Fluorine in PDB 2r25: Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-
Enzymatic activity of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-
All present enzymatic activity of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-:
2.7.13.3;
Protein crystallography data
The structure of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-, PDB code: 2r25
was solved by
D.M.Copeland,
X.Zhao,
A.S.Soares,
A.H.West,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
17.75 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.013,
75.544,
98.392,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
24
|
Other elements in 2r25:
The structure of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-
(pdb code 2r25). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-, PDB code: 2r25:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 2r25
Go back to
Fluorine Binding Sites List in 2r25
Fluorine binding site 1 out
of 3 in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F2
b:26.6
occ:1.00
|
F1
|
B:BEF2
|
0.0
|
26.6
|
1.0
|
BE
|
B:BEF2
|
1.5
|
28.5
|
1.0
|
MG
|
B:MG1
|
2.0
|
25.9
|
1.0
|
F3
|
B:BEF2
|
2.4
|
26.0
|
1.0
|
F2
|
B:BEF2
|
2.5
|
25.3
|
1.0
|
OD1
|
B:ASP1144
|
2.6
|
33.6
|
1.0
|
OD2
|
B:ASP1144
|
2.9
|
28.9
|
1.0
|
O
|
B:HOH160
|
2.9
|
27.9
|
1.0
|
O
|
B:GLN1146
|
3.0
|
25.0
|
1.0
|
O
|
B:HOH159
|
3.1
|
26.8
|
1.0
|
CG
|
B:ASP1144
|
3.1
|
33.2
|
1.0
|
CD2
|
A:HIS64
|
3.1
|
23.0
|
1.0
|
NE2
|
A:HIS64
|
3.2
|
27.5
|
1.0
|
O
|
A:HOH184
|
3.4
|
29.0
|
1.0
|
N
|
B:GLN1146
|
3.5
|
26.9
|
1.0
|
CB
|
B:GLN1146
|
3.7
|
29.0
|
1.0
|
C
|
B:GLN1146
|
3.8
|
26.9
|
1.0
|
CA
|
B:GLN1146
|
3.8
|
26.5
|
1.0
|
OD2
|
B:ASP1095
|
4.1
|
28.0
|
1.0
|
CG
|
B:GLN1146
|
4.4
|
33.7
|
1.0
|
NZ
|
B:LYS1195
|
4.4
|
23.7
|
1.0
|
CG
|
A:HIS64
|
4.4
|
27.2
|
1.0
|
O
|
B:HOH164
|
4.6
|
27.5
|
1.0
|
CE1
|
A:HIS64
|
4.6
|
28.3
|
1.0
|
C
|
B:VAL1145
|
4.6
|
29.6
|
1.0
|
N
|
B:VAL1145
|
4.6
|
26.0
|
1.0
|
CB
|
B:ASP1144
|
4.6
|
30.8
|
1.0
|
O
|
B:HOH189
|
4.9
|
48.9
|
1.0
|
OG1
|
B:THR1173
|
4.9
|
33.0
|
1.0
|
N
|
B:ALA1174
|
4.9
|
27.4
|
1.0
|
OE1
|
B:GLU1094
|
5.0
|
26.7
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 2r25
Go back to
Fluorine Binding Sites List in 2r25
Fluorine binding site 2 out
of 3 in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F2
b:25.3
occ:1.00
|
F2
|
B:BEF2
|
0.0
|
25.3
|
1.0
|
BE
|
B:BEF2
|
1.5
|
28.5
|
1.0
|
F1
|
B:BEF2
|
2.5
|
26.6
|
1.0
|
F3
|
B:BEF2
|
2.5
|
26.0
|
1.0
|
OD1
|
B:ASP1144
|
2.5
|
33.6
|
1.0
|
OG1
|
B:THR1173
|
2.6
|
33.0
|
1.0
|
NE2
|
A:HIS64
|
2.7
|
27.5
|
1.0
|
N
|
B:GLN1146
|
3.1
|
26.9
|
1.0
|
N
|
B:VAL1145
|
3.2
|
26.0
|
1.0
|
CB
|
B:THR1173
|
3.5
|
27.8
|
1.0
|
CB
|
B:VAL1145
|
3.5
|
30.5
|
1.0
|
CD2
|
A:HIS64
|
3.6
|
23.0
|
1.0
|
CG
|
B:ASP1144
|
3.6
|
33.2
|
1.0
|
CA
|
B:VAL1145
|
3.6
|
29.3
|
1.0
|
CE1
|
A:HIS64
|
3.8
|
28.3
|
1.0
|
N
|
B:ALA1174
|
3.8
|
27.4
|
1.0
|
C
|
B:VAL1145
|
3.8
|
29.6
|
1.0
|
CA
|
B:THR1173
|
3.9
|
30.2
|
1.0
|
CD2
|
B:PHE1175
|
4.1
|
28.5
|
1.0
|
OD2
|
B:ASP1144
|
4.2
|
28.9
|
1.0
|
CA
|
B:GLN1146
|
4.2
|
26.5
|
1.0
|
CG2
|
B:VAL1145
|
4.3
|
26.0
|
1.0
|
MG
|
B:MG1
|
4.3
|
25.9
|
1.0
|
CB
|
B:GLN1146
|
4.3
|
29.0
|
1.0
|
CG
|
B:GLN1146
|
4.3
|
33.7
|
1.0
|
CE2
|
B:PHE1175
|
4.3
|
32.2
|
1.0
|
C
|
B:THR1173
|
4.3
|
31.1
|
1.0
|
C
|
B:ASP1144
|
4.3
|
28.7
|
1.0
|
O
|
B:GLN1146
|
4.5
|
25.0
|
1.0
|
CA
|
B:ASP1144
|
4.7
|
30.6
|
1.0
|
CG1
|
B:VAL1145
|
4.7
|
30.1
|
1.0
|
CB
|
B:ASP1144
|
4.7
|
30.8
|
1.0
|
CG
|
A:HIS64
|
4.8
|
27.2
|
1.0
|
N
|
B:PHE1175
|
4.8
|
30.1
|
1.0
|
C
|
B:GLN1146
|
4.8
|
26.9
|
1.0
|
CG2
|
B:THR1173
|
4.9
|
32.0
|
1.0
|
ND1
|
A:HIS64
|
4.9
|
30.6
|
1.0
|
O
|
A:HOH184
|
4.9
|
29.0
|
1.0
|
CA
|
B:ALA1174
|
4.9
|
29.5
|
1.0
|
CG
|
B:PHE1175
|
5.0
|
29.7
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 2r25
Go back to
Fluorine Binding Sites List in 2r25
Fluorine binding site 3 out
of 3 in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F2
b:26.0
occ:1.00
|
F3
|
B:BEF2
|
0.0
|
26.0
|
1.0
|
BE
|
B:BEF2
|
1.5
|
28.5
|
1.0
|
F1
|
B:BEF2
|
2.4
|
26.6
|
1.0
|
F2
|
B:BEF2
|
2.5
|
25.3
|
1.0
|
OD1
|
B:ASP1144
|
2.6
|
33.6
|
1.0
|
N
|
B:ALA1174
|
2.7
|
27.4
|
1.0
|
NZ
|
B:LYS1195
|
2.9
|
23.7
|
1.0
|
O
|
A:HOH184
|
2.9
|
29.0
|
1.0
|
NE2
|
A:HIS64
|
3.3
|
27.5
|
1.0
|
CA
|
B:THR1173
|
3.5
|
30.2
|
1.0
|
C
|
B:THR1173
|
3.5
|
31.1
|
1.0
|
OG1
|
B:THR1173
|
3.6
|
33.0
|
1.0
|
CG
|
B:ASP1144
|
3.6
|
33.2
|
1.0
|
CB
|
B:ALA1174
|
3.6
|
30.3
|
1.0
|
CE
|
B:LYS1195
|
3.7
|
28.5
|
1.0
|
O
|
B:HOH160
|
3.7
|
27.9
|
1.0
|
CA
|
B:ALA1174
|
3.7
|
29.5
|
1.0
|
CD2
|
A:HIS64
|
3.8
|
23.0
|
1.0
|
MG
|
B:MG1
|
4.0
|
25.9
|
1.0
|
CD
|
B:LYS1195
|
4.0
|
26.4
|
1.0
|
CB
|
B:THR1173
|
4.1
|
27.8
|
1.0
|
OD2
|
B:ASP1144
|
4.1
|
28.9
|
1.0
|
O
|
B:HOH189
|
4.2
|
48.9
|
1.0
|
CE1
|
A:HIS64
|
4.3
|
28.3
|
1.0
|
O
|
B:LEU1172
|
4.6
|
31.4
|
1.0
|
O
|
B:THR1173
|
4.7
|
30.0
|
1.0
|
N
|
B:THR1173
|
4.7
|
30.1
|
1.0
|
OE2
|
B:GLU1094
|
4.7
|
26.9
|
1.0
|
C
|
B:ALA1174
|
4.8
|
33.1
|
1.0
|
CB
|
B:ASP1144
|
4.8
|
30.8
|
1.0
|
N
|
B:PHE1175
|
4.9
|
30.1
|
1.0
|
N
|
B:VAL1145
|
4.9
|
26.0
|
1.0
|
CG
|
A:HIS64
|
5.0
|
27.2
|
1.0
|
|
Reference:
X.Zhao,
D.M.Copeland,
A.S.Soares,
A.H.West.
Crystal Structure of A Complex Between the Phosphorelay Protein YPD1 and the Response Regulator Domain of SLN1 Bound to A Phosphoryl Analog J.Mol.Biol. V. 375 1141 2008.
ISSN: ISSN 0022-2836
PubMed: 18076904
DOI: 10.1016/J.JMB.2007.11.045
Page generated: Wed Jul 31 15:55:25 2024
|