Magnesium in PDB 3nrj: Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
Protein crystallography data
The structure of Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium, PDB code: 3nrj
was solved by
Y.Patskovsky,
U.Ramagopal,
R.Toro,
J.Freeman,
J.M.Sauder,
S.K.Burley,
S.C.Almo,
New York Sgx Research Center For Structural Genomics(Nysgxrc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.302,
126.733,
106.531,
90.00,
95.57,
90.00
|
R / Rfree (%)
|
17.9 /
24
|
Other elements in 3nrj:
The structure of Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
(pdb code 3nrj). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the
Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium, PDB code: 3nrj:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 12 in 3nrj
Go back to
Magnesium Binding Sites List in 3nrj
Magnesium binding site 1 out
of 12 in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
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 Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg190
b:36.3
occ:1.00
|
OD2
|
A:ASP23
|
2.0
|
39.2
|
1.0
|
OD1
|
A:ASP116
|
2.1
|
39.8
|
1.0
|
O
|
A:ASP25
|
2.1
|
36.3
|
1.0
|
O
|
A:HOH624
|
2.1
|
42.2
|
1.0
|
O
|
A:HOH630
|
2.1
|
34.5
|
1.0
|
O
|
A:HOH1223
|
2.2
|
41.6
|
1.0
|
CG
|
A:ASP116
|
3.0
|
43.9
|
1.0
|
CG
|
A:ASP23
|
3.1
|
44.4
|
1.0
|
C
|
A:ASP25
|
3.3
|
31.7
|
1.0
|
OD2
|
A:ASP116
|
3.3
|
40.4
|
1.0
|
OD1
|
A:ASP23
|
3.5
|
42.6
|
1.0
|
OD2
|
A:ASP120
|
3.9
|
38.3
|
1.0
|
CA
|
A:ASP25
|
4.1
|
35.1
|
1.0
|
N
|
A:ASP25
|
4.2
|
36.5
|
1.0
|
CB
|
A:ASP116
|
4.3
|
30.9
|
1.0
|
N
|
A:GLY26
|
4.3
|
36.0
|
1.0
|
O
|
A:HOH237
|
4.3
|
65.2
|
1.0
|
CB
|
A:ASP23
|
4.3
|
36.6
|
1.0
|
O2
|
A:PO4191
|
4.4
|
51.1
|
0.7
|
CA
|
A:GLY26
|
4.4
|
36.1
|
1.0
|
CB
|
A:ASP25
|
4.4
|
35.0
|
1.0
|
O1
|
A:PO4191
|
4.4
|
32.3
|
0.7
|
CB
|
A:ASP117
|
4.6
|
35.3
|
1.0
|
N
|
A:ASP117
|
4.6
|
37.0
|
1.0
|
N
|
A:ASP116
|
4.7
|
33.0
|
1.0
|
O
|
A:HOH214
|
4.7
|
47.8
|
1.0
|
P
|
A:PO4191
|
4.8
|
33.8
|
0.7
|
CA
|
A:ASP116
|
4.8
|
35.7
|
1.0
|
O3
|
A:PO4191
|
4.8
|
35.2
|
0.7
|
C
|
A:VAL24
|
4.8
|
41.6
|
1.0
|
OG1
|
H:THR47
|
4.9
|
43.9
|
1.0
|
C
|
A:ASP116
|
4.9
|
39.0
|
1.0
|
C
|
A:GLY26
|
4.9
|
40.5
|
1.0
|
CG
|
A:ASP120
|
4.9
|
33.0
|
1.0
|
O
|
A:HOH306
|
5.0
|
45.0
|
1.0
|
CG2
|
A:VAL27
|
5.0
|
32.8
|
1.0
|
N
|
A:VAL27
|
5.0
|
29.9
|
1.0
|
|
Magnesium binding site 2 out
of 12 in 3nrj
Go back to
Magnesium Binding Sites List in 3nrj
Magnesium binding site 2 out
of 12 in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
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 Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg190
b:49.3
occ:1.00
|
OD2
|
B:ASP23
|
2.0
|
47.3
|
1.0
|
O
|
B:HOH202
|
2.0
|
43.1
|
1.0
|
O
|
B:HOH565
|
2.1
|
41.0
|
1.0
|
O
|
B:HOH203
|
2.1
|
56.4
|
1.0
|
OD1
|
B:ASP116
|
2.1
|
50.0
|
1.0
|
O
|
B:ASP25
|
2.2
|
47.1
|
1.0
|
CG
|
B:ASP23
|
3.0
|
47.1
|
1.0
|
CG
|
B:ASP116
|
3.3
|
47.3
|
1.0
|
C
|
B:ASP25
|
3.4
|
44.6
|
1.0
|
OD1
|
B:ASP23
|
3.4
|
49.7
|
1.0
|
OD2
|
B:ASP116
|
3.7
|
52.0
|
1.0
|
OD2
|
B:ASP120
|
3.9
|
53.2
|
1.0
|
CA
|
B:ASP25
|
4.1
|
44.1
|
1.0
|
O2
|
B:PO4191
|
4.2
|
40.0
|
0.7
|
O
|
B:HOH461
|
4.2
|
47.0
|
1.0
|
N
|
B:ASP25
|
4.2
|
39.6
|
1.0
|
CB
|
B:ASP25
|
4.3
|
40.6
|
1.0
|
CB
|
B:ASP23
|
4.3
|
39.9
|
1.0
|
N
|
B:GLY26
|
4.4
|
43.7
|
1.0
|
O3
|
B:PO4191
|
4.5
|
67.3
|
0.7
|
CB
|
B:ASP116
|
4.5
|
47.3
|
1.0
|
CA
|
B:GLY26
|
4.6
|
39.3
|
1.0
|
CB
|
B:ASP117
|
4.6
|
41.8
|
1.0
|
N
|
B:ASP117
|
4.6
|
45.0
|
1.0
|
N
|
B:ASP116
|
4.7
|
43.9
|
1.0
|
P
|
B:PO4191
|
4.7
|
49.0
|
0.7
|
O1
|
B:PO4191
|
4.8
|
43.0
|
0.7
|
CG
|
B:ASP120
|
4.8
|
52.6
|
1.0
|
CG2
|
B:VAL27
|
4.8
|
38.8
|
1.0
|
O
|
B:HOH210
|
4.9
|
55.9
|
1.0
|
OD1
|
B:ASP120
|
4.9
|
44.8
|
1.0
|
C
|
B:ASP116
|
4.9
|
42.0
|
1.0
|
CA
|
B:ASP116
|
4.9
|
41.5
|
1.0
|
|
Magnesium binding site 3 out
of 12 in 3nrj
Go back to
Magnesium Binding Sites List in 3nrj
Magnesium binding site 3 out
of 12 in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
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 Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg189
b:38.5
occ:1.00
|
O
|
C:HOH1094
|
2.0
|
31.8
|
1.0
|
OD2
|
C:ASP23
|
2.0
|
40.4
|
1.0
|
O
|
C:HOH651
|
2.1
|
37.7
|
1.0
|
O
|
C:HOH662
|
2.2
|
44.3
|
1.0
|
O
|
C:ASP25
|
2.2
|
34.0
|
1.0
|
OD1
|
C:ASP116
|
2.2
|
38.3
|
1.0
|
CG
|
C:ASP23
|
3.1
|
37.5
|
1.0
|
CG
|
C:ASP116
|
3.2
|
42.8
|
1.0
|
C
|
C:ASP25
|
3.3
|
29.1
|
1.0
|
OD2
|
C:ASP116
|
3.5
|
46.7
|
1.0
|
OD1
|
C:ASP23
|
3.6
|
42.8
|
1.0
|
O1
|
C:PO4190
|
4.0
|
69.9
|
0.7
|
O2
|
C:PO4190
|
4.0
|
57.7
|
0.7
|
OD2
|
C:ASP120
|
4.1
|
36.9
|
1.0
|
CA
|
C:ASP25
|
4.1
|
34.5
|
1.0
|
O
|
C:HOH359
|
4.2
|
40.0
|
1.0
|
N
|
C:ASP25
|
4.2
|
33.8
|
1.0
|
CB
|
C:ASP25
|
4.2
|
29.4
|
1.0
|
N
|
C:GLY26
|
4.4
|
34.7
|
1.0
|
CB
|
C:ASP23
|
4.4
|
32.8
|
1.0
|
CB
|
C:ASP116
|
4.5
|
36.3
|
1.0
|
P
|
C:PO4190
|
4.5
|
47.7
|
0.7
|
CB
|
C:ASP117
|
4.6
|
33.1
|
1.0
|
CA
|
C:GLY26
|
4.6
|
35.7
|
1.0
|
N
|
C:ASP117
|
4.6
|
36.2
|
1.0
|
OG1
|
A:THR47
|
4.7
|
39.3
|
1.0
|
O
|
C:HOH195
|
4.7
|
46.7
|
1.0
|
N
|
C:ASP116
|
4.8
|
32.5
|
1.0
|
NH2
|
C:ARG69
|
4.9
|
51.5
|
0.5
|
C
|
C:VAL24
|
4.9
|
38.0
|
1.0
|
CA
|
C:ASP116
|
5.0
|
33.1
|
1.0
|
O4
|
C:PO4190
|
5.0
|
40.9
|
0.7
|
C
|
C:ASP116
|
5.0
|
38.4
|
1.0
|
|
Magnesium binding site 4 out
of 12 in 3nrj
Go back to
Magnesium Binding Sites List in 3nrj
Magnesium binding site 4 out
of 12 in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
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 Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg189
b:42.7
occ:1.00
|
OD1
|
D:ASP116
|
2.0
|
45.2
|
1.0
|
OD2
|
D:ASP23
|
2.0
|
41.0
|
1.0
|
O
|
D:HOH1057
|
2.0
|
43.9
|
1.0
|
O
|
D:HOH1201
|
2.1
|
48.7
|
1.0
|
O
|
D:ASP25
|
2.2
|
34.5
|
1.0
|
O
|
D:HOH467
|
2.2
|
35.5
|
1.0
|
CG
|
D:ASP116
|
2.9
|
45.9
|
1.0
|
CG
|
D:ASP23
|
3.1
|
34.0
|
1.0
|
OD2
|
D:ASP116
|
3.3
|
50.4
|
1.0
|
C
|
D:ASP25
|
3.4
|
39.8
|
1.0
|
OD1
|
D:ASP23
|
3.5
|
41.0
|
1.0
|
OD2
|
D:ASP120
|
4.1
|
37.3
|
1.0
|
O1
|
D:PO4190
|
4.2
|
63.8
|
0.7
|
CA
|
D:ASP25
|
4.2
|
34.4
|
1.0
|
CB
|
D:ASP116
|
4.3
|
33.8
|
1.0
|
O2
|
D:PO4190
|
4.3
|
54.1
|
0.7
|
N
|
D:ASP25
|
4.3
|
30.9
|
1.0
|
CB
|
D:ASP23
|
4.3
|
31.3
|
1.0
|
CB
|
D:ASP25
|
4.4
|
37.3
|
1.0
|
N
|
D:GLY26
|
4.4
|
35.4
|
1.0
|
N
|
D:ASP116
|
4.6
|
36.3
|
1.0
|
O
|
D:HOH718
|
4.6
|
41.5
|
1.0
|
CA
|
D:GLY26
|
4.7
|
37.1
|
1.0
|
CB
|
D:ASP117
|
4.7
|
38.2
|
1.0
|
P
|
D:PO4190
|
4.7
|
46.0
|
0.7
|
O
|
D:HOH206
|
4.7
|
47.4
|
1.0
|
N
|
D:ASP117
|
4.7
|
33.6
|
1.0
|
O
|
D:HOH389
|
4.7
|
44.3
|
0.5
|
CA
|
D:ASP116
|
4.8
|
37.1
|
1.0
|
OG1
|
C:THR47
|
4.8
|
44.4
|
1.0
|
C
|
D:ASP116
|
4.9
|
33.3
|
1.0
|
O4
|
D:PO4190
|
4.9
|
62.1
|
0.7
|
C
|
D:VAL24
|
5.0
|
26.7
|
1.0
|
|
Magnesium binding site 5 out
of 12 in 3nrj
Go back to
Magnesium Binding Sites List in 3nrj
Magnesium binding site 5 out
of 12 in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
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 Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg189
b:43.6
occ:1.00
|
OD1
|
E:ASP116
|
2.0
|
53.9
|
1.0
|
O
|
E:HOH627
|
2.1
|
47.7
|
1.0
|
OD2
|
E:ASP23
|
2.1
|
35.3
|
1.0
|
O
|
E:ASP25
|
2.2
|
36.6
|
1.0
|
O
|
E:HOH1502
|
2.2
|
46.2
|
1.0
|
O
|
E:HOH329
|
2.3
|
43.0
|
1.0
|
CG
|
E:ASP116
|
3.0
|
44.5
|
1.0
|
CG
|
E:ASP23
|
3.1
|
52.7
|
1.0
|
C
|
E:ASP25
|
3.3
|
38.3
|
1.0
|
OD2
|
E:ASP116
|
3.4
|
45.4
|
1.0
|
OD1
|
E:ASP23
|
3.5
|
50.2
|
1.0
|
OD2
|
E:ASP120
|
4.0
|
35.6
|
1.0
|
N
|
E:ASP25
|
4.1
|
37.7
|
1.0
|
O1
|
E:PO4190
|
4.1
|
47.3
|
0.7
|
CA
|
E:ASP25
|
4.1
|
36.8
|
1.0
|
O2
|
E:PO4190
|
4.2
|
57.8
|
0.7
|
CB
|
E:ASP25
|
4.3
|
36.4
|
1.0
|
CB
|
E:ASP116
|
4.3
|
39.9
|
1.0
|
N
|
E:GLY26
|
4.4
|
42.0
|
1.0
|
CB
|
E:ASP23
|
4.4
|
46.0
|
1.0
|
CA
|
E:GLY26
|
4.5
|
33.1
|
1.0
|
O
|
E:HOH221
|
4.6
|
45.2
|
1.0
|
P
|
E:PO4190
|
4.6
|
46.1
|
0.7
|
N
|
E:ASP116
|
4.7
|
38.2
|
1.0
|
OG1
|
F:THR47
|
4.7
|
48.4
|
1.0
|
CB
|
E:ASP117
|
4.8
|
37.4
|
1.0
|
O
|
E:HOH191
|
4.8
|
50.0
|
1.0
|
C
|
E:VAL24
|
4.8
|
41.7
|
1.0
|
O3
|
E:PO4190
|
4.8
|
33.9
|
0.7
|
N
|
E:ASP117
|
4.8
|
36.0
|
1.0
|
CA
|
E:ASP116
|
4.9
|
40.0
|
1.0
|
CG2
|
E:VAL27
|
4.9
|
39.9
|
1.0
|
CG
|
E:ASP120
|
5.0
|
50.1
|
1.0
|
|
Magnesium binding site 6 out
of 12 in 3nrj
Go back to
Magnesium Binding Sites List in 3nrj
Magnesium binding site 6 out
of 12 in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
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 Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg189
b:42.5
occ:1.00
|
O
|
F:ASP25
|
1.9
|
35.5
|
1.0
|
OD1
|
F:ASP116
|
2.0
|
43.1
|
1.0
|
OD2
|
F:ASP23
|
2.0
|
46.4
|
1.0
|
O
|
F:HOH959
|
2.1
|
38.9
|
1.0
|
O
|
F:HOH1546
|
2.1
|
36.2
|
1.0
|
O
|
F:HOH383
|
2.1
|
42.3
|
1.0
|
CG
|
F:ASP116
|
3.0
|
42.3
|
1.0
|
CG
|
F:ASP23
|
3.0
|
47.8
|
1.0
|
C
|
F:ASP25
|
3.1
|
37.1
|
1.0
|
OD2
|
F:ASP116
|
3.4
|
45.7
|
1.0
|
OD1
|
F:ASP23
|
3.4
|
41.1
|
1.0
|
CA
|
F:ASP25
|
3.9
|
34.7
|
1.0
|
N
|
F:ASP25
|
3.9
|
33.7
|
1.0
|
OD2
|
F:ASP120
|
4.0
|
42.3
|
1.0
|
CB
|
F:ASP25
|
4.2
|
32.8
|
1.0
|
N
|
F:GLY26
|
4.2
|
38.2
|
1.0
|
O
|
F:HOH606
|
4.2
|
46.5
|
1.0
|
O1
|
F:PO4190
|
4.3
|
60.5
|
0.7
|
CB
|
F:ASP116
|
4.3
|
33.6
|
1.0
|
CB
|
F:ASP23
|
4.4
|
42.9
|
1.0
|
O3
|
F:PO4190
|
4.5
|
58.6
|
0.7
|
CA
|
F:GLY26
|
4.5
|
32.3
|
1.0
|
O
|
F:HOH202
|
4.6
|
46.3
|
1.0
|
C
|
F:VAL24
|
4.7
|
34.0
|
1.0
|
N
|
F:ASP116
|
4.8
|
35.5
|
1.0
|
P
|
F:PO4190
|
4.8
|
43.2
|
0.7
|
OG1
|
G:THR47
|
4.9
|
43.7
|
1.0
|
N
|
F:ASP117
|
4.9
|
40.2
|
1.0
|
CB
|
F:ASP117
|
4.9
|
43.9
|
1.0
|
CG2
|
F:VAL27
|
4.9
|
33.7
|
1.0
|
CA
|
F:ASP116
|
4.9
|
34.8
|
1.0
|
O4
|
F:PO4190
|
4.9
|
49.8
|
0.7
|
N
|
F:VAL27
|
4.9
|
32.6
|
1.0
|
C
|
F:GLY26
|
5.0
|
32.6
|
1.0
|
|
Magnesium binding site 7 out
of 12 in 3nrj
Go back to
Magnesium Binding Sites List in 3nrj
Magnesium binding site 7 out
of 12 in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
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 Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg190
b:43.2
occ:1.00
|
OD2
|
G:ASP23
|
1.9
|
40.2
|
1.0
|
OD1
|
G:ASP116
|
2.0
|
44.5
|
1.0
|
O
|
G:HOH1126
|
2.0
|
40.6
|
1.0
|
O
|
G:HOH294
|
2.1
|
48.0
|
1.0
|
O
|
G:HOH929
|
2.1
|
52.3
|
1.0
|
O
|
G:ASP25
|
2.2
|
39.1
|
1.0
|
CG
|
G:ASP23
|
2.9
|
39.1
|
1.0
|
CG
|
G:ASP116
|
3.2
|
44.4
|
1.0
|
OD1
|
G:ASP23
|
3.2
|
43.9
|
1.0
|
C
|
G:ASP25
|
3.4
|
43.3
|
1.0
|
OD2
|
G:ASP116
|
3.7
|
46.1
|
1.0
|
OD2
|
G:ASP120
|
3.8
|
40.0
|
1.0
|
O2
|
G:PO4191
|
3.9
|
59.8
|
0.7
|
CA
|
G:ASP25
|
4.2
|
35.3
|
1.0
|
CB
|
G:ASP23
|
4.2
|
38.4
|
1.0
|
N
|
G:ASP25
|
4.2
|
36.4
|
1.0
|
O1
|
G:PO4191
|
4.3
|
64.9
|
0.7
|
O
|
G:HOH306
|
4.3
|
69.5
|
1.0
|
CB
|
G:ASP116
|
4.4
|
39.2
|
1.0
|
CB
|
G:ASP25
|
4.4
|
36.4
|
1.0
|
O
|
G:HOH332
|
4.5
|
48.8
|
1.0
|
N
|
G:GLY26
|
4.5
|
37.6
|
1.0
|
N
|
G:ASP116
|
4.6
|
44.6
|
1.0
|
P
|
G:PO4191
|
4.6
|
45.3
|
0.7
|
N
|
G:ASP117
|
4.6
|
35.8
|
1.0
|
O
|
G:HOH605
|
4.6
|
42.5
|
1.0
|
CB
|
G:ASP117
|
4.7
|
37.9
|
1.0
|
CA
|
G:GLY26
|
4.7
|
42.6
|
1.0
|
CG
|
G:ASP120
|
4.7
|
43.4
|
1.0
|
CA
|
G:ASP116
|
4.8
|
41.6
|
1.0
|
OD1
|
G:ASP120
|
4.9
|
40.4
|
1.0
|
O4
|
G:PO4191
|
4.9
|
38.0
|
0.7
|
C
|
G:ASP116
|
4.9
|
36.7
|
1.0
|
CG2
|
G:VAL27
|
4.9
|
39.6
|
1.0
|
C
|
G:VAL24
|
5.0
|
37.0
|
1.0
|
OG1
|
I:THR47
|
5.0
|
41.2
|
1.0
|
|
Magnesium binding site 8 out
of 12 in 3nrj
Go back to
Magnesium Binding Sites List in 3nrj
Magnesium binding site 8 out
of 12 in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
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 Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg188
b:35.8
occ:1.00
|
OD2
|
H:ASP23
|
1.9
|
39.6
|
1.0
|
O
|
H:HOH808
|
2.0
|
42.6
|
1.0
|
OD1
|
H:ASP116
|
2.0
|
38.7
|
1.0
|
O
|
H:HOH434
|
2.1
|
36.3
|
1.0
|
O
|
H:ASP25
|
2.1
|
38.3
|
1.0
|
O
|
H:HOH699
|
2.1
|
36.8
|
1.0
|
CG
|
H:ASP23
|
2.9
|
42.3
|
1.0
|
CG
|
H:ASP116
|
3.1
|
37.4
|
1.0
|
C
|
H:ASP25
|
3.3
|
34.7
|
1.0
|
OD1
|
H:ASP23
|
3.3
|
45.5
|
1.0
|
OD2
|
H:ASP116
|
3.4
|
39.9
|
1.0
|
OD2
|
H:ASP120
|
3.9
|
34.7
|
1.0
|
CA
|
H:ASP25
|
4.1
|
40.1
|
1.0
|
N
|
H:ASP25
|
4.1
|
34.4
|
1.0
|
O
|
H:HOH221
|
4.2
|
60.8
|
1.0
|
O2
|
H:PO4189
|
4.2
|
38.2
|
0.7
|
CB
|
H:ASP23
|
4.3
|
32.1
|
1.0
|
CB
|
H:ASP25
|
4.3
|
35.5
|
1.0
|
N
|
H:GLY26
|
4.3
|
41.0
|
1.0
|
O3
|
H:PO4189
|
4.3
|
49.6
|
0.7
|
CB
|
H:ASP116
|
4.3
|
26.2
|
1.0
|
O
|
H:HOH307
|
4.4
|
42.3
|
1.0
|
CA
|
H:GLY26
|
4.5
|
33.6
|
1.0
|
N
|
H:ASP116
|
4.5
|
35.4
|
1.0
|
O
|
H:HOH198
|
4.6
|
35.9
|
1.0
|
N
|
H:ASP117
|
4.8
|
32.5
|
1.0
|
CB
|
H:ASP117
|
4.8
|
31.6
|
1.0
|
P
|
H:PO4189
|
4.8
|
41.5
|
0.7
|
C
|
H:VAL24
|
4.8
|
36.1
|
1.0
|
CA
|
H:ASP116
|
4.8
|
29.9
|
1.0
|
CG
|
H:ASP120
|
4.9
|
39.9
|
1.0
|
CG2
|
H:VAL27
|
4.9
|
24.1
|
1.0
|
O1
|
H:PO4189
|
5.0
|
48.1
|
0.7
|
C
|
H:GLY26
|
5.0
|
39.4
|
1.0
|
N
|
H:VAL27
|
5.0
|
29.8
|
1.0
|
C
|
H:ASP116
|
5.0
|
35.4
|
1.0
|
|
Magnesium binding site 9 out
of 12 in 3nrj
Go back to
Magnesium Binding Sites List in 3nrj
Magnesium binding site 9 out
of 12 in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
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 Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg188
b:55.3
occ:1.00
|
OD1
|
I:ASP116
|
2.0
|
49.2
|
1.0
|
O
|
I:ASP25
|
2.0
|
43.1
|
1.0
|
O
|
I:HOH1036
|
2.0
|
48.4
|
1.0
|
O
|
I:HOH1141
|
2.2
|
25.9
|
0.5
|
OD2
|
I:ASP23
|
2.2
|
54.8
|
1.0
|
O
|
I:HOH1140
|
2.3
|
48.9
|
1.0
|
CG
|
I:ASP116
|
3.0
|
47.9
|
1.0
|
C
|
I:ASP25
|
3.2
|
44.3
|
1.0
|
CG
|
I:ASP23
|
3.2
|
45.9
|
1.0
|
OD2
|
I:ASP116
|
3.3
|
45.2
|
1.0
|
OD1
|
I:ASP23
|
3.5
|
46.3
|
1.0
|
CA
|
I:ASP25
|
4.0
|
42.6
|
1.0
|
O2
|
I:PO4189
|
4.0
|
56.9
|
0.7
|
CB
|
I:ASP25
|
4.1
|
36.4
|
1.0
|
N
|
I:ASP25
|
4.1
|
41.9
|
1.0
|
N
|
I:GLY26
|
4.2
|
38.7
|
1.0
|
OD2
|
I:ASP120
|
4.3
|
44.6
|
1.0
|
O1
|
I:PO4189
|
4.3
|
44.7
|
0.7
|
CB
|
I:ASP116
|
4.3
|
43.7
|
1.0
|
CA
|
I:GLY26
|
4.5
|
39.4
|
1.0
|
O
|
I:HOH506
|
4.5
|
51.1
|
1.0
|
O
|
I:HOH198
|
4.5
|
53.9
|
1.0
|
CB
|
I:ASP23
|
4.5
|
45.8
|
1.0
|
OG1
|
E:THR47
|
4.7
|
48.6
|
1.0
|
P
|
I:PO4189
|
4.7
|
43.3
|
0.7
|
CB
|
I:ASP117
|
4.7
|
48.0
|
1.0
|
N
|
I:ASP116
|
4.9
|
40.7
|
1.0
|
N
|
I:ASP117
|
4.9
|
42.8
|
1.0
|
C
|
I:VAL24
|
4.9
|
42.5
|
1.0
|
CA
|
I:ASP116
|
5.0
|
41.9
|
1.0
|
|
Magnesium binding site 10 out
of 12 in 3nrj
Go back to
Magnesium Binding Sites List in 3nrj
Magnesium binding site 10 out
of 12 in the Crystal Structure of Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium
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 Probable Yrbi Family Phosphatase From Pseudomonas Syringae Pv.Phaseolica 1448A Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg188
b:53.6
occ:1.00
|
O
|
J:HOH194
|
1.9
|
55.7
|
1.0
|
OD2
|
J:ASP23
|
2.1
|
51.7
|
1.0
|
O
|
J:HOH914
|
2.1
|
39.3
|
1.0
|
O
|
J:HOH761
|
2.1
|
48.5
|
1.0
|
OD1
|
J:ASP116
|
2.1
|
50.7
|
1.0
|
O
|
J:ASP25
|
2.2
|
45.1
|
1.0
|
CG
|
J:ASP23
|
3.1
|
49.2
|
1.0
|
CG
|
J:ASP116
|
3.2
|
47.8
|
1.0
|
C
|
J:ASP25
|
3.3
|
41.6
|
1.0
|
OD1
|
J:ASP23
|
3.5
|
45.7
|
1.0
|
OD2
|
J:ASP116
|
3.7
|
54.2
|
1.0
|
O
|
J:HOH205
|
3.8
|
66.8
|
1.0
|
O2
|
J:PO4189
|
3.9
|
56.1
|
0.7
|
OD2
|
J:ASP120
|
4.0
|
44.8
|
1.0
|
CA
|
J:ASP25
|
4.1
|
44.1
|
1.0
|
CB
|
J:ASP25
|
4.2
|
41.9
|
1.0
|
N
|
J:ASP25
|
4.2
|
41.8
|
1.0
|
O1
|
J:PO4189
|
4.3
|
61.9
|
0.7
|
N
|
J:GLY26
|
4.4
|
43.6
|
1.0
|
O
|
J:HOH198
|
4.4
|
58.2
|
1.0
|
CB
|
J:ASP23
|
4.4
|
43.8
|
1.0
|
CB
|
J:ASP116
|
4.5
|
47.5
|
1.0
|
CB
|
J:ASP117
|
4.6
|
54.1
|
1.0
|
P
|
J:PO4189
|
4.6
|
55.7
|
0.7
|
N
|
J:ASP117
|
4.6
|
47.1
|
1.0
|
CA
|
J:GLY26
|
4.6
|
40.7
|
1.0
|
O
|
J:HOH281
|
4.7
|
55.0
|
1.0
|
N
|
J:ASP116
|
4.8
|
45.2
|
1.0
|
O4
|
J:PO4189
|
4.9
|
57.8
|
0.7
|
CG
|
J:ASP120
|
4.9
|
53.7
|
1.0
|
CA
|
J:ASP116
|
5.0
|
43.6
|
1.0
|
OG1
|
L:THR47
|
5.0
|
43.9
|
1.0
|
C
|
J:ASP116
|
5.0
|
49.8
|
1.0
|
C
|
J:VAL24
|
5.0
|
41.0
|
1.0
|
|
Reference:
Y.Patskovsky,
U.Ramagopal,
R.Toro,
J.Freeman,
J.M.Sauder,
S.K.Burley,
S.C.Almo.
Crystal Structure of Had Family Hydrolase From Pseudomonas Syringae Pv.Phaseolica 1448A To Be Published.
Page generated: Thu Aug 15 08:06:30 2024
|