Magnesium in PDB 6gs8: Crystal Structure of Smba in Complex with C-Di-Gmp
Protein crystallography data
The structure of Crystal Structure of Smba in Complex with C-Di-Gmp, PDB code: 6gs8
was solved by
B.N.Dubey,
T.Schirmer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
127.910,
87.420,
130.270,
90.00,
119.48,
90.00
|
R / Rfree (%)
|
20.9 /
26
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Smba in Complex with C-Di-Gmp
(pdb code 6gs8). 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 Smba in Complex with C-Di-Gmp, PDB code: 6gs8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6gs8
Go back to
Magnesium Binding Sites List in 6gs8
Magnesium binding site 1 out
of 6 in the Crystal Structure of Smba in Complex with C-Di-Gmp
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 Smba in Complex with C-Di-Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:39.6
occ:1.00
|
O
|
A:ASN153
|
2.3
|
56.3
|
1.0
|
O
|
A:LEU151
|
2.3
|
50.4
|
1.0
|
O
|
A:VAL156
|
2.6
|
51.0
|
1.0
|
O
|
A:HOH501
|
3.4
|
52.4
|
1.0
|
C
|
A:ASN153
|
3.5
|
55.2
|
1.0
|
C
|
A:LEU151
|
3.6
|
52.5
|
1.0
|
C
|
A:VAL156
|
3.8
|
50.1
|
1.0
|
C
|
A:ALA152
|
4.0
|
52.3
|
1.0
|
O
|
A:ALA152
|
4.0
|
53.4
|
1.0
|
CE1
|
A:PHE183
|
4.0
|
54.8
|
1.0
|
CZ
|
A:PHE183
|
4.1
|
56.0
|
1.0
|
CA
|
A:ASP154
|
4.2
|
57.5
|
1.0
|
N
|
A:ASN153
|
4.3
|
50.8
|
1.0
|
N
|
A:VAL156
|
4.3
|
54.5
|
1.0
|
CA
|
A:ALA152
|
4.3
|
53.6
|
1.0
|
N
|
A:ASP154
|
4.3
|
56.6
|
1.0
|
O
|
A:ASP154
|
4.3
|
50.8
|
1.0
|
CA
|
A:VAL156
|
4.4
|
50.5
|
1.0
|
CB
|
A:VAL156
|
4.4
|
49.6
|
1.0
|
N
|
A:ALA152
|
4.4
|
52.4
|
1.0
|
C
|
A:ASP154
|
4.4
|
53.4
|
1.0
|
CA
|
A:ASN153
|
4.5
|
52.8
|
1.0
|
CA
|
A:LEU151
|
4.7
|
52.5
|
1.0
|
N
|
A:THR157
|
4.9
|
52.3
|
1.0
|
CG1
|
A:VAL156
|
4.9
|
47.7
|
1.0
|
OD1
|
A:ASP154
|
5.0
|
58.8
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6gs8
Go back to
Magnesium Binding Sites List in 6gs8
Magnesium binding site 2 out
of 6 in the Crystal Structure of Smba in Complex with C-Di-Gmp
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 Smba in Complex with C-Di-Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg503
b:62.6
occ:1.00
|
O
|
B:ASN153
|
2.1
|
68.9
|
1.0
|
O
|
B:LEU151
|
2.2
|
68.8
|
1.0
|
O
|
B:HOH602
|
2.6
|
60.0
|
1.0
|
O
|
B:VAL156
|
2.7
|
66.8
|
1.0
|
C
|
B:ASN153
|
3.3
|
75.5
|
1.0
|
C
|
B:LEU151
|
3.4
|
68.6
|
1.0
|
C
|
B:ALA152
|
3.7
|
78.0
|
1.0
|
O
|
B:ALA152
|
3.8
|
82.2
|
1.0
|
C
|
B:VAL156
|
3.8
|
65.2
|
1.0
|
N
|
B:ASN153
|
4.0
|
76.9
|
1.0
|
CE1
|
B:PHE183
|
4.1
|
67.9
|
1.0
|
N
|
B:ASP154
|
4.1
|
79.6
|
1.0
|
CA
|
B:ALA152
|
4.1
|
77.8
|
1.0
|
N
|
B:ALA152
|
4.2
|
75.9
|
1.0
|
CA
|
B:ASP154
|
4.2
|
81.1
|
1.0
|
N
|
B:VAL156
|
4.2
|
65.7
|
1.0
|
CZ
|
B:PHE183
|
4.2
|
69.4
|
1.0
|
CB
|
B:VAL156
|
4.2
|
66.9
|
1.0
|
CA
|
B:VAL156
|
4.3
|
64.9
|
1.0
|
CA
|
B:ASN153
|
4.3
|
76.0
|
1.0
|
O
|
B:ASP154
|
4.3
|
75.2
|
1.0
|
C
|
B:ASP154
|
4.4
|
77.2
|
1.0
|
CA
|
B:LEU151
|
4.6
|
65.4
|
1.0
|
CG1
|
B:VAL156
|
4.9
|
67.9
|
1.0
|
N
|
B:THR157
|
5.0
|
62.0
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6gs8
Go back to
Magnesium Binding Sites List in 6gs8
Magnesium binding site 3 out
of 6 in the Crystal Structure of Smba in Complex with C-Di-Gmp
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 Smba in Complex with C-Di-Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg503
b:52.3
occ:1.00
|
O
|
C:ASN153
|
2.1
|
64.3
|
1.0
|
O
|
C:LEU151
|
2.2
|
59.5
|
1.0
|
O
|
C:VAL156
|
2.8
|
69.8
|
1.0
|
C
|
C:ASN153
|
3.3
|
68.3
|
1.0
|
O
|
C:HOH615
|
3.4
|
58.4
|
1.0
|
C
|
C:LEU151
|
3.4
|
62.1
|
1.0
|
C
|
C:ALA152
|
3.6
|
69.3
|
1.0
|
O
|
C:ALA152
|
3.7
|
69.3
|
1.0
|
C
|
C:VAL156
|
3.9
|
61.6
|
1.0
|
N
|
C:ASN153
|
4.0
|
64.7
|
1.0
|
CA
|
C:ALA152
|
4.0
|
71.6
|
1.0
|
CE1
|
C:PHE183
|
4.1
|
58.7
|
1.0
|
N
|
C:ALA152
|
4.1
|
66.3
|
1.0
|
N
|
C:ASP154
|
4.1
|
71.7
|
1.0
|
CZ
|
C:PHE183
|
4.2
|
61.3
|
1.0
|
CA
|
C:ASP154
|
4.2
|
73.3
|
1.0
|
CA
|
C:ASN153
|
4.3
|
65.7
|
1.0
|
N
|
C:VAL156
|
4.3
|
60.8
|
1.0
|
CB
|
C:VAL156
|
4.3
|
56.0
|
1.0
|
CA
|
C:VAL156
|
4.4
|
58.5
|
1.0
|
C
|
C:ASP154
|
4.4
|
67.7
|
1.0
|
O
|
C:ASP154
|
4.4
|
69.2
|
1.0
|
CA
|
C:LEU151
|
4.6
|
63.3
|
1.0
|
CG1
|
C:VAL156
|
4.9
|
53.7
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6gs8
Go back to
Magnesium Binding Sites List in 6gs8
Magnesium binding site 4 out
of 6 in the Crystal Structure of Smba in Complex with C-Di-Gmp
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 Smba in Complex with C-Di-Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg503
b:66.3
occ:1.00
|
O
|
D:HOH606
|
1.6
|
79.3
|
1.0
|
O
|
D:ASN153
|
2.1
|
72.6
|
1.0
|
O
|
D:LEU151
|
2.2
|
73.4
|
1.0
|
O
|
D:VAL156
|
2.7
|
57.0
|
1.0
|
C
|
D:ASN153
|
3.3
|
70.6
|
1.0
|
C
|
D:LEU151
|
3.4
|
68.2
|
1.0
|
C
|
D:ALA152
|
3.7
|
64.7
|
1.0
|
O
|
D:ALA152
|
3.8
|
65.0
|
1.0
|
C
|
D:VAL156
|
3.8
|
58.2
|
1.0
|
N
|
D:ASN153
|
4.0
|
66.0
|
1.0
|
CE1
|
D:PHE183
|
4.1
|
56.2
|
1.0
|
CA
|
D:ALA152
|
4.1
|
67.9
|
1.0
|
N
|
D:ASP154
|
4.1
|
72.6
|
1.0
|
CZ
|
D:PHE183
|
4.2
|
56.4
|
1.0
|
N
|
D:ALA152
|
4.2
|
68.3
|
1.0
|
CA
|
D:ASP154
|
4.2
|
74.4
|
1.0
|
N
|
D:VAL156
|
4.2
|
61.0
|
1.0
|
CB
|
D:VAL156
|
4.3
|
63.5
|
1.0
|
CA
|
D:ASN153
|
4.3
|
70.5
|
1.0
|
CA
|
D:VAL156
|
4.3
|
60.4
|
1.0
|
O
|
D:ASP154
|
4.4
|
70.2
|
1.0
|
C
|
D:ASP154
|
4.4
|
69.8
|
1.0
|
CA
|
D:LEU151
|
4.6
|
67.9
|
1.0
|
CG1
|
D:VAL156
|
4.9
|
63.6
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6gs8
Go back to
Magnesium Binding Sites List in 6gs8
Magnesium binding site 5 out
of 6 in the Crystal Structure of Smba in Complex with C-Di-Gmp
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 Smba in Complex with C-Di-Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg503
b:46.0
occ:1.00
|
O
|
E:LEU151
|
2.2
|
58.5
|
1.0
|
O
|
E:ASN153
|
2.2
|
49.4
|
1.0
|
O
|
E:VAL156
|
2.7
|
52.8
|
1.0
|
C
|
E:ASN153
|
3.4
|
52.4
|
1.0
|
C
|
E:LEU151
|
3.4
|
55.9
|
1.0
|
O
|
E:HOH601
|
3.5
|
45.6
|
1.0
|
C
|
E:ALA152
|
3.7
|
57.8
|
1.0
|
O
|
E:ALA152
|
3.7
|
60.7
|
1.0
|
C
|
E:VAL156
|
3.8
|
49.6
|
1.0
|
CE1
|
E:PHE183
|
3.9
|
59.2
|
1.0
|
CZ
|
E:PHE183
|
4.0
|
58.2
|
1.0
|
N
|
E:ASN153
|
4.0
|
55.4
|
1.0
|
CA
|
E:ALA152
|
4.1
|
58.2
|
1.0
|
N
|
E:ALA152
|
4.2
|
57.8
|
1.0
|
N
|
E:ASP154
|
4.2
|
53.7
|
1.0
|
CA
|
E:ASP154
|
4.3
|
56.4
|
1.0
|
CB
|
E:VAL156
|
4.3
|
51.6
|
1.0
|
N
|
E:VAL156
|
4.3
|
50.0
|
1.0
|
CA
|
E:VAL156
|
4.3
|
50.9
|
1.0
|
CA
|
E:ASN153
|
4.3
|
53.6
|
1.0
|
O
|
E:ASP154
|
4.4
|
55.7
|
1.0
|
C
|
E:ASP154
|
4.4
|
55.1
|
1.0
|
CA
|
E:LEU151
|
4.6
|
53.4
|
1.0
|
CG1
|
E:VAL156
|
4.8
|
50.4
|
1.0
|
N
|
E:THR157
|
5.0
|
49.6
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6gs8
Go back to
Magnesium Binding Sites List in 6gs8
Magnesium binding site 6 out
of 6 in the Crystal Structure of Smba in Complex with C-Di-Gmp
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 Smba in Complex with C-Di-Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg503
b:83.3
occ:1.00
|
O
|
F:HOH601
|
2.1
|
49.0
|
1.0
|
O
|
F:ASN153
|
2.1
|
90.7
|
1.0
|
O
|
F:VAL156
|
2.2
|
82.9
|
1.0
|
O
|
F:LEU151
|
2.2
|
98.6
|
1.0
|
C
|
F:VAL156
|
3.3
|
75.8
|
1.0
|
C
|
F:ASN153
|
3.3
|
93.0
|
1.0
|
C
|
F:LEU151
|
3.4
|
96.3
|
1.0
|
CB
|
F:VAL156
|
3.7
|
79.0
|
1.0
|
CA
|
F:VAL156
|
3.8
|
77.0
|
1.0
|
N
|
F:VAL156
|
3.8
|
78.2
|
1.0
|
CE1
|
F:PHE183
|
3.9
|
78.9
|
1.0
|
C
|
F:ALA152
|
4.0
|
99.8
|
1.0
|
O
|
F:ALA152
|
4.1
|
99.9
|
1.0
|
N
|
F:ASN153
|
4.1
|
96.3
|
1.0
|
CZ
|
F:PHE183
|
4.1
|
78.7
|
1.0
|
N
|
F:ASP154
|
4.2
|
98.0
|
1.0
|
O
|
F:ASP154
|
4.3
|
85.1
|
1.0
|
N
|
F:ALA152
|
4.3
|
0.2
|
1.0
|
C
|
F:ASP154
|
4.3
|
88.7
|
1.0
|
CA
|
F:ASP154
|
4.3
|
97.6
|
1.0
|
CA
|
F:ASN153
|
4.3
|
93.0
|
1.0
|
CG1
|
F:VAL156
|
4.3
|
82.0
|
1.0
|
CA
|
F:ALA152
|
4.4
|
0.8
|
1.0
|
CA
|
F:LEU151
|
4.4
|
94.9
|
1.0
|
N
|
F:THR157
|
4.4
|
73.1
|
1.0
|
C
|
F:LEU155
|
4.8
|
80.4
|
1.0
|
O
|
F:LEU150
|
4.8
|
0.7
|
1.0
|
N
|
F:LEU155
|
4.9
|
81.5
|
1.0
|
CD1
|
F:PHE183
|
4.9
|
76.0
|
1.0
|
CA
|
F:THR157
|
5.0
|
75.4
|
1.0
|
CG2
|
F:VAL156
|
5.0
|
78.1
|
1.0
|
|
Reference:
V.Shyp,
B.N.Dubey,
R.Bohm,
J.Nesper,
S.Hiller,
U.Jenal,
T.Schirmer.
Reciprocal Regulation of Bacterial Growth and Development By Competitive Binding of Two Second Messengers to A (Central) Metabolic Switch To Be Published.
Page generated: Tue Oct 1 01:24:14 2024
|