Magnesium in PDB 6afz: Proton Pyrophosphatase-E225H Mutant
Enzymatic activity of Proton Pyrophosphatase-E225H Mutant
All present enzymatic activity of Proton Pyrophosphatase-E225H Mutant:
3.6.1.1;
Protein crystallography data
The structure of Proton Pyrophosphatase-E225H Mutant, PDB code: 6afz
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)
|
25.70 /
2.48
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
215.605,
88.023,
158.194,
90.00,
124.99,
90.00
|
|
R / Rfree (%)
|
20.1 /
23.5
|
Other elements in 6afz:
The structure of Proton Pyrophosphatase-E225H Mutant also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Proton Pyrophosphatase-E225H Mutant
(pdb code 6afz). 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-E225H Mutant, PDB code: 6afz:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 6afz
Go back to
Magnesium Binding Sites List in 6afz
Magnesium binding site 1 out
of 10 in the Proton Pyrophosphatase-E225H 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-E225H Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1003
b:36.6
occ:1.00
|
O
|
A:HOH1145
|
2.1
|
29.9
|
1.0
|
|
O2
|
A:PO41002
|
2.1
|
37.7
|
1.0
|
|
OD2
|
A:ASP257
|
2.1
|
41.2
|
1.0
|
|
OD1
|
A:ASP253
|
2.2
|
42.9
|
1.0
|
|
O
|
A:HOH1123
|
2.2
|
34.8
|
1.0
|
|
O
|
A:HOH1119
|
2.3
|
32.6
|
1.0
|
|
CG
|
A:ASP257
|
3.0
|
38.4
|
1.0
|
|
CG
|
A:ASP253
|
3.1
|
38.4
|
1.0
|
|
OD1
|
A:ASP257
|
3.2
|
34.6
|
1.0
|
|
P
|
A:PO41002
|
3.2
|
41.9
|
1.0
|
|
O3
|
A:PO41002
|
3.3
|
38.3
|
1.0
|
|
OD2
|
A:ASP253
|
3.4
|
38.9
|
1.0
|
|
MG
|
A:MG1005
|
3.6
|
37.9
|
1.0
|
|
O
|
A:HOH1182
|
3.8
|
33.3
|
1.0
|
|
OE1
|
A:GLU268
|
4.0
|
39.1
|
1.0
|
|
O
|
A:HOH1114
|
4.0
|
31.3
|
1.0
|
|
O4
|
A:PO41002
|
4.0
|
31.4
|
1.0
|
|
OD2
|
A:ASP723
|
4.1
|
33.6
|
1.0
|
|
OD2
|
A:ASP279
|
4.2
|
38.9
|
1.0
|
|
O
|
A:ASP253
|
4.3
|
37.0
|
1.0
|
|
CB
|
A:ASP257
|
4.3
|
40.0
|
1.0
|
|
O1
|
A:PO41002
|
4.4
|
40.1
|
1.0
|
|
O
|
A:HOH1118
|
4.4
|
32.9
|
1.0
|
|
CD
|
A:GLU268
|
4.4
|
44.3
|
1.0
|
|
CB
|
A:ASP253
|
4.5
|
38.0
|
1.0
|
|
O
|
A:HOH1109
|
4.6
|
32.6
|
1.0
|
|
OD2
|
A:ASP727
|
4.6
|
41.1
|
1.0
|
|
NZ
|
A:LYS694
|
4.7
|
34.8
|
1.0
|
|
CA
|
A:ASP253
|
4.8
|
38.2
|
1.0
|
|
C
|
A:ASP253
|
4.8
|
40.5
|
1.0
|
|
O4
|
A:PO41001
|
4.8
|
33.4
|
1.0
|
|
OE2
|
A:GLU268
|
4.9
|
36.6
|
1.0
|
|
MG
|
A:MG1004
|
4.9
|
46.9
|
1.0
|
|
CG
|
A:GLU268
|
5.0
|
37.7
|
1.0
|
|
OD1
|
A:ASP727
|
5.0
|
39.0
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 6afz
Go back to
Magnesium Binding Sites List in 6afz
Magnesium binding site 2 out
of 10 in the Proton Pyrophosphatase-E225H 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-E225H Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1004
b:46.9
occ:1.00
|
O
|
A:HOH1135
|
1.9
|
36.8
|
1.0
|
|
O
|
A:HOH1182
|
2.0
|
33.3
|
1.0
|
|
OD1
|
A:ASP507
|
2.0
|
42.0
|
1.0
|
|
O
|
A:HOH1103
|
2.0
|
41.0
|
1.0
|
|
O4
|
A:PO41002
|
2.2
|
31.4
|
1.0
|
|
O
|
A:HOH1108
|
2.5
|
42.9
|
1.0
|
|
CG
|
A:ASP507
|
2.8
|
39.5
|
1.0
|
|
OD2
|
A:ASP507
|
3.0
|
41.3
|
1.0
|
|
P
|
A:PO41002
|
3.4
|
41.9
|
1.0
|
|
O3
|
A:PO41002
|
3.4
|
38.3
|
1.0
|
|
MG
|
A:MG1006
|
3.6
|
42.1
|
1.0
|
|
O
|
A:HOH1118
|
3.9
|
32.9
|
1.0
|
|
OD1
|
A:ASP279
|
3.9
|
36.5
|
1.0
|
|
OD2
|
A:ASP283
|
4.0
|
43.3
|
1.0
|
|
CB
|
A:ASP507
|
4.2
|
40.5
|
1.0
|
|
O
|
A:HOH1145
|
4.2
|
29.9
|
1.0
|
|
O2
|
A:PO41002
|
4.3
|
37.7
|
1.0
|
|
OD1
|
A:ASP269
|
4.3
|
48.7
|
1.0
|
|
O
|
A:ASP507
|
4.3
|
38.1
|
1.0
|
|
OD2
|
A:ASP269
|
4.4
|
39.8
|
1.0
|
|
O2
|
A:PO41001
|
4.4
|
39.5
|
1.0
|
|
O1
|
A:PO41002
|
4.5
|
40.1
|
1.0
|
|
OE2
|
A:GLU268
|
4.5
|
36.6
|
1.0
|
|
O
|
A:HOH1140
|
4.6
|
33.1
|
1.0
|
|
C
|
A:ASP507
|
4.7
|
42.0
|
1.0
|
|
CA
|
A:ASP507
|
4.7
|
37.5
|
1.0
|
|
ND2
|
A:ASN280
|
4.7
|
37.2
|
1.0
|
|
CG
|
A:ASP269
|
4.8
|
45.9
|
1.0
|
|
CG
|
A:ASP279
|
4.8
|
36.5
|
1.0
|
|
OD1
|
A:ASP283
|
4.8
|
41.9
|
1.0
|
|
OD2
|
A:ASP279
|
4.8
|
38.9
|
1.0
|
|
CG
|
A:ASP283
|
4.8
|
41.3
|
1.0
|
|
OD1
|
A:ASP530
|
4.9
|
42.9
|
1.0
|
|
MG
|
A:MG1003
|
4.9
|
36.6
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 6afz
Go back to
Magnesium Binding Sites List in 6afz
Magnesium binding site 3 out
of 10 in the Proton Pyrophosphatase-E225H 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-E225H Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1005
b:37.9
occ:1.00
|
OD1
|
A:ASP727
|
1.9
|
39.0
|
1.0
|
|
O
|
A:HOH1109
|
2.0
|
32.6
|
1.0
|
|
O4
|
A:PO41001
|
2.1
|
33.4
|
1.0
|
|
O
|
A:HOH1119
|
2.2
|
32.6
|
1.0
|
|
O2
|
A:PO41002
|
2.3
|
37.7
|
1.0
|
|
OD2
|
A:ASP253
|
2.5
|
38.9
|
1.0
|
|
CG
|
A:ASP727
|
2.9
|
39.0
|
1.0
|
|
O1
|
A:PO41002
|
3.2
|
40.1
|
1.0
|
|
OD2
|
A:ASP727
|
3.2
|
41.1
|
1.0
|
|
CG
|
A:ASP253
|
3.3
|
38.4
|
1.0
|
|
P
|
A:PO41002
|
3.4
|
41.9
|
1.0
|
|
NZ
|
A:LYS730
|
3.4
|
32.0
|
1.0
|
|
OD1
|
A:ASP253
|
3.5
|
42.9
|
1.0
|
|
P
|
A:PO41001
|
3.5
|
60.8
|
1.0
|
|
MG
|
A:MG1003
|
3.6
|
36.6
|
1.0
|
|
NZ
|
A:LYS250
|
3.9
|
33.5
|
1.0
|
|
OD1
|
A:ASP723
|
4.0
|
37.4
|
1.0
|
|
OD2
|
A:ASP723
|
4.0
|
33.6
|
1.0
|
|
O3
|
A:PO41001
|
4.1
|
42.6
|
1.0
|
|
CB
|
A:ASP727
|
4.2
|
31.9
|
1.0
|
|
O2
|
A:PO41001
|
4.3
|
39.5
|
1.0
|
|
O4
|
A:PO41002
|
4.3
|
31.4
|
1.0
|
|
O
|
A:HOH1123
|
4.3
|
34.8
|
1.0
|
|
O
|
A:HOH1118
|
4.4
|
32.9
|
1.0
|
|
CG
|
A:ASP723
|
4.4
|
34.6
|
1.0
|
|
OD2
|
A:ASP691
|
4.4
|
37.8
|
1.0
|
|
O3
|
A:PO41002
|
4.5
|
38.3
|
1.0
|
|
O1
|
A:PO41001
|
4.5
|
44.4
|
1.0
|
|
CB
|
A:ASP253
|
4.5
|
38.0
|
1.0
|
|
O
|
A:HOH1152
|
4.5
|
36.4
|
1.0
|
|
CE
|
A:LYS730
|
4.7
|
34.4
|
1.0
|
|
OD2
|
A:ASP731
|
4.7
|
41.2
|
1.0
|
|
CA
|
A:ASP727
|
4.7
|
34.7
|
1.0
|
|
O
|
A:ASP723
|
4.8
|
38.0
|
1.0
|
|
CD
|
A:LYS250
|
4.9
|
32.8
|
1.0
|
|
OD2
|
A:ASP257
|
4.9
|
41.2
|
1.0
|
|
CE
|
A:LYS250
|
5.0
|
32.8
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 6afz
Go back to
Magnesium Binding Sites List in 6afz
Magnesium binding site 4 out
of 10 in the Proton Pyrophosphatase-E225H 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-E225H Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1006
b:42.1
occ:1.00
|
O2
|
A:PO41001
|
1.8
|
39.5
|
1.0
|
|
O
|
A:HOH1103
|
2.0
|
41.0
|
1.0
|
|
O
|
A:HOH1118
|
2.0
|
32.9
|
1.0
|
|
OD1
|
A:ASP283
|
2.1
|
41.9
|
1.0
|
|
OD2
|
A:ASP507
|
2.2
|
41.3
|
1.0
|
|
O4
|
A:PO41002
|
2.4
|
31.4
|
1.0
|
|
CG
|
A:ASP283
|
3.0
|
41.3
|
1.0
|
|
P
|
A:PO41001
|
3.2
|
60.8
|
1.0
|
|
O
|
A:HOH1117
|
3.2
|
30.9
|
1.0
|
|
OD2
|
A:ASP283
|
3.3
|
43.3
|
1.0
|
|
CG
|
A:ASP507
|
3.4
|
39.5
|
1.0
|
|
MG
|
A:MG1004
|
3.6
|
46.9
|
1.0
|
|
O4
|
A:PO41001
|
3.6
|
33.4
|
1.0
|
|
P
|
A:PO41002
|
3.7
|
41.9
|
1.0
|
|
O
|
A:HOH1183
|
3.8
|
40.0
|
1.0
|
|
OD1
|
A:ASP507
|
4.0
|
42.0
|
1.0
|
|
O1
|
A:PO41001
|
4.0
|
44.4
|
1.0
|
|
O
|
A:HOH1188
|
4.1
|
32.2
|
1.0
|
|
OD2
|
A:ASP253
|
4.1
|
38.9
|
1.0
|
|
O1
|
A:PO41002
|
4.1
|
40.1
|
1.0
|
|
NZ
|
A:LYS250
|
4.1
|
33.5
|
1.0
|
|
O2
|
A:PO41002
|
4.1
|
37.7
|
1.0
|
|
O
|
A:HOH1140
|
4.1
|
33.1
|
1.0
|
|
O3
|
A:PO41001
|
4.2
|
42.6
|
1.0
|
|
CB
|
A:ASP283
|
4.3
|
39.3
|
1.0
|
|
OD2
|
A:ASP287
|
4.4
|
41.0
|
1.0
|
|
OD1
|
A:ASP279
|
4.4
|
36.5
|
1.0
|
|
CB
|
A:ASP507
|
4.5
|
40.5
|
1.0
|
|
CA
|
A:ASP283
|
4.8
|
41.3
|
1.0
|
|
O
|
A:HOH1182
|
4.8
|
33.3
|
1.0
|
|
O3
|
A:PO41002
|
4.9
|
38.3
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 6afz
Go back to
Magnesium Binding Sites List in 6afz
Magnesium binding site 5 out
of 10 in the Proton Pyrophosphatase-E225H 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-E225H Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1007
b:42.7
occ:1.00
|
OD2
|
A:ASP691
|
2.0
|
37.8
|
1.0
|
|
O3
|
A:PO41001
|
2.0
|
42.6
|
1.0
|
|
OD1
|
A:ASN534
|
2.0
|
37.3
|
1.0
|
|
O
|
A:HOH1112
|
2.1
|
35.2
|
1.0
|
|
O1
|
A:PO41002
|
2.4
|
40.1
|
1.0
|
|
O
|
A:HOH1140
|
2.5
|
33.1
|
1.0
|
|
CG
|
A:ASN534
|
2.7
|
39.3
|
1.0
|
|
ND2
|
A:ASN534
|
3.0
|
34.6
|
1.0
|
|
CG
|
A:ASP691
|
3.0
|
35.8
|
1.0
|
|
OD1
|
A:ASP691
|
3.5
|
38.5
|
1.0
|
|
P
|
A:PO41001
|
3.5
|
60.8
|
1.0
|
|
O
|
A:HOH1201
|
3.8
|
42.8
|
1.0
|
|
P
|
A:PO41002
|
3.8
|
41.9
|
1.0
|
|
K
|
A:K1008
|
3.8
|
48.5
|
1.0
|
|
O2
|
A:PO41001
|
4.0
|
39.5
|
1.0
|
|
CB
|
A:ASN534
|
4.0
|
35.8
|
1.0
|
|
O
|
A:HOH1109
|
4.1
|
32.6
|
1.0
|
|
O4
|
A:PO41001
|
4.1
|
33.4
|
1.0
|
|
OD2
|
A:ASP530
|
4.2
|
44.5
|
1.0
|
|
CB
|
A:ASP691
|
4.3
|
31.4
|
1.0
|
|
O3
|
A:PO41002
|
4.3
|
38.3
|
1.0
|
|
OD1
|
A:ASP530
|
4.4
|
42.9
|
1.0
|
|
O4
|
A:PO41002
|
4.4
|
31.4
|
1.0
|
|
O1
|
A:PO41001
|
4.5
|
44.4
|
1.0
|
|
CA
|
A:ASN534
|
4.6
|
38.4
|
1.0
|
|
CG
|
A:ASP530
|
4.6
|
44.7
|
1.0
|
|
O
|
A:ASP530
|
4.7
|
39.0
|
1.0
|
|
CE
|
A:LYS730
|
4.8
|
34.4
|
1.0
|
|
O
|
A:HOH1168
|
4.8
|
37.1
|
1.0
|
|
O2
|
A:PO41002
|
4.9
|
37.7
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 6afz
Go back to
Magnesium Binding Sites List in 6afz
Magnesium binding site 6 out
of 10 in the Proton Pyrophosphatase-E225H 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-E225H Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1003
b:52.2
occ:1.00
|
OD1
|
B:ASP253
|
2.0
|
51.8
|
1.0
|
|
O
|
B:HOH1106
|
2.1
|
48.4
|
1.0
|
|
O
|
B:HOH1101
|
2.1
|
46.0
|
1.0
|
|
OD2
|
B:ASP257
|
2.2
|
51.1
|
1.0
|
|
O
|
B:HOH1134
|
2.3
|
50.2
|
1.0
|
|
O2
|
B:PO41002
|
2.4
|
45.7
|
1.0
|
|
CG
|
B:ASP253
|
2.8
|
48.1
|
1.0
|
|
OD2
|
B:ASP253
|
2.9
|
45.2
|
1.0
|
|
MG
|
B:MG1005
|
3.1
|
50.3
|
1.0
|
|
O4
|
B:PO41002
|
3.1
|
52.7
|
1.0
|
|
P
|
B:PO41002
|
3.2
|
54.3
|
1.0
|
|
CG
|
B:ASP257
|
3.3
|
50.9
|
1.0
|
|
O3
|
B:PO41002
|
3.7
|
49.8
|
1.0
|
|
OD1
|
B:ASP257
|
3.9
|
51.7
|
1.0
|
|
OD2
|
B:ASP723
|
3.9
|
43.3
|
1.0
|
|
OD2
|
B:ASP727
|
4.0
|
43.3
|
1.0
|
|
CB
|
B:ASP253
|
4.2
|
45.5
|
1.0
|
|
O
|
B:HOH1114
|
4.2
|
44.7
|
1.0
|
|
O
|
B:HOH1123
|
4.3
|
41.4
|
1.0
|
|
O
|
B:HOH1151
|
4.3
|
43.9
|
1.0
|
|
O
|
B:ASP253
|
4.3
|
52.0
|
1.0
|
|
OD1
|
B:ASP727
|
4.4
|
47.2
|
1.0
|
|
OD2
|
B:ASP279
|
4.5
|
46.4
|
1.0
|
|
NZ
|
B:LYS694
|
4.5
|
44.8
|
1.0
|
|
OE2
|
B:GLU268
|
4.5
|
54.6
|
1.0
|
|
O1
|
B:PO41002
|
4.5
|
55.4
|
1.0
|
|
CB
|
B:ASP257
|
4.6
|
47.4
|
1.0
|
|
O2
|
B:PO41001
|
4.6
|
49.2
|
1.0
|
|
CG
|
B:ASP727
|
4.6
|
46.3
|
1.0
|
|
CA
|
B:ASP253
|
4.7
|
49.5
|
1.0
|
|
C
|
B:ASP253
|
4.7
|
51.5
|
1.0
|
|
CG
|
B:ASP723
|
5.0
|
46.0
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 6afz
Go back to
Magnesium Binding Sites List in 6afz
Magnesium binding site 7 out
of 10 in the Proton Pyrophosphatase-E225H 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-E225H Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1004
b:58.8
occ:1.00
|
OD1
|
B:ASP507
|
1.9
|
60.0
|
1.0
|
|
O
|
B:HOH1102
|
2.1
|
55.7
|
1.0
|
|
O
|
B:HOH1113
|
2.1
|
48.6
|
1.0
|
|
O
|
B:HOH1151
|
2.1
|
43.9
|
1.0
|
|
O
|
B:HOH1112
|
2.2
|
51.3
|
1.0
|
|
O3
|
B:PO41002
|
2.3
|
49.8
|
1.0
|
|
CG
|
B:ASP507
|
2.7
|
58.4
|
1.0
|
|
OD2
|
B:ASP507
|
2.7
|
59.3
|
1.0
|
|
MG
|
B:MG1006
|
3.0
|
54.9
|
1.0
|
|
P
|
B:PO41002
|
3.6
|
54.3
|
1.0
|
|
O4
|
B:PO41002
|
3.8
|
52.7
|
1.0
|
|
OD2
|
B:ASP283
|
3.8
|
58.8
|
1.0
|
|
OD1
|
B:ASP279
|
4.0
|
45.7
|
1.0
|
|
O
|
B:HOH1123
|
4.1
|
41.4
|
1.0
|
|
O4
|
B:PO41001
|
4.1
|
52.2
|
1.0
|
|
CB
|
B:ASP507
|
4.1
|
56.9
|
1.0
|
|
O1
|
B:PO41002
|
4.2
|
55.4
|
1.0
|
|
O
|
B:ASP507
|
4.2
|
61.7
|
1.0
|
|
O
|
B:HOH1134
|
4.3
|
50.2
|
1.0
|
|
OD2
|
B:ASP269
|
4.3
|
57.0
|
1.0
|
|
OD1
|
B:ASP283
|
4.6
|
60.2
|
1.0
|
|
C
|
B:ASP507
|
4.6
|
58.0
|
1.0
|
|
CG
|
B:ASP283
|
4.6
|
58.6
|
1.0
|
|
OE1
|
B:GLU268
|
4.6
|
48.9
|
1.0
|
|
OD1
|
B:ASP269
|
4.6
|
60.7
|
1.0
|
|
CA
|
B:ASP507
|
4.7
|
54.4
|
1.0
|
|
O2
|
B:PO41002
|
4.7
|
45.7
|
1.0
|
|
OD2
|
B:ASP530
|
4.8
|
58.2
|
1.0
|
|
O
|
B:HOH1127
|
4.9
|
51.2
|
1.0
|
|
CG
|
B:ASP269
|
4.9
|
61.2
|
1.0
|
|
OD2
|
B:ASP279
|
4.9
|
46.4
|
1.0
|
|
CG
|
B:ASP279
|
4.9
|
48.4
|
1.0
|
|
ND2
|
B:ASN280
|
5.0
|
55.4
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 6afz
Go back to
Magnesium Binding Sites List in 6afz
Magnesium binding site 8 out
of 10 in the Proton Pyrophosphatase-E225H 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-E225H Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1005
b:50.3
occ:1.00
|
O2
|
B:PO41002
|
1.8
|
45.7
|
1.0
|
|
OD1
|
B:ASP727
|
2.0
|
47.2
|
1.0
|
|
O
|
B:HOH1106
|
2.0
|
48.4
|
1.0
|
|
O2
|
B:PO41001
|
2.2
|
49.2
|
1.0
|
|
O
|
B:HOH1114
|
2.3
|
44.7
|
1.0
|
|
OD2
|
B:ASP253
|
2.3
|
45.2
|
1.0
|
|
CG
|
B:ASP727
|
2.9
|
46.3
|
1.0
|
|
MG
|
B:MG1003
|
3.1
|
52.2
|
1.0
|
|
CG
|
B:ASP253
|
3.2
|
48.1
|
1.0
|
|
P
|
B:PO41002
|
3.2
|
54.3
|
1.0
|
|
OD2
|
B:ASP727
|
3.2
|
43.3
|
1.0
|
|
NZ
|
B:LYS730
|
3.4
|
44.9
|
1.0
|
|
OD1
|
B:ASP253
|
3.6
|
51.8
|
1.0
|
|
P
|
B:PO41001
|
3.6
|
65.7
|
1.0
|
|
O1
|
B:PO41002
|
3.7
|
55.4
|
1.0
|
|
CE
|
B:LYS250
|
3.8
|
40.2
|
1.0
|
|
NZ
|
B:LYS250
|
3.8
|
44.1
|
1.0
|
|
O4
|
B:PO41002
|
4.1
|
52.7
|
1.0
|
|
O3
|
B:PO41002
|
4.1
|
49.8
|
1.0
|
|
CB
|
B:ASP727
|
4.2
|
43.6
|
1.0
|
|
O3
|
B:PO41001
|
4.2
|
55.0
|
1.0
|
|
O4
|
B:PO41001
|
4.3
|
52.2
|
1.0
|
|
OD1
|
B:ASP723
|
4.3
|
48.5
|
1.0
|
|
OD2
|
B:ASP723
|
4.3
|
43.3
|
1.0
|
|
O
|
B:HOH1123
|
4.3
|
41.4
|
1.0
|
|
O
|
B:HOH1101
|
4.4
|
46.0
|
1.0
|
|
CB
|
B:ASP253
|
4.4
|
45.5
|
1.0
|
|
CE
|
B:LYS730
|
4.5
|
42.2
|
1.0
|
|
OD2
|
B:ASP731
|
4.6
|
48.2
|
1.0
|
|
O1
|
B:PO41001
|
4.6
|
61.1
|
1.0
|
|
CA
|
B:ASP727
|
4.7
|
41.6
|
1.0
|
|
CG
|
B:ASP723
|
4.7
|
46.0
|
1.0
|
|
O
|
B:HOH1133
|
4.8
|
42.6
|
1.0
|
|
OD2
|
B:ASP691
|
4.8
|
49.9
|
1.0
|
|
MG
|
B:MG1007
|
5.0
|
56.5
|
1.0
|
|
OD2
|
B:ASP257
|
5.0
|
51.1
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 6afz
Go back to
Magnesium Binding Sites List in 6afz
Magnesium binding site 9 out
of 10 in the Proton Pyrophosphatase-E225H 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-E225H Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1006
b:54.9
occ:1.00
|
OD1
|
B:ASP283
|
2.0
|
60.2
|
1.0
|
|
O
|
B:HOH1123
|
2.1
|
41.4
|
1.0
|
|
O4
|
B:PO41001
|
2.1
|
52.2
|
1.0
|
|
OD2
|
B:ASP507
|
2.2
|
59.3
|
1.0
|
|
O3
|
B:PO41002
|
2.4
|
49.8
|
1.0
|
|
CG
|
B:ASP283
|
2.7
|
58.6
|
1.0
|
|
O
|
B:HOH1102
|
2.7
|
55.7
|
1.0
|
|
OD2
|
B:ASP283
|
2.8
|
58.8
|
1.0
|
|
MG
|
B:MG1004
|
3.0
|
58.8
|
1.0
|
|
CG
|
B:ASP507
|
3.3
|
58.4
|
1.0
|
|
P
|
B:PO41001
|
3.5
|
65.7
|
1.0
|
|
O
|
B:HOH1103
|
3.5
|
49.5
|
1.0
|
|
P
|
B:PO41002
|
3.6
|
54.3
|
1.0
|
|
OD1
|
B:ASP507
|
3.8
|
60.0
|
1.0
|
|
O2
|
B:PO41001
|
3.8
|
49.2
|
1.0
|
|
O1
|
B:PO41002
|
3.9
|
55.4
|
1.0
|
|
O
|
B:HOH1140
|
4.0
|
41.8
|
1.0
|
|
OD1
|
B:ASP279
|
4.0
|
45.7
|
1.0
|
|
O2
|
B:PO41002
|
4.1
|
45.7
|
1.0
|
|
CB
|
B:ASP283
|
4.1
|
56.9
|
1.0
|
|
O1
|
B:PO41001
|
4.2
|
61.1
|
1.0
|
|
O
|
B:HOH1151
|
4.3
|
43.9
|
1.0
|
|
OD2
|
B:ASP253
|
4.3
|
45.2
|
1.0
|
|
O
|
B:HOH1154
|
4.3
|
54.7
|
1.0
|
|
NZ
|
B:LYS250
|
4.4
|
44.1
|
1.0
|
|
O
|
B:ASP279
|
4.6
|
55.4
|
1.0
|
|
CB
|
B:ASP507
|
4.6
|
56.9
|
1.0
|
|
O3
|
B:PO41001
|
4.6
|
55.0
|
1.0
|
|
O
|
B:HOH1127
|
4.7
|
51.2
|
1.0
|
|
CG
|
B:ASP279
|
4.7
|
48.4
|
1.0
|
|
OD2
|
B:ASP279
|
4.8
|
46.4
|
1.0
|
|
O4
|
B:PO41002
|
4.8
|
52.7
|
1.0
|
|
O
|
B:HOH1113
|
4.8
|
48.6
|
1.0
|
|
CA
|
B:ASP283
|
4.8
|
55.9
|
1.0
|
|
O
|
B:HOH1112
|
4.8
|
51.3
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 6afz
Go back to
Magnesium Binding Sites List in 6afz
Magnesium binding site 10 out
of 10 in the Proton Pyrophosphatase-E225H 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-E225H Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1007
b:56.5
occ:1.00
|
O3
|
B:PO41001
|
2.0
|
55.0
|
1.0
|
|
OD1
|
B:ASN534
|
2.1
|
54.0
|
1.0
|
|
O1
|
B:PO41002
|
2.1
|
55.4
|
1.0
|
|
OD2
|
B:ASP691
|
2.2
|
49.9
|
1.0
|
|
O
|
B:HOH1127
|
2.3
|
51.2
|
1.0
|
|
CG
|
B:ASN534
|
2.9
|
55.6
|
1.0
|
|
ND2
|
B:ASN534
|
3.1
|
55.9
|
1.0
|
|
CG
|
B:ASP691
|
3.2
|
48.5
|
1.0
|
|
P
|
B:PO41001
|
3.3
|
65.7
|
1.0
|
|
O
|
B:HOH1114
|
3.5
|
44.7
|
1.0
|
|
P
|
B:PO41002
|
3.6
|
54.3
|
1.0
|
|
OD1
|
B:ASP691
|
3.6
|
52.6
|
1.0
|
|
K
|
B:K1008
|
3.7
|
63.8
|
1.0
|
|
O4
|
B:PO41001
|
3.8
|
52.2
|
1.0
|
|
O2
|
B:PO41001
|
4.0
|
49.2
|
1.0
|
|
O4
|
B:PO41002
|
4.1
|
52.7
|
1.0
|
|
O2
|
B:PO41002
|
4.2
|
45.7
|
1.0
|
|
CB
|
B:ASN534
|
4.3
|
56.0
|
1.0
|
|
O1
|
B:PO41001
|
4.3
|
61.1
|
1.0
|
|
OD2
|
B:ASP530
|
4.3
|
58.2
|
1.0
|
|
O3
|
B:PO41002
|
4.4
|
49.8
|
1.0
|
|
OD1
|
B:ASP530
|
4.5
|
61.6
|
1.0
|
|
CB
|
B:ASP691
|
4.6
|
43.2
|
1.0
|
|
CE
|
B:LYS730
|
4.7
|
42.2
|
1.0
|
|
CG
|
B:ASP530
|
4.8
|
62.5
|
1.0
|
|
CA
|
B:ASN534
|
4.8
|
56.1
|
1.0
|
|
NZ
|
B:LYS730
|
4.8
|
44.9
|
1.0
|
|
O
|
B:HOH1138
|
4.9
|
52.7
|
1.0
|
|
MG
|
B:MG1005
|
5.0
|
50.3
|
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: Mon Sep 30 19:09:47 2024
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