Fluorine in PDB 2v0n: Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S
Protein crystallography data
The structure of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S, PDB code: 2v0n
was solved by
P.Wassmann,
T.Schirmer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.71
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.965,
132.557,
88.425,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.5 /
25.2
|
Other elements in 2v0n:
The structure of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S
(pdb code 2v0n). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S, PDB code: 2v0n:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 2v0n
Go back to
Fluorine Binding Sites List in 2v0n
Fluorine binding site 1 out
of 6 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:39.1
occ:1.00
|
F1
|
A:BEF501
|
0.0
|
39.1
|
1.0
|
BE
|
A:BEF501
|
1.5
|
39.4
|
1.0
|
F2
|
A:BEF501
|
2.4
|
35.4
|
1.0
|
F3
|
A:BEF501
|
2.5
|
35.3
|
1.0
|
OD1
|
A:ASP53
|
2.5
|
40.6
|
1.0
|
NZ
|
A:LYS105
|
2.6
|
44.3
|
1.0
|
N
|
A:ALA84
|
2.9
|
42.3
|
1.0
|
CA
|
A:THR83
|
3.5
|
41.0
|
1.0
|
CG
|
A:ASP53
|
3.5
|
37.4
|
1.0
|
CE
|
A:LYS105
|
3.5
|
46.8
|
1.0
|
CE
|
A:MET55
|
3.6
|
44.2
|
1.0
|
C
|
A:THR83
|
3.7
|
41.6
|
1.0
|
CB
|
A:ALA84
|
3.7
|
42.4
|
1.0
|
OG1
|
A:THR83
|
3.7
|
41.4
|
1.0
|
OD2
|
A:ASP53
|
3.9
|
33.2
|
1.0
|
CA
|
A:ALA84
|
3.9
|
42.8
|
1.0
|
O
|
A:HOH2001
|
3.9
|
25.7
|
1.0
|
CD
|
A:LYS105
|
4.0
|
45.3
|
1.0
|
CB
|
A:THR83
|
4.1
|
41.3
|
1.0
|
MG
|
A:MG502
|
4.4
|
37.2
|
1.0
|
O
|
A:ILE82
|
4.4
|
40.8
|
1.0
|
N
|
A:THR83
|
4.6
|
40.6
|
1.0
|
O
|
A:THR83
|
4.8
|
40.8
|
1.0
|
CB
|
A:ASP53
|
4.8
|
39.6
|
1.0
|
OD2
|
A:ASP9
|
4.9
|
45.6
|
1.0
|
N
|
A:VAL54
|
5.0
|
40.2
|
1.0
|
CG
|
A:LYS105
|
5.0
|
45.4
|
1.0
|
C
|
A:ILE82
|
5.0
|
40.4
|
1.0
|
N
|
A:MET55
|
5.0
|
41.2
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 2v0n
Go back to
Fluorine Binding Sites List in 2v0n
Fluorine binding site 2 out
of 6 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:35.4
occ:1.00
|
F2
|
A:BEF501
|
0.0
|
35.4
|
1.0
|
BE
|
A:BEF501
|
1.5
|
39.4
|
1.0
|
MG
|
A:MG502
|
2.2
|
37.2
|
1.0
|
OD2
|
A:ASP53
|
2.2
|
33.2
|
1.0
|
F3
|
A:BEF501
|
2.4
|
35.3
|
1.0
|
F1
|
A:BEF501
|
2.4
|
39.1
|
1.0
|
OD1
|
A:ASP53
|
2.5
|
40.6
|
1.0
|
O
|
A:HOH2001
|
2.6
|
25.7
|
1.0
|
CG
|
A:ASP53
|
2.6
|
37.4
|
1.0
|
O
|
A:MET55
|
3.0
|
38.6
|
1.0
|
CB
|
A:MET55
|
3.5
|
41.5
|
1.0
|
CE
|
A:MET55
|
3.6
|
44.2
|
1.0
|
N
|
A:MET55
|
3.7
|
41.2
|
1.0
|
C
|
A:MET55
|
3.8
|
40.3
|
1.0
|
CA
|
A:MET55
|
3.8
|
41.5
|
1.0
|
NZ
|
A:LYS105
|
3.9
|
44.3
|
1.0
|
OD1
|
A:ASP10
|
4.0
|
40.8
|
1.0
|
CB
|
A:ASP53
|
4.1
|
39.6
|
1.0
|
CG
|
A:MET55
|
4.4
|
41.4
|
1.0
|
N
|
A:VAL54
|
4.6
|
40.2
|
1.0
|
SD
|
A:MET55
|
4.7
|
48.0
|
1.0
|
C
|
A:VAL54
|
4.8
|
41.1
|
1.0
|
OD2
|
A:ASP10
|
4.8
|
38.9
|
1.0
|
CG
|
A:ASP10
|
4.9
|
40.2
|
1.0
|
OD2
|
A:ASP9
|
4.9
|
45.6
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 2v0n
Go back to
Fluorine Binding Sites List in 2v0n
Fluorine binding site 3 out
of 6 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:35.3
occ:1.00
|
F3
|
A:BEF501
|
0.0
|
35.3
|
1.0
|
BE
|
A:BEF501
|
1.5
|
39.4
|
1.0
|
F2
|
A:BEF501
|
2.4
|
35.4
|
1.0
|
F1
|
A:BEF501
|
2.5
|
39.1
|
1.0
|
OD1
|
A:ASP53
|
2.5
|
40.6
|
1.0
|
N
|
A:MET55
|
2.7
|
41.2
|
1.0
|
OG1
|
A:THR83
|
2.9
|
41.4
|
1.0
|
CE
|
A:MET55
|
3.2
|
44.2
|
1.0
|
CG
|
A:ASP53
|
3.2
|
37.4
|
1.0
|
N
|
A:VAL54
|
3.2
|
40.2
|
1.0
|
CB
|
A:MET55
|
3.4
|
41.5
|
1.0
|
OD2
|
A:ASP53
|
3.5
|
33.2
|
1.0
|
CG
|
A:MET55
|
3.5
|
41.4
|
1.0
|
CA
|
A:MET55
|
3.6
|
41.5
|
1.0
|
CB
|
A:THR83
|
3.6
|
41.3
|
1.0
|
CB
|
A:VAL54
|
3.6
|
41.0
|
1.0
|
C
|
A:VAL54
|
3.6
|
41.1
|
1.0
|
CA
|
A:VAL54
|
3.6
|
40.4
|
1.0
|
CA
|
A:THR83
|
3.9
|
41.0
|
1.0
|
SD
|
A:MET55
|
4.1
|
48.0
|
1.0
|
N
|
A:ALA84
|
4.1
|
42.3
|
1.0
|
O
|
A:MET55
|
4.2
|
38.6
|
1.0
|
C
|
A:ASP53
|
4.3
|
39.9
|
1.0
|
C
|
A:MET55
|
4.4
|
40.3
|
1.0
|
MG
|
A:MG502
|
4.4
|
37.2
|
1.0
|
CB
|
A:ASP53
|
4.4
|
39.6
|
1.0
|
CA
|
A:ASP53
|
4.5
|
39.0
|
1.0
|
CG2
|
A:VAL54
|
4.6
|
39.6
|
1.0
|
C
|
A:THR83
|
4.6
|
41.6
|
1.0
|
CG1
|
A:VAL54
|
4.6
|
39.3
|
1.0
|
NZ
|
A:LYS105
|
4.7
|
44.3
|
1.0
|
O
|
A:VAL54
|
4.8
|
42.2
|
1.0
|
O
|
A:ILE82
|
4.8
|
40.8
|
1.0
|
O
|
A:HOH2001
|
4.9
|
25.7
|
1.0
|
CG
|
A:LEU85
|
4.9
|
40.6
|
1.0
|
CD1
|
A:LEU85
|
4.9
|
31.8
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 2v0n
Go back to
Fluorine Binding Sites List in 2v0n
Fluorine binding site 4 out
of 6 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:39.9
occ:1.00
|
F1
|
B:BEF501
|
0.0
|
39.9
|
1.0
|
BE
|
B:BEF501
|
1.5
|
39.6
|
1.0
|
F2
|
B:BEF501
|
2.5
|
35.0
|
1.0
|
F3
|
B:BEF501
|
2.5
|
35.5
|
1.0
|
OD1
|
B:ASP53
|
2.5
|
39.9
|
1.0
|
NZ
|
B:LYS105
|
2.8
|
47.2
|
1.0
|
N
|
B:ALA84
|
2.9
|
39.0
|
1.0
|
CA
|
B:THR83
|
3.4
|
40.4
|
1.0
|
CG
|
B:ASP53
|
3.5
|
37.0
|
1.0
|
C
|
B:THR83
|
3.6
|
41.0
|
1.0
|
CE
|
B:LYS105
|
3.7
|
48.9
|
1.0
|
CB
|
B:ALA84
|
3.8
|
39.2
|
1.0
|
OG1
|
B:THR83
|
3.8
|
41.5
|
1.0
|
OD2
|
B:ASP53
|
3.9
|
31.4
|
1.0
|
CA
|
B:ALA84
|
3.9
|
40.1
|
1.0
|
CD
|
B:LYS105
|
4.1
|
46.4
|
1.0
|
CE
|
B:MET55
|
4.1
|
44.4
|
1.0
|
CB
|
B:THR83
|
4.1
|
41.3
|
1.0
|
O
|
B:HOH2001
|
4.3
|
22.7
|
1.0
|
O
|
B:ILE82
|
4.3
|
41.2
|
1.0
|
MG
|
B:MG502
|
4.4
|
36.8
|
1.0
|
N
|
B:THR83
|
4.6
|
39.8
|
1.0
|
OD2
|
B:ASP9
|
4.7
|
45.1
|
1.0
|
O
|
B:THR83
|
4.7
|
41.1
|
1.0
|
CB
|
B:ASP53
|
4.8
|
37.0
|
1.0
|
C
|
B:ILE82
|
4.9
|
40.6
|
1.0
|
N
|
B:VAL54
|
5.0
|
40.1
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 2v0n
Go back to
Fluorine Binding Sites List in 2v0n
Fluorine binding site 5 out
of 6 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:35.0
occ:1.00
|
F2
|
B:BEF501
|
0.0
|
35.0
|
1.0
|
BE
|
B:BEF501
|
1.5
|
39.6
|
1.0
|
MG
|
B:MG502
|
2.1
|
36.8
|
1.0
|
OD2
|
B:ASP53
|
2.2
|
31.4
|
1.0
|
F3
|
B:BEF501
|
2.4
|
35.5
|
1.0
|
F1
|
B:BEF501
|
2.5
|
39.9
|
1.0
|
OD1
|
B:ASP53
|
2.5
|
39.9
|
1.0
|
CG
|
B:ASP53
|
2.6
|
37.0
|
1.0
|
O
|
B:MET55
|
2.9
|
38.5
|
1.0
|
O
|
B:HOH2001
|
3.1
|
22.7
|
1.0
|
CB
|
B:MET55
|
3.5
|
41.2
|
1.0
|
N
|
B:MET55
|
3.6
|
40.4
|
1.0
|
C
|
B:MET55
|
3.7
|
40.3
|
1.0
|
CA
|
B:MET55
|
3.7
|
41.0
|
1.0
|
CE
|
B:MET55
|
3.8
|
44.4
|
1.0
|
OD1
|
B:ASP10
|
4.0
|
46.1
|
1.0
|
CB
|
B:ASP53
|
4.1
|
37.0
|
1.0
|
NZ
|
B:LYS105
|
4.2
|
47.2
|
1.0
|
CG
|
B:MET55
|
4.4
|
41.0
|
1.0
|
N
|
B:VAL54
|
4.5
|
40.1
|
1.0
|
OD2
|
B:ASP9
|
4.7
|
45.1
|
1.0
|
C
|
B:VAL54
|
4.7
|
41.0
|
1.0
|
CG
|
B:ASP10
|
4.9
|
43.4
|
1.0
|
SD
|
B:MET55
|
5.0
|
44.9
|
1.0
|
CA
|
B:ASP53
|
5.0
|
37.7
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 2v0n
Go back to
Fluorine Binding Sites List in 2v0n
Fluorine binding site 6 out
of 6 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:35.5
occ:1.00
|
F3
|
B:BEF501
|
0.0
|
35.5
|
1.0
|
BE
|
B:BEF501
|
1.5
|
39.6
|
1.0
|
F2
|
B:BEF501
|
2.4
|
35.0
|
1.0
|
F1
|
B:BEF501
|
2.5
|
39.9
|
1.0
|
OD1
|
B:ASP53
|
2.5
|
39.9
|
1.0
|
N
|
B:MET55
|
2.7
|
40.4
|
1.0
|
OG1
|
B:THR83
|
3.0
|
41.5
|
1.0
|
N
|
B:VAL54
|
3.2
|
40.1
|
1.0
|
CG
|
B:ASP53
|
3.2
|
37.0
|
1.0
|
CB
|
B:MET55
|
3.4
|
41.2
|
1.0
|
CE
|
B:MET55
|
3.5
|
44.4
|
1.0
|
CA
|
B:MET55
|
3.6
|
41.0
|
1.0
|
CB
|
B:THR83
|
3.6
|
41.3
|
1.0
|
CG
|
B:MET55
|
3.6
|
41.0
|
1.0
|
OD2
|
B:ASP53
|
3.6
|
31.4
|
1.0
|
C
|
B:VAL54
|
3.6
|
41.0
|
1.0
|
CA
|
B:VAL54
|
3.7
|
40.1
|
1.0
|
CB
|
B:VAL54
|
3.7
|
41.0
|
1.0
|
CA
|
B:THR83
|
3.9
|
40.4
|
1.0
|
N
|
B:ALA84
|
4.0
|
39.0
|
1.0
|
O
|
B:MET55
|
4.2
|
38.5
|
1.0
|
C
|
B:ASP53
|
4.3
|
38.7
|
1.0
|
C
|
B:MET55
|
4.4
|
40.3
|
1.0
|
MG
|
B:MG502
|
4.4
|
36.8
|
1.0
|
SD
|
B:MET55
|
4.4
|
44.9
|
1.0
|
CB
|
B:ASP53
|
4.4
|
37.0
|
1.0
|
CA
|
B:ASP53
|
4.5
|
37.7
|
1.0
|
C
|
B:THR83
|
4.5
|
41.0
|
1.0
|
CG2
|
B:VAL54
|
4.7
|
39.6
|
1.0
|
CG1
|
B:VAL54
|
4.7
|
39.4
|
1.0
|
O
|
B:ILE82
|
4.8
|
41.2
|
1.0
|
O
|
B:VAL54
|
4.8
|
42.5
|
1.0
|
CD1
|
B:LEU85
|
4.8
|
38.2
|
1.0
|
NZ
|
B:LYS105
|
4.9
|
47.2
|
1.0
|
|
Reference:
P.Wassmann,
C.Chan,
R.Paul,
A.Beck,
H.Heerklotz,
U.Jenal,
T.Schirmer.
Structure of BEF3--Modified Response Regulator Pled: Implications For Diguanylate Cyclase Activation, Catalysis, and Feedback Inhibition Structure V. 15 915 2007.
ISSN: ISSN 0969-2126
PubMed: 17697997
DOI: 10.1016/J.STR.2007.06.016
Page generated: Wed Jul 31 16:02:08 2024
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