.0
|
|
OD1
|
A:ASP257
|
3.3
|
12.9
|
1.0
|
|
OD2
|
A:ASP253
|
3.3
|
11.5
|
1.0
|
|
MG
|
A:MG1005
|
3.3
|
11.9
|
1.0
|
|
O3
|
A:PO41002
|
3.5
|
12.0
|
1.0
|
|
O
|
A:HOH1135
|
3.9
|
12.0
|
1.0
|
|
O4
|
A:PO41002
|
4.0
|
9.3
|
1.0
|
|
OD2
|
A:ASP723
|
4.1
|
10.6
|
1.0
|
|
O
|
A:HOH1211
|
4.1
|
11.9
|
1.0
|
|
O
|
A:HOH1203
|
4.2
|
10.6
|
1.0
|
|
OD2
|
A:ASP279
|
4.3
|
27.0
|
1.0
|
|
OE1
|
A:GLU268
|
4.3
|
16.9
|
1.0
|
|
CB
|
A:ASP257
|
4.4
|
10.5
|
1.0
|
|
O
|
A:HOH1109
|
4.4
|
7.9
|
1.0
|
|
OD2
|
A:ASP727
|
4.4
|
8.8
|
1.0
|
|
O
|
A:ASP253
|
4.4
|
9.1
|
1.0
|
|
O1
|
A:PO41002
|
4.5
|
12.4
|
1.0
|
|
CB
|
A:ASP253
|
4.5
|
11.4
|
1.0
|
|
NZ
|
A:LYS694
|
4.5
|
14.1
|
1.0
|
|
CD
|
A:GLU268
|
4.7
|
18.9
|
1.0
|
|
CA
|
A:ASP253
|
4.8
|
10.0
|
1.0
|
|
C
|
A:ASP253
|
4.8
|
10.8
|
1.0
|
|
OD1
|
A:ASP727
|
4.8
|
11.4
|
1.0
|
|
O3
|
A:PO41001
|
4.9
|
5.8
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 6afx
Go back to
Magnesium Binding Sites List in 6afx
Magnesium binding site 2 out
of 10 in the Proton Pyrophosphatase - E225A
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Proton Pyrophosphatase - E225A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1004
b:16.3
occ:1.00
|
O
|
A:HOH1124
|
2.0
|
16.9
|
1.0
|
|
OD1
|
A:ASP507
|
2.0
|
14.1
|
1.0
|
|
O
|
A:HOH1211
|
2.1
|
11.9
|
1.0
|
|
O
|
A:HOH1111
|
2.2
|
14.2
|
1.0
|
|
O
|
A:HOH1115
|
2.2
|
11.3
|
1.0
|
|
O4
|
A:PO41002
|
2.2
|
9.3
|
1.0
|
|
CG
|
A:ASP507
|
3.0
|
14.6
|
1.0
|
|
MG
|
A:MG1006
|
3.2
|
15.8
|
1.0
|
|
OD2
|
A:ASP507
|
3.3
|
13.4
|
1.0
|
|
P
|
A:PO41002
|
3.4
|
10.3
|
1.0
|
|
O3
|
A:PO41002
|
3.5
|
12.0
|
1.0
|
|
O
|
A:HOH1305
|
3.9
|
17.2
|
1.0
|
|
OD2
|
A:ASP269
|
4.0
|
20.4
|
1.0
|
|
OD1
|
A:ASP279
|
4.1
|
24.1
|
1.0
|
|
O
|
A:HOH1203
|
4.2
|
10.6
|
1.0
|
|
OD2
|
A:ASP283
|
4.2
|
16.7
|
1.0
|
|
O
|
A:ASP507
|
4.2
|
15.3
|
1.0
|
|
OE2
|
A:GLU268
|
4.2
|
17.5
|
1.0
|
|
O
|
A:HOH1130
|
4.3
|
11.2
|
1.0
|
|
OD1
|
A:ASP269
|
4.3
|
19.7
|
1.0
|
|
CB
|
A:ASP507
|
4.4
|
16.3
|
1.0
|
|
O2
|
A:PO41002
|
4.4
|
8.0
|
1.0
|
|
O1
|
A:PO41002
|
4.4
|
12.4
|
1.0
|
|
C
|
A:ASP507
|
4.6
|
14.7
|
1.0
|
|
CG
|
A:ASP269
|
4.6
|
22.1
|
1.0
|
|
CA
|
A:ASP507
|
4.7
|
15.0
|
1.0
|
|
O2
|
A:PO41001
|
4.7
|
8.2
|
1.0
|
|
OD1
|
A:ASP283
|
4.8
|
15.9
|
1.0
|
|
O
|
A:HOH1153
|
4.8
|
11.1
|
1.0
|
|
ND2
|
A:ASN280
|
4.9
|
20.5
|
1.0
|
|
OD2
|
A:ASP530
|
4.9
|
17.4
|
1.0
|
|
CG
|
A:ASP283
|
4.9
|
14.9
|
1.0
|
|
CD
|
A:GLU268
|
5.0
|
18.9
|
1.0
|
|
CG
|
A:ASP279
|
5.0
|
27.1
|
1.0
|
|
OD2
|
A:ASP279
|
5.0
|
27.0
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 6afx
Go back to
Magnesium Binding Sites List in 6afx
Magnesium binding site 3 out
of 10 in the Proton Pyrophosphatase - E225A
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Proton Pyrophosphatase - E225A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1005
b:11.9
occ:1.00
|
OD1
|
A:ASP727
|
2.1
|
11.4
|
1.0
|
|
O3
|
A:PO41001
|
2.1
|
5.8
|
1.0
|
|
O2
|
A:PO41002
|
2.1
|
8.0
|
1.0
|
|
O
|
A:HOH1127
|
2.2
|
8.4
|
1.0
|
|
OD2
|
A:ASP253
|
2.2
|
11.5
|
1.0
|
|
O
|
A:HOH1109
|
2.3
|
7.9
|
1.0
|
|
CG
|
A:ASP727
|
3.0
|
9.6
|
1.0
|
|
CG
|
A:ASP253
|
3.2
|
11.5
|
1.0
|
|
OD2
|
A:ASP727
|
3.3
|
8.8
|
1.0
|
|
P
|
A:PO41002
|
3.3
|
10.3
|
1.0
|
|
MG
|
A:MG1003
|
3.3
|
13.2
|
1.0
|
|
O1
|
A:PO41002
|
3.4
|
12.4
|
1.0
|
|
NZ
|
A:LYS730
|
3.5
|
7.6
|
1.0
|
|
NZ
|
A:LYS250
|
3.5
|
8.3
|
1.0
|
|
OD1
|
A:ASP253
|
3.6
|
11.2
|
1.0
|
|
P
|
A:PO41001
|
3.6
|
36.4
|
1.0
|
|
O
|
A:HOH1203
|
3.9
|
10.6
|
1.0
|
|
O2
|
A:PO41001
|
4.1
|
8.2
|
1.0
|
|
OD1
|
A:ASP723
|
4.1
|
7.7
|
1.0
|
|
OD2
|
A:ASP723
|
4.2
|
10.6
|
1.0
|
|
CB
|
A:ASP727
|
4.3
|
7.8
|
1.0
|
|
O4
|
A:PO41002
|
4.3
|
9.3
|
1.0
|
|
O4
|
A:PO41001
|
4.3
|
12.6
|
1.0
|
|
O
|
A:HOH1112
|
4.3
|
10.0
|
1.0
|
|
O3
|
A:PO41002
|
4.4
|
12.0
|
1.0
|
|
CB
|
A:ASP253
|
4.5
|
11.4
|
1.0
|
|
CG
|
A:ASP723
|
4.5
|
9.9
|
1.0
|
|
OD2
|
A:ASP691
|
4.6
|
10.1
|
1.0
|
|
O1
|
A:PO41001
|
4.6
|
15.4
|
1.0
|
|
CE
|
A:LYS730
|
4.7
|
9.7
|
1.0
|
|
OD2
|
A:ASP731
|
4.8
|
13.6
|
1.0
|
|
CE
|
A:LYS250
|
4.8
|
9.7
|
1.0
|
|
OD2
|
A:ASP257
|
4.8
|
11.3
|
1.0
|
|
CA
|
A:ASP727
|
4.8
|
8.1
|
1.0
|
|
CD
|
A:LYS250
|
4.9
|
8.2
|
1.0
|
|
O
|
A:HOH1197
|
4.9
|
8.5
|
1.0
|
|
MG
|
A:MG1007
|
5.0
|
12.4
|
1.0
|
|
O
|
A:ASP723
|
5.0
|
6.8
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 6afx
Go back to
Magnesium Binding Sites List in 6afx
Magnesium binding site 4 out
of 10 in the Proton Pyrophosphatase - E225A
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Proton Pyrophosphatase - E225A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1006
b:15.8
occ:1.00
|
O
|
A:HOH1203
|
2.0
|
10.6
|
1.0
|
|
OD1
|
A:ASP283
|
2.1
|
15.9
|
1.0
|
|
OD2
|
A:ASP507
|
2.1
|
13.4
|
1.0
|
|
O
|
A:HOH1115
|
2.2
|
11.3
|
1.0
|
|
O2
|
A:PO41001
|
2.2
|
8.2
|
1.0
|
|
O4
|
A:PO41002
|
2.2
|
9.3
|
1.0
|
|
CG
|
A:ASP283
|
2.9
|
14.9
|
1.0
|
|
OD2
|
A:ASP283
|
3.1
|
16.7
|
1.0
|
|
CG
|
A:ASP507
|
3.1
|
14.6
|
1.0
|
|
MG
|
A:MG1004
|
3.2
|
16.3
|
1.0
|
|
P
|
A:PO41002
|
3.4
|
10.3
|
1.0
|
|
OD1
|
A:ASP507
|
3.5
|
14.1
|
1.0
|
|
P
|
A:PO41001
|
3.7
|
36.4
|
1.0
|
|
O
|
A:HOH1131
|
3.7
|
10.3
|
1.0
|
|
O1
|
A:PO41002
|
3.8
|
12.4
|
1.0
|
|
OD1
|
A:ASP279
|
3.9
|
24.1
|
1.0
|
|
O2
|
A:PO41002
|
4.0
|
8.0
|
1.0
|
|
O
|
A:HOH1201
|
4.0
|
16.2
|
1.0
|
|
O
|
A:HOH1241
|
4.1
|
15.2
|
1.0
|
|
O3
|
A:PO41001
|
4.2
|
5.8
|
1.0
|
|
CB
|
A:ASP283
|
4.3
|
11.7
|
1.0
|
|
O
|
A:HOH1153
|
4.3
|
11.1
|
1.0
|
|
CB
|
A:ASP507
|
4.4
|
16.3
|
1.0
|
|
O
|
A:HOH1211
|
4.5
|
11.9
|
1.0
|
|
O1
|
A:PO41001
|
4.6
|
15.4
|
1.0
|
|
O4
|
A:PO41001
|
4.6
|
12.6
|
1.0
|
|
NZ
|
A:LYS250
|
4.6
|
8.3
|
1.0
|
|
O3
|
A:PO41002
|
4.7
|
12.0
|
1.0
|
|
OD2
|
A:ASP253
|
4.7
|
11.5
|
1.0
|
|
O
|
A:HOH1124
|
4.8
|
16.9
|
1.0
|
|
O
|
A:HOH1111
|
4.9
|
14.2
|
1.0
|
|
O
|
A:ASP279
|
4.9
|
17.3
|
1.0
|
|
CG
|
A:ASP279
|
4.9
|
27.1
|
1.0
|
|
CA
|
A:ASP283
|
5.0
|
14.5
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 6afx
Go back to
Magnesium Binding Sites List in 6afx
Magnesium binding site 5 out
of 10 in the Proton Pyrophosphatase - E225A
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Proton Pyrophosphatase - E225A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1007
b:12.4
occ:1.00
|
OD2
|
A:ASP691
|
2.0
|
10.1
|
1.0
|
|
O4
|
A:PO41001
|
2.1
|
12.6
|
1.0
|
|
O
|
A:HOH1177
|
2.1
|
8.9
|
1.0
|
|
OD1
|
A:ASN534
|
2.1
|
11.9
|
1.0
|
|
O
|
A:HOH1153
|
2.1
|
11.1
|
1.0
|
|
O1
|
A:PO41002
|
2.1
|
12.4
|
1.0
|
|
CG
|
A:ASN534
|
2.9
|
12.1
|
1.0
|
|
CG
|
A:ASP691
|
3.1
|
10.3
|
1.0
|
|
ND2
|
A:ASN534
|
3.2
|
8.3
|
1.0
|
|
P
|
A:PO41001
|
3.4
|
36.4
|
1.0
|
|
OD1
|
A:ASP691
|
3.6
|
10.9
|
1.0
|
|
P
|
A:PO41002
|
3.6
|
10.3
|
1.0
|
|
K
|
A:K1008
|
3.6
|
21.9
|
1.0
|
|
O2
|
A:PO41001
|
3.8
|
8.2
|
1.0
|
|
O3
|
A:PO41001
|
3.9
|
5.8
|
1.0
|
|
O
|
A:HOH1109
|
3.9
|
7.9
|
1.0
|
|
O3
|
A:PO41002
|
4.0
|
12.0
|
1.0
|
|
O
|
A:HOH1278
|
4.0
|
14.8
|
1.0
|
|
OD1
|
A:ASP530
|
4.2
|
20.0
|
1.0
|
|
CB
|
A:ASN534
|
4.3
|
9.2
|
1.0
|
|
O4
|
A:PO41002
|
4.3
|
9.3
|
1.0
|
|
OD2
|
A:ASP530
|
4.3
|
17.4
|
1.0
|
|
CB
|
A:ASP691
|
4.4
|
7.7
|
1.0
|
|
O2
|
A:PO41002
|
4.6
|
8.0
|
1.0
|
|
O1
|
A:PO41001
|
4.6
|
15.4
|
1.0
|
|
CG
|
A:ASP530
|
4.6
|
16.1
|
1.0
|
|
O
|
A:HOH1164
|
4.7
|
11.0
|
1.0
|
|
CE
|
A:LYS730
|
4.8
|
9.7
|
1.0
|
|
CA
|
A:ASN534
|
4.8
|
10.4
|
1.0
|
|
OD2
|
A:ASP507
|
4.9
|
13.4
|
1.0
|
|
NZ
|
A:LYS730
|
4.9
|
7.6
|
1.0
|
|
MG
|
A:MG1005
|
5.0
|
11.9
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 6afx
Go back to
Magnesium Binding Sites List in 6afx
Magnesium binding site 6 out
of 10 in the Proton Pyrophosphatase - E225A
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Proton Pyrophosphatase - E225A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1003
b:13.3
occ:1.00
|
OD1
|
B:ASP253
|
2.0
|
15.5
|
1.0
|
|
OD2
|
B:ASP257
|
2.1
|
16.6
|
1.0
|
|
O
|
B:HOH1103
|
2.1
|
12.0
|
1.0
|
|
O2
|
B:PO41002
|
2.1
|
7.8
|
1.0
|
|
O
|
B:HOH1113
|
2.3
|
18.2
|
1.0
|
|
O
|
B:HOH1109
|
2.3
|
12.3
|
1.0
|
|
CG
|
B:ASP253
|
2.9
|
15.9
|
1.0
|
|
CG
|
B:ASP257
|
3.1
|
14.5
|
1.0
|
|
OD2
|
B:ASP253
|
3.2
|
12.5
|
1.0
|
|
P
|
B:PO41002
|
3.3
|
16.9
|
1.0
|
|
MG
|
B:MG1005
|
3.4
|
15.2
|
1.0
|
|
OD1
|
B:ASP257
|
3.5
|
16.5
|
1.0
|
|
O4
|
B:PO41002
|
3.6
|
13.8
|
1.0
|
|
O3
|
B:PO41002
|
3.9
|
16.6
|
1.0
|
|
O
|
B:HOH1240
|
4.0
|
16.5
|
1.0
|
|
OD2
|
B:ASP723
|
4.1
|
15.2
|
1.0
|
|
O
|
B:HOH1222
|
4.1
|
16.3
|
1.0
|
|
O
|
B:HOH1152
|
4.1
|
14.2
|
1.0
|
|
OD2
|
B:ASP279
|
4.2
|
29.1
|
1.0
|
|
OE1
|
B:GLU268
|
4.3
|
23.7
|
1.0
|
|
CB
|
B:ASP253
|
4.3
|
16.3
|
1.0
|
|
O
|
B:ASP253
|
4.4
|
16.9
|
1.0
|
|
CB
|
B:ASP257
|
4.4
|
12.9
|
1.0
|
|
OD2
|
B:ASP727
|
4.5
|
10.8
|
1.0
|
|
O
|
B:HOH1116
|
4.5
|
10.4
|
1.0
|
|
O1
|
B:PO41002
|
4.5
|
15.1
|
1.0
|
|
CA
|
B:ASP253
|
4.7
|
16.9
|
1.0
|
|
CD
|
B:GLU268
|
4.7
|
23.9
|
1.0
|
|
OD1
|
B:ASP727
|
4.7
|
14.1
|
1.0
|
|
C
|
B:ASP253
|
4.8
|
18.3
|
1.0
|
|
NZ
|
B:LYS694
|
4.8
|
16.6
|
1.0
|
|
O2
|
B:PO41001
|
4.9
|
11.1
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 6afx
Go back to
Magnesium Binding Sites List in 6afx
Magnesium binding site 7 out
of 10 in the Proton Pyrophosphatase - E225A
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Proton Pyrophosphatase - E225A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1004
b:22.2
occ:1.00
|
OD1
|
B:ASP507
|
1.9
|
18.8
|
1.0
|
|
O
|
B:HOH1240
|
2.0
|
16.5
|
1.0
|
|
O
|
B:HOH1155
|
2.1
|
21.3
|
1.0
|
|
O
|
B:HOH1111
|
2.1
|
20.5
|
1.0
|
|
O
|
B:HOH1182
|
2.2
|
22.1
|
1.0
|
|
O3
|
B:PO41002
|
2.4
|
16.6
|
1.0
|
|
CG
|
B:ASP507
|
2.9
|
19.7
|
1.0
|
|
OD2
|
B:ASP507
|
3.2
|
16.5
|
1.0
|
|
MG
|
B:MG1006
|
3.5
|
18.1
|
1.0
|
|
P
|
B:PO41002
|
3.6
|
16.9
|
1.0
|
|
O4
|
B:PO41002
|
3.7
|
13.8
|
1.0
|
|
O
|
B:ASP507
|
4.0
|
22.9
|
1.0
|
|
OD2
|
B:ASP269
|
4.0
|
27.6
|
1.0
|
|
O
|
B:HOH1260
|
4.1
|
28.7
|
1.0
|
|
OD1
|
B:ASP279
|
4.2
|
25.4
|
1.0
|
|
OD2
|
B:ASP283
|
4.2
|
25.5
|
1.0
|
|
CB
|
B:ASP507
|
4.3
|
17.0
|
1.0
|
|
OE2
|
B:GLU268
|
4.3
|
26.4
|
1.0
|
|
OD1
|
B:ASP269
|
4.3
|
29.8
|
1.0
|
|
O
|
B:HOH1222
|
4.4
|
16.3
|
1.0
|
|
C
|
B:ASP507
|
4.4
|
22.9
|
1.0
|
|
O
|
B:HOH1113
|
4.5
|
18.2
|
1.0
|
|
O1
|
B:PO41002
|
4.6
|
15.1
|
1.0
|
|
CA
|
B:ASP507
|
4.6
|
19.0
|
1.0
|
|
O2
|
B:PO41002
|
4.6
|
7.8
|
1.0
|
|
CG
|
B:ASP269
|
4.6
|
28.8
|
1.0
|
|
ND2
|
B:ASN280
|
4.8
|
24.1
|
1.0
|
|
OD2
|
B:ASP530
|
4.8
|
25.8
|
1.0
|
|
O4
|
B:PO41001
|
4.9
|
15.7
|
1.0
|
|
OD1
|
B:ASP283
|
4.9
|
25.7
|
1.0
|
|
O
|
B:HOH1133
|
4.9
|
17.4
|
1.0
|
|
CG
|
B:ASP283
|
5.0
|
23.3
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 6afx
Go back to
Magnesium Binding Sites List in 6afx
Magnesium binding site 8 out
of 10 in the Proton Pyrophosphatase - E225A
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Proton Pyrophosphatase - E225A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1005
b:15.2
occ:1.00
|
O2
|
B:PO41001
|
2.0
|
11.1
|
1.0
|
|
O
|
B:HOH1109
|
2.1
|
12.3
|
1.0
|
|
O2
|
B:PO41002
|
2.1
|
7.8
|
1.0
|
|
OD1
|
B:ASP727
|
2.1
|
14.1
|
1.0
|
|
O
|
B:HOH1116
|
2.2
|
10.4
|
1.0
|
|
OD2
|
B:ASP253
|
2.2
|
12.5
|
1.0
|
|
CG
|
B:ASP727
|
3.2
|
12.4
|
1.0
|
|
P
|
B:PO41002
|
3.2
|
16.9
|
1.0
|
|
CG
|
B:ASP253
|
3.3
|
15.9
|
1.0
|
|
O1
|
B:PO41002
|
3.3
|
15.1
|
1.0
|
|
MG
|
B:MG1003
|
3.4
|
13.3
|
1.0
|
|
NZ
|
B:LYS730
|
3.4
|
12.7
|
1.0
|
|
P
|
B:PO41001
|
3.5
|
44.8
|
1.0
|
|
OD2
|
B:ASP727
|
3.5
|
10.8
|
1.0
|
|
NZ
|
B:LYS250
|
3.6
|
14.3
|
1.0
|
|
OD1
|
B:ASP253
|
3.7
|
15.5
|
1.0
|
|
O
|
B:HOH1222
|
4.1
|
16.3
|
1.0
|
|
O4
|
B:PO41001
|
4.1
|
15.7
|
1.0
|
|
OD1
|
B:ASP723
|
4.2
|
15.9
|
1.0
|
|
O3
|
B:PO41002
|
4.2
|
16.6
|
1.0
|
|
O3
|
B:PO41001
|
4.2
|
15.5
|
1.0
|
|
O4
|
B:PO41002
|
4.3
|
13.8
|
1.0
|
|
OD2
|
B:ASP723
|
4.3
|
15.2
|
1.0
|
|
O
|
B:HOH1103
|
4.3
|
12.0
|
1.0
|
|
OD2
|
B:ASP691
|
4.4
|
17.3
|
1.0
|
|
CB
|
B:ASP727
|
4.5
|
13.0
|
1.0
|
|
O1
|
B:PO41001
|
4.5
|
20.1
|
1.0
|
|
CE
|
B:LYS730
|
4.5
|
14.1
|
1.0
|
|
CB
|
B:ASP253
|
4.6
|
16.3
|
1.0
|
|
CG
|
B:ASP723
|
4.6
|
15.2
|
1.0
|
|
OD2
|
B:ASP731
|
4.7
|
16.4
|
1.0
|
|
CE
|
B:LYS250
|
4.8
|
14.7
|
1.0
|
|
MG
|
B:MG1007
|
4.8
|
18.6
|
1.0
|
|
MG
|
B:MG1006
|
4.9
|
18.1
|
1.0
|
|
CD
|
B:LYS250
|
4.9
|
13.8
|
1.0
|
|
O
|
B:HOH1171
|
4.9
|
11.1
|
1.0
|
|
CA
|
B:ASP727
|
4.9
|
11.8
|
1.0
|
|
OD2
|
B:ASP257
|
5.0
|
16.6
|
1.0
|
|
CG
|
B:ASP691
|
5.0
|
17.3
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 6afx
Go back to
Magnesium Binding Sites List in 6afx
Magnesium binding site 9 out
of 10 in the Proton Pyrophosphatase - E225A
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Proton Pyrophosphatase - E225A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1006
b:18.1
occ:1.00
|
O
|
B:HOH1222
|
2.0
|
16.3
|
1.0
|
|
O4
|
B:PO41001
|
2.1
|
15.7
|
1.0
|
|
OD1
|
B:ASP283
|
2.1
|
25.7
|
1.0
|
|
OD2
|
B:ASP507
|
2.2
|
16.5
|
1.0
|
|
O3
|
B:PO41002
|
2.3
|
16.6
|
1.0
|
|
O
|
B:HOH1111
|
2.3
|
20.5
|
1.0
|
|
CG
|
B:ASP283
|
3.0
|
23.3
|
1.0
|
|
OD2
|
B:ASP283
|
3.3
|
25.5
|
1.0
|
|
CG
|
B:ASP507
|
3.3
|
19.7
|
1.0
|
|
P
|
B:PO41002
|
3.4
|
16.9
|
1.0
|
|
O
|
B:HOH1141
|
3.5
|
15.4
|
1.0
|
|
P
|
B:PO41001
|
3.5
|
44.8
|
1.0
|
|
MG
|
B:MG1004
|
3.5
|
22.2
|
1.0
|
|
OD1
|
B:ASP507
|
3.7
|
18.8
|
1.0
|
|
O1
|
B:PO41002
|
3.8
|
15.1
|
1.0
|
|
O2
|
B:PO41002
|
3.9
|
7.8
|
1.0
|
|
O2
|
B:PO41001
|
3.9
|
11.1
|
1.0
|
|
O
|
B:HOH1199
|
4.0
|
20.9
|
1.0
|
|
O
|
B:HOH1231
|
4.0
|
20.2
|
1.0
|
|
OD1
|
B:ASP279
|
4.1
|
25.4
|
1.0
|
|
CB
|
B:ASP283
|
4.3
|
19.6
|
1.0
|
|
O
|
B:HOH1240
|
4.3
|
16.5
|
1.0
|
|
NZ
|
B:LYS250
|
4.4
|
14.3
|
1.0
|
|
O
|
B:HOH1133
|
4.4
|
17.4
|
1.0
|
|
O1
|
B:PO41001
|
4.4
|
20.1
|
1.0
|
|
O3
|
B:PO41001
|
4.4
|
15.5
|
1.0
|
|
CB
|
B:ASP507
|
4.5
|
17.0
|
1.0
|
|
OD2
|
B:ASP253
|
4.6
|
12.5
|
1.0
|
|
O4
|
B:PO41002
|
4.7
|
13.8
|
1.0
|
|
MG
|
B:MG1005
|
4.9
|
15.2
|
1.0
|
|
CA
|
B:ASP283
|
4.9
|
20.6
|
1.0
|
|
O
|
B:ASP279
|
4.9
|
25.3
|
1.0
|
|
CG
|
B:ASP279
|
5.0
|
26.9
|
1.0
|
|
OD2
|
B:ASP287
|
5.0
|
23.4
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 6afx
Go back to
Magnesium Binding Sites List in 6afx
Magnesium binding site 10 out
of 10 in the Proton Pyrophosphatase - E225A
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Proton Pyrophosphatase - E225A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1007
b:18.6
occ:1.00
|
OD1
|
B:ASN534
|
2.1
|
16.8
|
1.0
|
|
O1
|
B:PO41002
|
2.1
|
15.1
|
1.0
|
|
O3
|
B:PO41001
|
2.1
|
15.5
|
1.0
|
|
O
|
B:HOH1137
|
2.2
|
17.8
|
1.0
|
|
OD2
|
B:ASP691
|
2.2
|
17.3
|
1.0
|
|
O
|
B:HOH1133
|
2.2
|
17.4
|
1.0
|
|
CG
|
B:ASN534
|
2.9
|
20.2
|
1.0
|
|
ND2
|
B:ASN534
|
3.1
|
16.8
|
1.0
|
|
CG
|
B:ASP691
|
3.3
|
17.3
|
1.0
|
|
P
|
B:PO41001
|
3.4
|
44.8
|
1.0
|
|
P
|
B:PO41002
|
3.5
|
16.9
|
1.0
|
|
OD1
|
B:ASP691
|
3.7
|
16.8
|
1.0
|
|
K
|
B:K1008
|
3.7
|
27.2
|
1.0
|
|
O
|
B:HOH1173
|
3.7
|
19.1
|
1.0
|
|
O2
|
B:PO41001
|
3.8
|
11.1
|
1.0
|
|
O4
|
B:PO41002
|
3.8
|
13.8
|
1.0
|
|
O4
|
B:PO41001
|
3.9
|
15.7
|
1.0
|
|
O
|
B:HOH1116
|
3.9
|
10.4
|
1.0
|
|
OD1
|
B:ASP530
|
4.2
|
23.9
|
1.0
|
|
OD2
|
B:ASP530
|
4.2
|
25.8
|
1.0
|
|
CB
|
B:ASN534
|
4.2
|
15.6
|
1.0
|
|
O3
|
B:PO41002
|
4.3
|
16.6
|
1.0
|
|
CB
|
B:ASP691
|
4.5
|
13.6
|
1.0
|
|
O2
|
B:PO41002
|
4.5
|
7.8
|
1.0
|
|
CG
|
B:ASP530
|
4.6
|
26.0
|
1.0
|
|
O1
|
B:PO41001
|
4.6
|
20.1
|
1.0
|
|
O
|
B:HOH1216
|
4.7
|
18.2
|
1.0
|
|
CA
|
B:ASN534
|
4.7
|
13.8
|
1.0
|
|
MG
|
B:MG1005
|
4.8
|
15.2
|
1.0
|
|
CE
|
B:LYS730
|
4.9
|
14.1
|
1.0
|
|
OD2
|
B:ASP507
|
4.9
|
16.5
|
1.0
|
|
O
|
B:ASP530
|
5.0
|
20.4
|
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 02:11:30 2025
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