Magnesium in PDB 7ssi: Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer State
Enzymatic activity of Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer State
All present enzymatic activity of Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer State:
2.7.13.3;
Protein crystallography data
The structure of Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer State, PDB code: 7ssi
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)
|
34.41 /
3.41
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.067,
115.634,
91.374,
90,
116.74,
90
|
R / Rfree (%)
|
25.2 /
28.3
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer State
(pdb code 7ssi). 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-Q10A Complex in the Phosphotransfer State, PDB code: 7ssi:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 7ssi
Go back to
Magnesium Binding Sites List in 7ssi
Magnesium binding site 1 out
of 6 in the Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer 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-Q10A Complex in the Phosphotransfer State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:131.2
occ:1.00
|
O2B
|
A:ACP401
|
2.1
|
159.7
|
1.0
|
OD1
|
A:ASN293
|
2.1
|
143.5
|
1.0
|
OE2
|
A:GLU289
|
2.3
|
144.4
|
1.0
|
O3G
|
A:ACP401
|
2.3
|
159.4
|
1.0
|
O1A
|
A:ACP401
|
2.3
|
158.4
|
1.0
|
O2G
|
A:ACP401
|
3.0
|
159.2
|
1.0
|
PG
|
A:ACP401
|
3.1
|
159.4
|
1.0
|
PB
|
A:ACP401
|
3.1
|
159.6
|
1.0
|
CG
|
A:ASN293
|
3.2
|
142.2
|
1.0
|
CD
|
A:GLU289
|
3.3
|
140.5
|
1.0
|
O3A
|
A:ACP401
|
3.3
|
159.0
|
1.0
|
PA
|
A:ACP401
|
3.4
|
158.3
|
1.0
|
C3B
|
A:ACP401
|
3.5
|
159.5
|
1.0
|
ND2
|
A:ASN293
|
3.7
|
142.3
|
1.0
|
OE1
|
A:GLU289
|
3.7
|
142.4
|
1.0
|
NZ
|
A:LYS296
|
4.0
|
164.1
|
1.0
|
CE
|
A:LYS296
|
4.1
|
162.4
|
1.0
|
NE2
|
A:HIS297
|
4.1
|
159.2
|
1.0
|
O5'
|
A:ACP401
|
4.3
|
157.7
|
1.0
|
O1B
|
A:ACP401
|
4.4
|
159.7
|
1.0
|
O1G
|
A:ACP401
|
4.5
|
159.5
|
1.0
|
CA
|
A:GLY336
|
4.5
|
130.5
|
1.0
|
O2A
|
A:ACP401
|
4.5
|
158.2
|
1.0
|
CB
|
A:ASN293
|
4.5
|
139.4
|
1.0
|
N
|
A:GLY336
|
4.5
|
132.2
|
1.0
|
CG
|
A:GLU289
|
4.6
|
130.3
|
1.0
|
CA
|
A:ASN293
|
4.8
|
138.7
|
1.0
|
CD2
|
A:HIS297
|
4.8
|
158.0
|
1.0
|
N
|
A:ASN293
|
5.0
|
136.7
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 7ssi
Go back to
Magnesium Binding Sites List in 7ssi
Magnesium binding site 2 out
of 6 in the Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer 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-Q10A Complex in the Phosphotransfer State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:300.0
occ:1.00
|
O
|
B:HOH501
|
1.9
|
99.4
|
1.0
|
O1A
|
B:ACP401
|
2.1
|
126.4
|
1.0
|
O2B
|
B:ACP401
|
2.1
|
126.3
|
1.0
|
OD1
|
B:ASN293
|
2.2
|
120.2
|
1.0
|
OE2
|
B:GLU289
|
2.2
|
134.3
|
1.0
|
O3G
|
B:ACP401
|
2.2
|
125.3
|
1.0
|
PB
|
B:ACP401
|
3.1
|
126.3
|
1.0
|
PG
|
B:ACP401
|
3.1
|
125.5
|
1.0
|
PA
|
B:ACP401
|
3.2
|
126.6
|
1.0
|
CG
|
B:ASN293
|
3.2
|
118.9
|
1.0
|
O2G
|
B:ACP401
|
3.2
|
125.5
|
1.0
|
O3A
|
B:ACP401
|
3.2
|
126.5
|
1.0
|
CD
|
B:GLU289
|
3.3
|
130.8
|
1.0
|
ND2
|
B:ASN293
|
3.6
|
119.1
|
1.0
|
C3B
|
B:ACP401
|
3.6
|
126.0
|
1.0
|
OE1
|
B:GLU289
|
3.8
|
133.2
|
1.0
|
O5'
|
B:ACP401
|
4.1
|
127.8
|
1.0
|
NE2
|
B:HIS297
|
4.2
|
135.2
|
1.0
|
CA
|
B:GLY336
|
4.3
|
124.8
|
1.0
|
NZ
|
B:LYS296
|
4.3
|
142.9
|
1.0
|
O2A
|
B:ACP401
|
4.3
|
126.3
|
1.0
|
N
|
B:GLY336
|
4.3
|
126.3
|
1.0
|
CE
|
B:LYS296
|
4.3
|
140.7
|
1.0
|
O1B
|
B:ACP401
|
4.4
|
126.5
|
1.0
|
O1G
|
B:ACP401
|
4.5
|
125.3
|
1.0
|
CB
|
B:ASN293
|
4.5
|
116.8
|
1.0
|
CG
|
B:GLU289
|
4.5
|
120.5
|
1.0
|
CA
|
B:ASN293
|
4.8
|
116.2
|
1.0
|
CD2
|
B:HIS297
|
4.9
|
134.1
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 7ssi
Go back to
Magnesium Binding Sites List in 7ssi
Magnesium binding site 3 out
of 6 in the Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer 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-Q10A Complex in the Phosphotransfer State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg201
b:81.4
occ:1.00
|
O
|
C:HOH303
|
2.7
|
37.3
|
1.0
|
OD2
|
C:ASP54
|
2.9
|
106.6
|
1.0
|
O
|
C:GLU56
|
3.0
|
112.6
|
1.0
|
OD1
|
C:ASP9
|
3.2
|
110.8
|
1.0
|
NZ
|
C:LYS102
|
3.3
|
99.4
|
1.0
|
O
|
C:HOH302
|
3.3
|
38.9
|
1.0
|
OD1
|
C:ASP54
|
3.4
|
105.3
|
1.0
|
CG
|
C:ASP54
|
3.5
|
105.4
|
1.0
|
C
|
C:GLU56
|
4.0
|
112.4
|
1.0
|
OE2
|
C:GLU8
|
4.2
|
109.5
|
1.0
|
CB
|
C:GLU56
|
4.2
|
115.1
|
1.0
|
CG
|
C:ASP9
|
4.2
|
110.4
|
1.0
|
NE2
|
B:GLN193
|
4.3
|
117.1
|
1.0
|
OD2
|
C:ASP9
|
4.4
|
111.7
|
1.0
|
CA
|
C:GLU56
|
4.4
|
111.9
|
1.0
|
N
|
C:GLU56
|
4.6
|
110.4
|
1.0
|
CE
|
C:LYS102
|
4.6
|
96.1
|
1.0
|
CD
|
B:GLN193
|
4.6
|
115.8
|
1.0
|
OE1
|
C:GLU8
|
4.9
|
109.5
|
1.0
|
OE1
|
B:GLN193
|
4.9
|
118.7
|
1.0
|
CD
|
C:GLU8
|
5.0
|
109.2
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 7ssi
Go back to
Magnesium Binding Sites List in 7ssi
Magnesium binding site 4 out
of 6 in the Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer 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-Q10A Complex in the Phosphotransfer State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg402
b:300.0
occ:1.00
|
O
|
D:HOH501
|
1.9
|
82.5
|
1.0
|
O1A
|
D:ACP401
|
2.1
|
168.1
|
1.0
|
O2B
|
D:ACP401
|
2.1
|
168.2
|
1.0
|
OD1
|
D:ASN293
|
2.1
|
135.6
|
1.0
|
OE2
|
D:GLU289
|
2.2
|
142.7
|
1.0
|
O3G
|
D:ACP401
|
2.2
|
168.2
|
1.0
|
PB
|
D:ACP401
|
3.1
|
168.1
|
1.0
|
PG
|
D:ACP401
|
3.2
|
168.1
|
1.0
|
CG
|
D:ASN293
|
3.2
|
134.6
|
1.0
|
PA
|
D:ACP401
|
3.2
|
168.0
|
1.0
|
O2G
|
D:ACP401
|
3.2
|
168.0
|
1.0
|
O3A
|
D:ACP401
|
3.2
|
168.1
|
1.0
|
CD
|
D:GLU289
|
3.3
|
138.5
|
1.0
|
ND2
|
D:ASN293
|
3.6
|
134.5
|
1.0
|
C3B
|
D:ACP401
|
3.6
|
168.0
|
1.0
|
OE1
|
D:GLU289
|
3.8
|
139.9
|
1.0
|
NE2
|
D:HIS297
|
4.1
|
157.4
|
1.0
|
O5'
|
D:ACP401
|
4.2
|
167.3
|
1.0
|
NZ
|
D:LYS296
|
4.2
|
165.9
|
1.0
|
CE
|
D:LYS296
|
4.3
|
163.8
|
1.0
|
O2A
|
D:ACP401
|
4.3
|
168.0
|
1.0
|
CA
|
D:GLY336
|
4.4
|
140.9
|
1.0
|
N
|
D:GLY336
|
4.4
|
142.4
|
1.0
|
O1B
|
D:ACP401
|
4.4
|
168.0
|
1.0
|
CB
|
D:ASN293
|
4.5
|
132.7
|
1.0
|
O1G
|
D:ACP401
|
4.5
|
168.1
|
1.0
|
CG
|
D:GLU289
|
4.6
|
128.3
|
1.0
|
CA
|
D:ASN293
|
4.8
|
133.4
|
1.0
|
CD2
|
D:HIS297
|
4.8
|
156.3
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 7ssi
Go back to
Magnesium Binding Sites List in 7ssi
Magnesium binding site 5 out
of 6 in the Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer 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-Q10A Complex in the Phosphotransfer State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg402
b:292.9
occ:1.00
|
O
|
E:HOH501
|
1.9
|
44.7
|
1.0
|
O1A
|
E:ACP401
|
2.0
|
118.6
|
1.0
|
O2B
|
E:ACP401
|
2.1
|
118.7
|
1.0
|
OD1
|
E:ASN293
|
2.1
|
113.6
|
1.0
|
OE2
|
E:GLU289
|
2.2
|
125.5
|
1.0
|
O3G
|
E:ACP401
|
2.2
|
118.0
|
1.0
|
PB
|
E:ACP401
|
3.1
|
118.7
|
1.0
|
PG
|
E:ACP401
|
3.1
|
118.3
|
1.0
|
PA
|
E:ACP401
|
3.2
|
118.5
|
1.0
|
CG
|
E:ASN293
|
3.2
|
112.7
|
1.0
|
O2G
|
E:ACP401
|
3.2
|
118.4
|
1.0
|
O3A
|
E:ACP401
|
3.2
|
118.5
|
1.0
|
CD
|
E:GLU289
|
3.3
|
121.7
|
1.0
|
ND2
|
E:ASN293
|
3.5
|
112.0
|
1.0
|
C3B
|
E:ACP401
|
3.6
|
118.5
|
1.0
|
OE1
|
E:GLU289
|
3.8
|
123.2
|
1.0
|
O5'
|
E:ACP401
|
4.1
|
119.3
|
1.0
|
NE2
|
E:HIS297
|
4.2
|
131.7
|
1.0
|
CA
|
E:GLY336
|
4.3
|
130.3
|
1.0
|
O2A
|
E:ACP401
|
4.3
|
118.0
|
1.0
|
NZ
|
E:LYS296
|
4.3
|
139.1
|
1.0
|
N
|
E:GLY336
|
4.3
|
131.6
|
1.0
|
CE
|
E:LYS296
|
4.3
|
137.0
|
1.0
|
O1B
|
E:ACP401
|
4.4
|
118.8
|
1.0
|
O1G
|
E:ACP401
|
4.5
|
118.2
|
1.0
|
CB
|
E:ASN293
|
4.5
|
112.2
|
1.0
|
CG
|
E:GLU289
|
4.5
|
112.9
|
1.0
|
CA
|
E:ASN293
|
4.8
|
112.5
|
1.0
|
CD2
|
E:HIS297
|
4.9
|
130.3
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 7ssi
Go back to
Magnesium Binding Sites List in 7ssi
Magnesium binding site 6 out
of 6 in the Crystal Structure of the Desk:Desr-Q10A Complex in the Phosphotransfer 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-Q10A Complex in the Phosphotransfer State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg201
b:73.5
occ:1.00
|
OD1
|
F:ASP54
|
3.0
|
111.9
|
1.0
|
OD2
|
F:ASP54
|
3.6
|
114.0
|
1.0
|
NZ
|
F:LYS102
|
3.6
|
100.1
|
1.0
|
CG
|
F:ASP54
|
3.7
|
112.0
|
1.0
|
O
|
F:GLU56
|
3.8
|
112.3
|
1.0
|
CB
|
F:GLU56
|
3.8
|
116.3
|
1.0
|
N
|
F:GLU56
|
4.0
|
110.9
|
1.0
|
CE
|
F:LYS102
|
4.1
|
98.0
|
1.0
|
CA
|
F:GLU56
|
4.3
|
112.3
|
1.0
|
OE1
|
E:GLN193
|
4.3
|
116.0
|
1.0
|
CG
|
F:GLU56
|
4.5
|
123.8
|
1.0
|
C
|
F:GLU56
|
4.5
|
112.2
|
1.0
|
NE2
|
E:GLN193
|
4.8
|
111.2
|
1.0
|
CD
|
E:GLN193
|
4.9
|
112.0
|
1.0
|
NH2
|
F:ARG84
|
4.9
|
134.8
|
1.0
|
OD1
|
F:ASP9
|
4.9
|
124.1
|
1.0
|
N
|
F:ILE55
|
5.0
|
108.6
|
1.0
|
OG1
|
F:THR81
|
5.0
|
101.4
|
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
|