Magnesium in PDB 7ssj: Crystal Structure of the Desk-Desr Complex in the Phosphatase State
Enzymatic activity of Crystal Structure of the Desk-Desr Complex in the Phosphatase State
All present enzymatic activity of Crystal Structure of the Desk-Desr Complex in the Phosphatase State:
2.7.13.3;
Protein crystallography data
The structure of Crystal Structure of the Desk-Desr Complex in the Phosphatase State, PDB code: 7ssj
was solved by
F.Trajtenberg,
A.Buschiazzo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
82.00 /
2.52
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.691,
94.691,
240.85,
90,
90,
120
|
R / Rfree (%)
|
25.3 /
28.9
|
Other elements in 7ssj:
The structure of Crystal Structure of the Desk-Desr Complex in the Phosphatase State also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State
(pdb code 7ssj). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Crystal Structure of the Desk-Desr Complex in the Phosphatase State, PDB code: 7ssj:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 7ssj
Go back to
Magnesium Binding Sites List in 7ssj
Magnesium binding site 1 out
of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State
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 the Desk-Desr Complex in the Phosphatase State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:84.8
occ:1.00
|
O3G
|
A:ACP401
|
2.0
|
95.4
|
1.0
|
OE2
|
A:GLU289
|
2.0
|
88.0
|
1.0
|
O1A
|
A:ACP401
|
2.1
|
92.1
|
1.0
|
OD1
|
A:ASN293
|
2.1
|
85.4
|
1.0
|
O2B
|
A:ACP401
|
2.1
|
96.8
|
1.0
|
O
|
A:HOH503
|
2.2
|
104.5
|
1.0
|
CG
|
A:ASN293
|
3.1
|
85.0
|
1.0
|
PB
|
A:ACP401
|
3.2
|
96.9
|
1.0
|
PA
|
A:ACP401
|
3.2
|
92.5
|
1.0
|
CD
|
A:GLU289
|
3.2
|
87.1
|
1.0
|
O3A
|
A:ACP401
|
3.3
|
94.9
|
1.0
|
PG
|
A:ACP401
|
3.4
|
96.5
|
1.0
|
ND2
|
A:ASN293
|
3.6
|
85.3
|
1.0
|
C3B
|
A:ACP401
|
3.7
|
97.2
|
1.0
|
OE1
|
A:GLU289
|
3.8
|
89.5
|
1.0
|
O2G
|
A:ACP401
|
4.1
|
97.1
|
1.0
|
O5'
|
A:ACP401
|
4.2
|
91.8
|
1.0
|
CA
|
A:GLY336
|
4.3
|
94.5
|
1.0
|
O2A
|
A:ACP401
|
4.3
|
91.9
|
1.0
|
NZ
|
A:LYS296
|
4.3
|
105.0
|
1.0
|
NE2
|
A:HIS297
|
4.3
|
97.6
|
1.0
|
N
|
A:GLY336
|
4.4
|
97.4
|
1.0
|
CG
|
A:GLU289
|
4.4
|
81.8
|
1.0
|
O1G
|
A:ACP401
|
4.5
|
96.6
|
1.0
|
CB
|
A:ASN293
|
4.5
|
84.1
|
1.0
|
O1B
|
A:ACP401
|
4.5
|
97.7
|
1.0
|
CE
|
A:LYS296
|
4.5
|
104.7
|
1.0
|
CA
|
A:ASN293
|
4.8
|
84.1
|
1.0
|
O
|
A:GLU289
|
4.9
|
78.2
|
1.0
|
N
|
A:ASN293
|
4.9
|
83.4
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 7ssj
Go back to
Magnesium Binding Sites List in 7ssj
Magnesium binding site 2 out
of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State
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 the Desk-Desr Complex in the Phosphatase State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg201
b:51.6
occ:1.00
|
OD2
|
B:ASP54
|
2.0
|
59.4
|
1.0
|
O
|
B:HOH303
|
2.1
|
70.7
|
1.0
|
O
|
A:HOH501
|
2.1
|
62.8
|
1.0
|
F3
|
B:BEF202
|
2.1
|
73.3
|
1.0
|
OD1
|
B:ASP9
|
2.1
|
68.1
|
1.0
|
O
|
B:GLU56
|
2.2
|
70.9
|
1.0
|
CG
|
B:ASP54
|
3.0
|
61.1
|
1.0
|
BE
|
B:BEF202
|
3.1
|
72.6
|
1.0
|
CG
|
B:ASP9
|
3.2
|
66.1
|
1.0
|
OD1
|
B:ASP54
|
3.3
|
62.7
|
1.0
|
C
|
B:GLU56
|
3.3
|
70.4
|
1.0
|
OD2
|
B:ASP9
|
3.6
|
67.3
|
1.0
|
OE2
|
B:GLU8
|
3.8
|
88.3
|
1.0
|
OE1
|
A:GLN193
|
3.9
|
72.0
|
1.0
|
NZ
|
B:LYS102
|
4.0
|
78.5
|
1.0
|
CB
|
B:GLU56
|
4.1
|
71.8
|
1.0
|
CA
|
B:GLU56
|
4.1
|
69.4
|
1.0
|
F2
|
B:BEF202
|
4.1
|
72.0
|
1.0
|
F1
|
B:BEF202
|
4.3
|
73.6
|
1.0
|
CB
|
B:ASP54
|
4.3
|
60.8
|
1.0
|
N
|
B:GLU56
|
4.3
|
68.3
|
1.0
|
N
|
B:MET57
|
4.4
|
70.8
|
1.0
|
CB
|
B:ASP9
|
4.4
|
61.4
|
1.0
|
CD
|
A:GLN193
|
4.5
|
71.8
|
1.0
|
NE2
|
A:GLN193
|
4.5
|
73.3
|
1.0
|
CG
|
B:MET57
|
4.6
|
69.5
|
1.0
|
N
|
B:ASP9
|
4.6
|
60.0
|
1.0
|
CD
|
B:GLU8
|
4.6
|
82.6
|
1.0
|
CA
|
B:MET57
|
4.7
|
71.7
|
1.0
|
CG
|
B:GLN10
|
4.7
|
63.1
|
1.0
|
OE1
|
B:GLU8
|
4.9
|
86.4
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 7ssj
Go back to
Magnesium Binding Sites List in 7ssj
Magnesium binding site 3 out
of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State
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 the Desk-Desr Complex in the Phosphatase State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg402
b:188.1
occ:1.00
|
O
|
C:HOH502
|
2.1
|
117.9
|
1.0
|
O3G
|
C:ACP401
|
2.1
|
155.9
|
1.0
|
OD1
|
C:ASN293
|
2.1
|
151.9
|
1.0
|
O1A
|
C:ACP401
|
2.1
|
154.3
|
1.0
|
OE2
|
C:GLU289
|
2.1
|
143.8
|
1.0
|
O2B
|
C:ACP401
|
2.1
|
157.5
|
1.0
|
CG
|
C:ASN293
|
3.1
|
150.4
|
1.0
|
PB
|
C:ACP401
|
3.2
|
156.5
|
1.0
|
PA
|
C:ACP401
|
3.3
|
154.1
|
1.0
|
PG
|
C:ACP401
|
3.3
|
156.4
|
1.0
|
CD
|
C:GLU289
|
3.3
|
141.9
|
1.0
|
O3A
|
C:ACP401
|
3.4
|
154.9
|
1.0
|
ND2
|
C:ASN293
|
3.5
|
149.0
|
1.0
|
O2G
|
C:ACP401
|
3.7
|
158.0
|
1.0
|
C3B
|
C:ACP401
|
3.8
|
156.5
|
1.0
|
OE1
|
C:GLU289
|
3.9
|
142.2
|
1.0
|
O5'
|
C:ACP401
|
4.2
|
154.2
|
1.0
|
CA
|
C:GLY336
|
4.4
|
128.6
|
1.0
|
CB
|
C:ASN293
|
4.4
|
149.3
|
1.0
|
O2A
|
C:ACP401
|
4.4
|
152.8
|
1.0
|
CG
|
C:GLU289
|
4.5
|
137.3
|
1.0
|
NE2
|
C:HIS297
|
4.5
|
164.0
|
1.0
|
N
|
C:GLY336
|
4.5
|
130.1
|
1.0
|
O1B
|
C:ACP401
|
4.5
|
157.1
|
1.0
|
O1G
|
C:ACP401
|
4.5
|
155.3
|
1.0
|
NZ
|
C:LYS296
|
4.6
|
171.9
|
1.0
|
CA
|
C:ASN293
|
4.6
|
150.1
|
1.0
|
CE
|
C:LYS296
|
4.7
|
171.1
|
1.0
|
N
|
C:ASN293
|
4.9
|
149.6
|
1.0
|
O
|
C:GLU289
|
5.0
|
137.3
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 7ssj
Go back to
Magnesium Binding Sites List in 7ssj
Magnesium binding site 4 out
of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State
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 the Desk-Desr Complex in the Phosphatase State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg402
b:90.0
occ:1.00
|
OE2
|
D:GLU289
|
2.0
|
102.2
|
1.0
|
OD1
|
D:ASN293
|
2.1
|
82.8
|
1.0
|
O
|
D:HOH502
|
2.1
|
85.7
|
1.0
|
O2B
|
D:ACP401
|
2.1
|
88.8
|
1.0
|
O3G
|
D:ACP401
|
2.1
|
89.9
|
1.0
|
O1A
|
D:ACP401
|
2.2
|
87.5
|
1.0
|
CG
|
D:ASN293
|
3.0
|
82.1
|
1.0
|
PB
|
D:ACP401
|
3.1
|
89.3
|
1.0
|
O3A
|
D:ACP401
|
3.2
|
88.9
|
1.0
|
CD
|
D:GLU289
|
3.2
|
100.5
|
1.0
|
PG
|
D:ACP401
|
3.2
|
90.6
|
1.0
|
PA
|
D:ACP401
|
3.2
|
88.1
|
1.0
|
ND2
|
D:ASN293
|
3.4
|
81.3
|
1.0
|
O2G
|
D:ACP401
|
3.5
|
91.1
|
1.0
|
C3B
|
D:ACP401
|
3.6
|
90.5
|
1.0
|
OE1
|
D:GLU289
|
3.8
|
102.5
|
1.0
|
O5'
|
D:ACP401
|
4.3
|
88.8
|
1.0
|
CA
|
D:GLY336
|
4.3
|
83.5
|
1.0
|
NE2
|
D:HIS297
|
4.3
|
98.2
|
1.0
|
NZ
|
D:LYS296
|
4.3
|
109.8
|
1.0
|
CG
|
D:GLU289
|
4.3
|
92.9
|
1.0
|
N
|
D:GLY336
|
4.4
|
86.3
|
1.0
|
O2A
|
D:ACP401
|
4.4
|
87.7
|
1.0
|
CB
|
D:ASN293
|
4.4
|
82.3
|
1.0
|
O1B
|
D:ACP401
|
4.5
|
89.6
|
1.0
|
CE
|
D:LYS296
|
4.5
|
107.3
|
1.0
|
O1G
|
D:ACP401
|
4.6
|
90.8
|
1.0
|
CA
|
D:ASN293
|
4.8
|
83.3
|
1.0
|
O
|
D:GLU289
|
4.9
|
83.6
|
1.0
|
N
|
D:ASN293
|
5.0
|
83.5
|
1.0
|
CD2
|
D:HIS297
|
5.0
|
97.2
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 7ssj
Go back to
Magnesium Binding Sites List in 7ssj
Magnesium binding site 5 out
of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State
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 the Desk-Desr Complex in the Phosphatase State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg201
b:77.6
occ:1.00
|
OD2
|
E:ASP54
|
1.9
|
67.8
|
1.0
|
O
|
E:HOH304
|
2.0
|
70.6
|
1.0
|
F3
|
E:BEF202
|
2.1
|
75.3
|
1.0
|
OD1
|
E:ASP9
|
2.1
|
75.4
|
1.0
|
O
|
C:HOH501
|
2.2
|
75.5
|
1.0
|
O
|
E:GLU56
|
2.2
|
78.8
|
1.0
|
CG
|
E:ASP54
|
2.9
|
67.8
|
1.0
|
CG
|
E:ASP9
|
3.1
|
75.4
|
1.0
|
BE
|
E:BEF202
|
3.2
|
75.6
|
1.0
|
OD1
|
E:ASP54
|
3.3
|
66.2
|
1.0
|
C
|
E:GLU56
|
3.4
|
77.9
|
1.0
|
OD2
|
E:ASP9
|
3.5
|
77.6
|
1.0
|
OE2
|
E:GLU8
|
3.8
|
89.3
|
1.0
|
NZ
|
E:LYS102
|
4.0
|
82.4
|
1.0
|
CB
|
E:GLU56
|
4.1
|
79.0
|
1.0
|
CA
|
E:GLU56
|
4.1
|
76.4
|
1.0
|
NE2
|
C:GLN193
|
4.1
|
84.4
|
1.0
|
F2
|
E:BEF202
|
4.2
|
74.8
|
1.0
|
CB
|
E:ASP54
|
4.3
|
70.4
|
1.0
|
OE1
|
C:GLN193
|
4.4
|
88.7
|
1.0
|
F1
|
E:BEF202
|
4.4
|
77.8
|
1.0
|
N
|
E:MET57
|
4.4
|
78.3
|
1.0
|
N
|
E:GLU56
|
4.4
|
74.8
|
1.0
|
CB
|
E:ASP9
|
4.4
|
70.8
|
1.0
|
CG
|
E:MET57
|
4.6
|
77.9
|
1.0
|
CD
|
C:GLN193
|
4.6
|
84.5
|
1.0
|
N
|
E:ASP9
|
4.6
|
68.5
|
1.0
|
CD
|
E:GLU8
|
4.6
|
86.7
|
1.0
|
CA
|
E:MET57
|
4.7
|
79.6
|
1.0
|
CG
|
E:GLN10
|
4.7
|
74.5
|
1.0
|
OE1
|
E:GLU8
|
4.9
|
91.0
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 7ssj
Go back to
Magnesium Binding Sites List in 7ssj
Magnesium binding site 6 out
of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State
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 the Desk-Desr Complex in the Phosphatase State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg201
b:133.6
occ:1.00
|
OD1
|
F:ASP9
|
2.0
|
111.5
|
1.0
|
F3
|
F:BEF202
|
2.1
|
123.4
|
1.0
|
O
|
F:GLU56
|
2.1
|
115.5
|
1.0
|
O
|
D:HOH503
|
2.1
|
92.4
|
1.0
|
OD2
|
F:ASP54
|
2.2
|
116.5
|
1.0
|
O
|
F:HOH301
|
2.2
|
106.1
|
1.0
|
CG
|
F:ASP9
|
2.9
|
110.7
|
1.0
|
CG
|
F:ASP54
|
3.2
|
116.1
|
1.0
|
OD2
|
F:ASP9
|
3.3
|
112.9
|
1.0
|
BE
|
F:BEF202
|
3.3
|
122.4
|
1.0
|
C
|
F:GLU56
|
3.3
|
115.1
|
1.0
|
OD1
|
F:ASP54
|
3.5
|
118.2
|
1.0
|
OE2
|
F:GLU8
|
4.1
|
112.6
|
1.0
|
F2
|
F:BEF202
|
4.1
|
122.2
|
1.0
|
CA
|
F:GLU56
|
4.2
|
114.4
|
1.0
|
CG
|
F:MET57
|
4.2
|
116.2
|
1.0
|
CB
|
F:GLU56
|
4.2
|
117.2
|
1.0
|
CB
|
F:ASP9
|
4.2
|
105.6
|
1.0
|
OE1
|
D:GLN193
|
4.3
|
100.1
|
1.0
|
NE2
|
D:GLN193
|
4.3
|
96.6
|
1.0
|
N
|
F:MET57
|
4.3
|
115.1
|
1.0
|
F1
|
F:BEF202
|
4.4
|
122.2
|
1.0
|
N
|
F:GLU56
|
4.5
|
113.2
|
1.0
|
CA
|
F:MET57
|
4.5
|
115.6
|
1.0
|
NZ
|
F:LYS102
|
4.5
|
112.4
|
1.0
|
CB
|
F:ASP54
|
4.5
|
112.1
|
1.0
|
CD
|
D:GLN193
|
4.5
|
96.9
|
1.0
|
N
|
F:ASP9
|
4.6
|
103.0
|
1.0
|
CG
|
F:GLN10
|
4.8
|
108.2
|
1.0
|
CD
|
F:GLU8
|
4.9
|
113.0
|
1.0
|
CA
|
F:ASP9
|
5.0
|
103.8
|
1.0
|
CB
|
F:MET57
|
5.0
|
115.3
|
1.0
|
|
Reference:
S.Lima,
J.Blanco,
F.Olivieri,
J.A.Imelio,
F.Carrion,
B.Alvarez,
A.Buschiazzo,
M.Marti,
F.Trajtenberg.
Molecular Basis of Unidirectional Information Transmission in Two-Component Systems: Lessons From the Desk-Desr Thermosensor To Be Published.
Page generated: Thu Oct 3 08:51:40 2024
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