Magnesium in PDB 3f79: Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb
Protein crystallography data
The structure of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb, PDB code: 3f79
was solved by
I.Levchenko,
R.A.Grant,
R.T.Sauer,
T.A.Baker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
2.80
|
Space group
|
P 31
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.872,
124.872,
92.900,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
24.3 /
29.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb
(pdb code 3f79). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb, PDB code: 3f79:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 3f79
Go back to
Magnesium Binding Sites List in 3f79
Magnesium binding site 1 out
of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1
b:61.1
occ:1.00
|
OD2
|
B:ASP210
|
2.7
|
28.5
|
1.0
|
OD1
|
B:ASP382
|
2.8
|
54.1
|
1.0
|
OD1
|
B:ASP210
|
2.8
|
0.2
|
1.0
|
O
|
B:GLY213
|
2.9
|
0.4
|
1.0
|
OD2
|
B:ASP382
|
3.0
|
49.2
|
1.0
|
CG
|
B:ASP210
|
3.1
|
55.0
|
1.0
|
CG
|
B:ASP382
|
3.2
|
74.6
|
1.0
|
OD2
|
B:ASP336
|
3.3
|
45.5
|
1.0
|
O
|
B:VAL211
|
3.5
|
83.0
|
1.0
|
C
|
B:GLY213
|
3.8
|
0.8
|
1.0
|
N
|
B:GLY213
|
3.9
|
0.2
|
1.0
|
CA
|
B:GLY213
|
4.1
|
0.8
|
1.0
|
CG
|
B:ASP336
|
4.3
|
78.0
|
1.0
|
OD1
|
B:ASP192
|
4.4
|
0.2
|
1.0
|
CB
|
B:ASP336
|
4.5
|
94.9
|
1.0
|
CB
|
B:ASP210
|
4.6
|
72.6
|
1.0
|
C
|
B:VAL211
|
4.6
|
83.8
|
1.0
|
CB
|
B:ASP382
|
4.7
|
59.2
|
1.0
|
C
|
B:SER212
|
4.8
|
0.1
|
1.0
|
N
|
B:HIS214
|
5.0
|
0.1
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 3f79
Go back to
Magnesium Binding Sites List in 3f79
Magnesium binding site 2 out
of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg5
b:50.1
occ:1.00
|
OD1
|
C:ASP336
|
2.8
|
65.0
|
1.0
|
CG
|
C:ASP336
|
3.6
|
0.4
|
1.0
|
CB
|
C:ASP382
|
3.9
|
91.4
|
1.0
|
O
|
C:ASP336
|
4.2
|
0.8
|
1.0
|
OD2
|
C:ASP336
|
4.2
|
61.7
|
1.0
|
CG
|
C:ASP382
|
4.2
|
83.8
|
1.0
|
OD2
|
C:ASP382
|
4.2
|
93.0
|
1.0
|
C
|
C:ASP336
|
4.6
|
68.9
|
1.0
|
CB
|
C:ASP336
|
4.6
|
0.1
|
1.0
|
OD1
|
C:ASP382
|
4.9
|
57.0
|
1.0
|
N
|
C:GLY337
|
5.0
|
39.4
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 3f79
Go back to
Magnesium Binding Sites List in 3f79
Magnesium binding site 3 out
of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg6
b:78.6
occ:1.00
|
OD2
|
D:ASP336
|
2.9
|
36.5
|
1.0
|
OD2
|
D:ASP210
|
3.0
|
62.3
|
1.0
|
OD2
|
D:ASP382
|
3.0
|
47.9
|
1.0
|
OD1
|
D:ASP210
|
3.2
|
91.8
|
1.0
|
CG
|
D:ASP210
|
3.4
|
83.7
|
1.0
|
N
|
D:GLY213
|
3.6
|
99.1
|
1.0
|
O
|
D:VAL211
|
3.6
|
81.1
|
1.0
|
O
|
D:GLY213
|
3.7
|
96.3
|
1.0
|
CG
|
D:ASP382
|
3.9
|
87.2
|
1.0
|
OD1
|
D:ASP382
|
3.9
|
92.8
|
1.0
|
CG
|
D:ASP336
|
3.9
|
61.1
|
1.0
|
MG
|
D:MG7
|
4.2
|
41.0
|
1.0
|
CA
|
D:GLY213
|
4.2
|
86.1
|
1.0
|
CB
|
D:ASP336
|
4.2
|
46.2
|
1.0
|
C
|
D:GLY213
|
4.4
|
95.2
|
1.0
|
C
|
D:SER212
|
4.4
|
88.5
|
1.0
|
CA
|
D:SER212
|
4.5
|
97.3
|
1.0
|
C
|
D:VAL211
|
4.6
|
79.9
|
1.0
|
CB
|
D:ASP210
|
4.9
|
67.2
|
1.0
|
N
|
D:SER212
|
4.9
|
68.2
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 3f79
Go back to
Magnesium Binding Sites List in 3f79
Magnesium binding site 4 out
of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg7
b:41.0
occ:1.00
|
O
|
D:GLY213
|
2.7
|
96.3
|
1.0
|
OD1
|
D:ASP210
|
2.7
|
91.8
|
1.0
|
OD1
|
D:ASP192
|
3.0
|
66.4
|
1.0
|
O
|
D:VAL211
|
3.3
|
81.1
|
1.0
|
CA
|
D:GLY191
|
3.3
|
46.2
|
1.0
|
C
|
D:GLY191
|
3.5
|
66.2
|
1.0
|
N
|
D:GLY191
|
3.5
|
97.3
|
1.0
|
N
|
D:ASP192
|
3.6
|
79.1
|
1.0
|
CG
|
D:ASP210
|
3.8
|
83.7
|
1.0
|
CG
|
D:ASP192
|
3.8
|
0.3
|
1.0
|
C
|
D:GLY213
|
3.9
|
95.2
|
1.0
|
OD1
|
D:ASP382
|
3.9
|
92.8
|
1.0
|
CB
|
D:ASP383
|
4.1
|
91.7
|
1.0
|
CB
|
D:HIS214
|
4.1
|
0.4
|
1.0
|
O
|
D:GLY191
|
4.2
|
0.5
|
1.0
|
CA
|
D:HIS214
|
4.2
|
0.5
|
1.0
|
MG
|
D:MG6
|
4.2
|
78.6
|
1.0
|
N
|
D:VAL211
|
4.3
|
71.0
|
1.0
|
OD2
|
D:ASP210
|
4.3
|
62.3
|
1.0
|
OD2
|
D:ASP192
|
4.3
|
0.4
|
1.0
|
C
|
D:VAL211
|
4.4
|
79.9
|
1.0
|
CA
|
D:ASP192
|
4.5
|
94.4
|
1.0
|
N
|
D:HIS214
|
4.5
|
0.8
|
1.0
|
CB
|
D:ASP192
|
4.7
|
60.6
|
1.0
|
OG
|
D:SER218
|
4.8
|
0.4
|
1.0
|
C
|
D:ASP210
|
4.8
|
38.1
|
1.0
|
CA
|
D:ASP210
|
4.8
|
26.1
|
1.0
|
C
|
D:SER190
|
4.8
|
99.7
|
1.0
|
CB
|
D:ASP210
|
4.8
|
67.2
|
1.0
|
CA
|
D:VAL211
|
4.8
|
43.3
|
1.0
|
N
|
D:ASP383
|
4.9
|
85.0
|
1.0
|
CG
|
D:ASP382
|
4.9
|
87.2
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 3f79
Go back to
Magnesium Binding Sites List in 3f79
Magnesium binding site 5 out
of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg2
b:39.8
occ:1.00
|
O
|
E:GLY213
|
2.6
|
0.6
|
1.0
|
OD1
|
E:ASP210
|
2.7
|
89.7
|
1.0
|
OD1
|
E:ASP192
|
2.7
|
0.1
|
1.0
|
O
|
E:VAL211
|
2.9
|
73.8
|
1.0
|
OD1
|
E:ASP382
|
3.0
|
41.6
|
1.0
|
OD2
|
E:ASP336
|
3.4
|
48.5
|
1.0
|
CG
|
E:ASP210
|
3.5
|
16.9
|
1.0
|
OD2
|
E:ASP383
|
3.8
|
26.7
|
1.0
|
C
|
E:GLY213
|
3.8
|
0.1
|
1.0
|
CG
|
E:ASP192
|
3.9
|
0.8
|
1.0
|
OD2
|
E:ASP210
|
3.9
|
73.2
|
1.0
|
CG
|
E:ASP382
|
4.0
|
65.6
|
1.0
|
C
|
E:VAL211
|
4.1
|
76.1
|
1.0
|
OD2
|
E:ASP382
|
4.3
|
0.1
|
1.0
|
OD2
|
E:ASP192
|
4.3
|
0.8
|
1.0
|
N
|
E:VAL211
|
4.3
|
68.1
|
1.0
|
C
|
E:GLY191
|
4.4
|
53.2
|
1.0
|
CA
|
E:GLY191
|
4.4
|
35.5
|
1.0
|
N
|
E:GLY213
|
4.4
|
0.6
|
1.0
|
CG
|
E:ASP336
|
4.5
|
67.1
|
1.0
|
C
|
E:ASP210
|
4.5
|
41.6
|
1.0
|
N
|
E:ASP192
|
4.6
|
72.1
|
1.0
|
CB
|
E:ASP383
|
4.6
|
0.2
|
1.0
|
CG
|
E:ASP383
|
4.6
|
33.7
|
1.0
|
CA
|
E:GLY213
|
4.6
|
92.8
|
1.0
|
CB
|
E:ASP210
|
4.7
|
16.3
|
1.0
|
N
|
E:GLY191
|
4.7
|
90.1
|
1.0
|
O
|
E:GLY191
|
4.7
|
99.3
|
1.0
|
N
|
E:ASP383
|
4.7
|
84.4
|
1.0
|
N
|
E:HIS214
|
4.7
|
0.5
|
1.0
|
CA
|
E:ASP210
|
4.8
|
27.1
|
1.0
|
CA
|
E:HIS214
|
4.8
|
0.5
|
1.0
|
CA
|
E:VAL211
|
4.8
|
38.1
|
1.0
|
C
|
E:SER212
|
4.8
|
85.7
|
1.0
|
CB
|
E:HIS214
|
4.8
|
88.7
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 3f79
Go back to
Magnesium Binding Sites List in 3f79
Magnesium binding site 6 out
of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg3
b:47.6
occ:1.00
|
O
|
F:GLY213
|
2.8
|
0.4
|
1.0
|
OD1
|
F:ASP210
|
3.0
|
28.6
|
1.0
|
OD1
|
F:ASP382
|
3.2
|
51.9
|
1.0
|
OD2
|
F:ASP210
|
3.2
|
28.8
|
1.0
|
O
|
F:VAL211
|
3.3
|
74.0
|
1.0
|
OD2
|
F:ASP382
|
3.4
|
0.1
|
1.0
|
N
|
F:GLY213
|
3.4
|
0.2
|
1.0
|
CG
|
F:ASP210
|
3.5
|
63.0
|
1.0
|
C
|
F:GLY213
|
3.6
|
0.6
|
1.0
|
CG
|
F:ASP382
|
3.7
|
89.8
|
1.0
|
MG
|
F:MG4
|
3.7
|
94.5
|
1.0
|
CA
|
F:GLY213
|
3.7
|
0.5
|
1.0
|
OD2
|
F:ASP336
|
4.2
|
83.4
|
1.0
|
C
|
F:SER212
|
4.3
|
0.1
|
1.0
|
C
|
F:VAL211
|
4.4
|
71.7
|
1.0
|
OD1
|
F:ASP192
|
4.6
|
0.5
|
1.0
|
CA
|
F:SER212
|
4.7
|
0.0
|
1.0
|
N
|
F:HIS214
|
4.7
|
0.8
|
1.0
|
CB
|
F:ASP210
|
5.0
|
59.8
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 3f79
Go back to
Magnesium Binding Sites List in 3f79
Magnesium binding site 7 out
of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg4
b:94.5
occ:1.00
|
OD2
|
F:ASP210
|
2.7
|
28.8
|
1.0
|
O
|
F:ASP383
|
2.8
|
74.8
|
1.0
|
OD2
|
F:ASP382
|
2.8
|
0.1
|
1.0
|
OD2
|
F:ASP192
|
3.1
|
0.0
|
1.0
|
OD1
|
F:ASP382
|
3.2
|
51.9
|
1.0
|
CG
|
F:ASP382
|
3.2
|
89.8
|
1.0
|
CG
|
F:ASP210
|
3.3
|
63.0
|
1.0
|
CB
|
F:ASP336
|
3.3
|
66.9
|
1.0
|
N
|
F:ASP336
|
3.5
|
0.6
|
1.0
|
OD1
|
F:ASP192
|
3.5
|
0.5
|
1.0
|
OD1
|
F:ASP210
|
3.6
|
28.6
|
1.0
|
MG
|
F:MG3
|
3.7
|
47.6
|
1.0
|
CG
|
F:ASP192
|
3.7
|
0.2
|
1.0
|
C
|
F:ASP383
|
3.9
|
98.9
|
1.0
|
CA
|
F:ASP336
|
3.9
|
75.0
|
1.0
|
CB
|
F:SER335
|
3.9
|
0.8
|
1.0
|
OD2
|
F:ASP336
|
4.1
|
83.4
|
1.0
|
CG
|
F:ASP336
|
4.1
|
69.5
|
1.0
|
N
|
F:ASP383
|
4.2
|
84.2
|
1.0
|
CB
|
F:ASP210
|
4.4
|
59.8
|
1.0
|
CB
|
F:ASP382
|
4.4
|
0.7
|
1.0
|
N
|
F:GLY337
|
4.4
|
56.4
|
1.0
|
CA
|
F:ASP383
|
4.4
|
93.2
|
1.0
|
C
|
F:SER335
|
4.5
|
62.6
|
1.0
|
CB
|
F:ASP383
|
4.5
|
63.9
|
1.0
|
C
|
F:ASP336
|
4.7
|
69.5
|
1.0
|
C
|
F:ASP382
|
4.7
|
94.2
|
1.0
|
OG
|
F:SER335
|
4.7
|
0.5
|
1.0
|
CA
|
F:SER335
|
4.8
|
76.0
|
1.0
|
N
|
F:ILE384
|
5.0
|
94.9
|
1.0
|
|
Reference:
I.Levchenko,
R.A.Grant,
R.T.Sauer,
T.A.Baker.
The Structure of Rssb, A Clpx Adaptor Protein That Regulates Sigma S To Be Published.
Page generated: Wed Aug 14 13:35:15 2024
|