Magnesium in PDB 1rmt: Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine.
Enzymatic activity of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine.
All present enzymatic activity of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine.:
3.1.3.2;
Protein crystallography data
The structure of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine., PDB code: 1rmt
was solved by
V.Calderone,
C.Forleo,
M.Benvenuti,
G.M.Rossolini,
M.C.Thaller,
S.Mangani,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
74.54 /
1.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.740,
66.704,
88.556,
90.00,
117.13,
90.00
|
R / Rfree (%)
|
16.7 /
19.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine.
(pdb code 1rmt). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine., PDB code: 1rmt:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1rmt
Go back to
Magnesium Binding Sites List in 1rmt
Magnesium binding site 1 out
of 4 in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine.
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 Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1413
b:9.6
occ:1.00
|
OD2
|
A:ASP44
|
2.0
|
6.0
|
1.0
|
O
|
A:ASP46
|
2.1
|
5.3
|
1.0
|
O
|
A:HOH1775
|
2.1
|
7.6
|
1.0
|
OD1
|
A:ASP167
|
2.1
|
6.9
|
1.0
|
O
|
A:HOH1797
|
2.1
|
6.6
|
1.0
|
O
|
A:HOH1812
|
2.1
|
7.3
|
1.0
|
CG
|
A:ASP44
|
3.0
|
6.7
|
1.0
|
CG
|
A:ASP167
|
3.1
|
5.6
|
1.0
|
C
|
A:ASP46
|
3.2
|
4.8
|
1.0
|
OD1
|
A:ASP44
|
3.3
|
7.5
|
1.0
|
OD2
|
A:ASP167
|
3.4
|
5.8
|
1.0
|
CA
|
A:ASP46
|
3.9
|
6.2
|
1.0
|
N
|
A:ASP46
|
3.9
|
7.0
|
1.0
|
OG1
|
A:THR48
|
3.9
|
6.4
|
1.0
|
OG
|
A:SER168
|
4.0
|
8.0
|
1.0
|
OD2
|
A:ASP171
|
4.1
|
8.3
|
1.0
|
O
|
A:HOH1503
|
4.1
|
7.9
|
1.0
|
CB
|
A:ASP46
|
4.2
|
6.0
|
1.0
|
O
|
A:HOH1813
|
4.2
|
19.7
|
1.0
|
N
|
A:ASP47
|
4.3
|
5.3
|
1.0
|
CB
|
A:ASP44
|
4.3
|
7.1
|
1.0
|
O
|
A:HOH1530
|
4.4
|
14.4
|
1.0
|
CB
|
A:ASP167
|
4.4
|
5.7
|
1.0
|
CB
|
A:ASP47
|
4.5
|
5.7
|
1.0
|
N
|
A:ASP167
|
4.6
|
6.0
|
1.0
|
N
|
A:THR48
|
4.6
|
5.5
|
1.0
|
CA
|
A:ASP47
|
4.7
|
5.4
|
1.0
|
C
|
A:ASP47
|
4.7
|
5.5
|
1.0
|
C
|
A:ILE45
|
4.7
|
7.0
|
1.0
|
N
|
A:SER168
|
4.8
|
7.2
|
1.0
|
O
|
A:HOH1510
|
4.8
|
9.8
|
1.0
|
O
|
A:HOH1505
|
4.9
|
10.8
|
1.0
|
CB
|
A:THR48
|
4.9
|
7.2
|
1.0
|
O
|
A:HOH1641
|
4.9
|
22.7
|
1.0
|
CA
|
A:ASP167
|
5.0
|
5.1
|
1.0
|
CB
|
A:SER168
|
5.0
|
8.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1rmt
Go back to
Magnesium Binding Sites List in 1rmt
Magnesium binding site 2 out
of 4 in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine.
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 Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1414
b:9.5
occ:1.00
|
O
|
B:HOH1831
|
2.0
|
9.3
|
1.0
|
O
|
B:HOH1800
|
2.0
|
8.2
|
1.0
|
O
|
B:ASP46
|
2.0
|
4.7
|
1.0
|
OD2
|
B:ASP44
|
2.1
|
6.7
|
1.0
|
OD1
|
B:ASP167
|
2.1
|
6.4
|
1.0
|
O
|
B:HOH1818
|
2.1
|
6.3
|
1.0
|
CG
|
B:ASP44
|
3.0
|
6.3
|
1.0
|
CG
|
B:ASP167
|
3.1
|
4.5
|
1.0
|
C
|
B:ASP46
|
3.2
|
5.7
|
1.0
|
OD1
|
B:ASP44
|
3.3
|
8.4
|
1.0
|
OD2
|
B:ASP167
|
3.4
|
6.2
|
1.0
|
CA
|
B:ASP46
|
3.9
|
6.6
|
1.0
|
N
|
B:ASP46
|
4.0
|
6.1
|
1.0
|
OG1
|
B:THR48
|
4.0
|
6.7
|
1.0
|
OG
|
B:SER168
|
4.0
|
9.8
|
1.0
|
O
|
B:HOH1523
|
4.1
|
9.7
|
1.0
|
O
|
B:HOH1654
|
4.1
|
17.6
|
1.0
|
OD2
|
B:ASP171
|
4.1
|
9.0
|
1.0
|
CB
|
B:ASP46
|
4.1
|
6.8
|
1.0
|
O
|
B:HOH1575
|
4.3
|
13.8
|
1.0
|
N
|
B:ASP47
|
4.3
|
6.2
|
1.0
|
CB
|
B:ASP44
|
4.4
|
6.9
|
1.0
|
CB
|
B:ASP167
|
4.5
|
5.3
|
1.0
|
CB
|
B:ASP47
|
4.6
|
5.2
|
1.0
|
N
|
B:THR48
|
4.6
|
4.9
|
1.0
|
N
|
B:ASP167
|
4.6
|
5.7
|
1.0
|
CA
|
B:ASP47
|
4.7
|
6.2
|
1.0
|
C
|
B:ASP47
|
4.7
|
5.4
|
1.0
|
C
|
B:ILE45
|
4.8
|
5.9
|
1.0
|
N
|
B:SER168
|
4.8
|
6.7
|
1.0
|
O
|
B:HOH1512
|
4.8
|
8.7
|
1.0
|
O
|
B:HOH1530
|
4.9
|
12.1
|
1.0
|
CB
|
B:SER168
|
4.9
|
8.3
|
1.0
|
CB
|
B:THR48
|
4.9
|
5.9
|
1.0
|
CA
|
B:ASP167
|
5.0
|
5.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1rmt
Go back to
Magnesium Binding Sites List in 1rmt
Magnesium binding site 3 out
of 4 in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine.
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 Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1415
b:12.4
occ:1.00
|
OD2
|
C:ASP44
|
2.0
|
9.0
|
1.0
|
OD1
|
C:ASP167
|
2.1
|
8.1
|
1.0
|
O
|
C:ASP46
|
2.1
|
7.3
|
1.0
|
O
|
C:HOH1787
|
2.1
|
11.4
|
1.0
|
O
|
C:HOH1771
|
2.1
|
9.2
|
1.0
|
O
|
C:HOH1750
|
2.1
|
10.7
|
1.0
|
CG
|
C:ASP44
|
3.0
|
9.6
|
1.0
|
CG
|
C:ASP167
|
3.1
|
7.1
|
1.0
|
C
|
C:ASP46
|
3.3
|
7.1
|
1.0
|
OD2
|
C:ASP167
|
3.4
|
8.6
|
1.0
|
OD1
|
C:ASP44
|
3.4
|
10.6
|
1.0
|
OG
|
C:SER168
|
4.0
|
10.6
|
1.0
|
OG1
|
C:THR48
|
4.0
|
8.3
|
1.0
|
O
|
C:HOH1671
|
4.0
|
33.5
|
1.0
|
CA
|
C:ASP46
|
4.0
|
8.0
|
1.0
|
OD2
|
C:ASP171
|
4.0
|
11.6
|
1.0
|
N
|
C:ASP46
|
4.0
|
8.7
|
1.0
|
O2'
|
C:ADN1503
|
4.1
|
36.3
|
1.0
|
O
|
C:HOH1526
|
4.1
|
16.7
|
1.0
|
CB
|
C:ASP46
|
4.2
|
8.6
|
1.0
|
O
|
C:HOH1531
|
4.2
|
11.5
|
1.0
|
CB
|
C:ASP44
|
4.3
|
8.5
|
1.0
|
O
|
C:HOH1504
|
4.4
|
10.9
|
1.0
|
N
|
C:ASP47
|
4.4
|
7.0
|
1.0
|
CB
|
C:ASP167
|
4.4
|
8.1
|
1.0
|
N
|
C:ASP167
|
4.6
|
7.8
|
1.0
|
CB
|
C:ASP47
|
4.6
|
7.6
|
1.0
|
N
|
C:THR48
|
4.6
|
6.8
|
1.0
|
CA
|
C:ASP47
|
4.7
|
7.4
|
1.0
|
C
|
C:ASP47
|
4.8
|
6.5
|
1.0
|
C
|
C:ILE45
|
4.8
|
8.8
|
1.0
|
C2'
|
C:ADN1503
|
4.8
|
35.4
|
1.0
|
CB
|
C:SER168
|
4.8
|
8.9
|
1.0
|
N
|
C:SER168
|
4.8
|
7.8
|
1.0
|
CB
|
C:THR48
|
4.9
|
7.8
|
1.0
|
CA
|
C:ASP167
|
5.0
|
7.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1rmt
Go back to
Magnesium Binding Sites List in 1rmt
Magnesium binding site 4 out
of 4 in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine.
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 Apha Class B Acid Phosphatase/Phosphotransferase Complexed with Adenosine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1416
b:10.2
occ:1.00
|
OD2
|
D:ASP44
|
2.0
|
6.5
|
1.0
|
O
|
D:HOH1778
|
2.1
|
6.8
|
1.0
|
O
|
D:ASP46
|
2.1
|
5.4
|
1.0
|
OD1
|
D:ASP167
|
2.1
|
6.8
|
1.0
|
O
|
D:HOH1797
|
2.1
|
9.0
|
1.0
|
O
|
D:HOH1811
|
2.1
|
10.0
|
1.0
|
CG
|
D:ASP44
|
3.0
|
7.1
|
1.0
|
CG
|
D:ASP167
|
3.1
|
5.8
|
1.0
|
C
|
D:ASP46
|
3.2
|
6.2
|
1.0
|
OD1
|
D:ASP44
|
3.4
|
7.2
|
1.0
|
OD2
|
D:ASP167
|
3.4
|
6.9
|
1.0
|
OG1
|
D:THR48
|
3.9
|
6.1
|
1.0
|
CA
|
D:ASP46
|
4.0
|
7.2
|
1.0
|
OG
|
D:SER168
|
4.0
|
9.8
|
1.0
|
OD2
|
D:ASP171
|
4.0
|
8.2
|
1.0
|
O2'
|
D:ADN1504
|
4.1
|
28.8
|
1.0
|
N
|
D:ASP46
|
4.1
|
6.9
|
1.0
|
CB
|
D:ASP46
|
4.1
|
7.3
|
1.0
|
O
|
D:HOH1523
|
4.2
|
12.1
|
1.0
|
CB
|
D:ASP44
|
4.3
|
6.4
|
1.0
|
O
|
D:HOH1510
|
4.3
|
10.2
|
1.0
|
N
|
D:ASP47
|
4.3
|
6.5
|
1.0
|
O
|
D:HOH1537
|
4.4
|
15.0
|
1.0
|
CB
|
D:ASP167
|
4.4
|
7.0
|
1.0
|
CB
|
D:ASP47
|
4.6
|
6.1
|
1.0
|
N
|
D:ASP167
|
4.6
|
5.8
|
1.0
|
N
|
D:THR48
|
4.7
|
5.8
|
1.0
|
CA
|
D:ASP47
|
4.7
|
5.6
|
1.0
|
C
|
D:ASP47
|
4.8
|
5.8
|
1.0
|
C
|
D:ILE45
|
4.8
|
7.4
|
1.0
|
N
|
D:SER168
|
4.8
|
7.4
|
1.0
|
CB
|
D:SER168
|
4.9
|
9.2
|
1.0
|
CB
|
D:THR48
|
4.9
|
6.9
|
1.0
|
C2'
|
D:ADN1504
|
5.0
|
31.9
|
1.0
|
CA
|
D:ASP167
|
5.0
|
6.1
|
1.0
|
|
Reference:
V.Calderone,
C.Forleo,
M.Benvenuti,
G.M.Rossolini,
M.C.Thaller,
S.Mangani.
Insights in the Catalytic Mechanism of Apha From Escherichia Coli To Be Published.
Page generated: Tue Aug 13 13:03:27 2024
|